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Kim JM, Lee JW, Seo JS, Ha BK, Kwon SJ. Differentially Expressed Genes Related to Isoflavone Biosynthesis in a Soybean Mutant Revealed by a Comparative Transcriptomic Analysis. Plants (Basel) 2024; 13:584. [PMID: 38475431 DOI: 10.3390/plants13050584] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/15/2024] [Revised: 02/13/2024] [Accepted: 02/20/2024] [Indexed: 03/14/2024]
Abstract
Soybean [Glycine max (L.) Merr.] isoflavones, which are secondary metabolites with various functions, are included in food, cosmetics, and medicine. However, the molecular mechanisms regulating the glycosylation and malonylation of isoflavone glycoconjugates remain unclear. In this study, we conducted an RNA-seq analysis to compare soybean genotypes with different isoflavone contents, including Danbaek and Hwanggeum (low-isoflavone cultivars) as well as DB-088 (high-isoflavone mutant). The transcriptome analysis yielded over 278 million clean reads, representing 39,156 transcripts. The analysis of differentially expressed genes (DEGs) detected 2654 up-regulated and 1805 down-regulated genes between the low- and high-isoflavone genotypes. The putative functions of these 4459 DEGs were annotated on the basis of GO and KEGG pathway enrichment analyses. These DEGs were further analyzed to compare the expression patterns of the genes involved in the biosynthesis of secondary metabolites and the genes encoding transcription factors. The examination of the relative expression levels of 70 isoflavone biosynthetic genes revealed the HID, IFS, UGT, and MAT expression levels were significantly up/down-regulated depending on the genotype and seed developmental stage. These expression patterns were confirmed by quantitative real-time PCR. Moreover, a gene co-expression analysis detected potential protein-protein interactions, suggestive of common functions. The study findings provide valuable insights into the structural genes responsible for isoflavone biosynthesis and accumulation in soybean seeds.
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Affiliation(s)
- Jung Min Kim
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
| | - Jeong Woo Lee
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Ji Su Seo
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, College of Agriculture and Life Sciences, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Soon-Jae Kwon
- Advanced Radiation Technology Institute, Korea Atomic Energy Research Institute, Jeongeup 56212, Republic of Korea
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Han F, Li H, Lyu E, Zhang Q, Gai H, Xu Y, Bai X, He X, Khan AQ, Li X, Xie F, Li F, Fang X, Wei M. Soybean-mediated suppression of BjaI/BjaR 1 quorum sensing in Bradyrhizobium diazoefficiens impacts symbiotic nitrogen fixation. Appl Environ Microbiol 2024; 90:e0137423. [PMID: 38251894 PMCID: PMC10880635 DOI: 10.1128/aem.01374-23] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2023] [Accepted: 11/23/2023] [Indexed: 01/23/2024] Open
Abstract
The acyl-homoserine lactones (AHLs)-mediated LuxI/LuxR quorum sensing (QS) system orchestrates diverse bacterial behaviors in response to changes in population density. The role of the BjaI/BjaR1 QS system in Bradyrhizobium diazoefficiens USDA 110, which shares homology with LuxI/LuxR, remains elusive during symbiotic interaction with soybean. Here this genetic system in wild-type (WT) bacteria residing inside nodules exhibited significantly reduced activity compared to free-living cells, potentially attributed to soybean-mediated suppression. The deletion mutant strain ΔbjaR1 showed significantly enhanced nodulation induction and nitrogen fixation ability. Nevertheless, its ultimate symbiotic outcome (plant dry weight) in soybeans was compromised. Furthermore, comparative analysis of the transcriptome, proteome, and promoter activity revealed that the inactivation of BjaR1 systematically activated and inhibited genomic modules associated with nodulation and nitrogen metabolism. The former appeared to be linked to a significant decrease in the expression of NodD2, a key cell-density-dependent repressor of nodulation genes, while the latter conferred bacterial growth and nitrogen fixation insensitivity to environmental nitrogen. In addition, BjaR1 exerted a positive influence on the transcription of multiple genes involved in a so-called central intermediate metabolism within the nodule. In conclusion, our findings highlight the crucial role of the BjaI/BjaR1 QS circuit in positively regulating bacterial nitrogen metabolism and emphasize the significance of the soybean-mediated suppression of this genetic system for promoting efficient symbiotic nitrogen fixation by B. diazoefficiens.IMPORTANCEThe present study demonstrates, for the first time, that the BjaI/BjaR1 QS system of Bradyrhizobium diazoefficiens has a significant impact on its nodulation and nitrogen fixation capability in soybean by positively regulating NodD2 expression and bacterial nitrogen metabolism. Moreover, it provides novel insights into the importance of suppressing the activity of this QS circuit by the soybean host plant in establishing an efficient mutual relationship between the two symbiotic partners. This research expands our understanding of legumes' role in modulating symbiotic nitrogen fixation through rhizobial QS-mediated metabolic functioning, thereby deepening our comprehension of symbiotic coevolution theory. In addition, these findings may hold great promise for developing quorum quenching technology in agriculture.
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Affiliation(s)
- Fang Han
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Huiquan Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Ermeng Lyu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Qianqian Zhang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Haoyu Gai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Yunfang Xu
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xuemei Bai
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xueqian He
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Abdul Qadir Khan
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiaolin Li
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
- University of the Chinese Academy of Sciences, Beijing, China
| | - Fang Xie
- National Key Laboratory of Plant Molecular Genetics, CAS Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, Shanghai, China
| | - Fengmin Li
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Xiangwen Fang
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
| | - Min Wei
- State Key Laboratory of Herbage Improvement and Grassland Agro-ecosystems, College of Ecology, Lanzhou University, Lanzhou, China
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53
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Otake T, Aoyagi Y, Yarita T. Assessment of the long-term stability of pesticide residues under freezing conditions in brown rice and soybean certified reference materials. J Pestic Sci 2024; 49:46-51. [PMID: 38450090 PMCID: PMC10912925 DOI: 10.1584/jpestics.d23-047] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/29/2023] [Accepted: 10/16/2023] [Indexed: 03/08/2024]
Abstract
The objective of this study was to assess the long-term stability of pesticide residues in brown rice and soybean. The long-term stability of pesticide residues in brown rice and soybean was assessed for 5415 days (over 14 years) and 1801 days (about 5 years), respectively. The samples-certified reference materials (CRMs) 7504-a (brown rice) and 7509-a (soybean) -were prepared by freeze-pulverization. Two target pesticides (etofenprox and fenitrothion) were selected for brown rice and four (chlorpyrifos, diazinon, fenitrothion, and permethrin) for soybean. Our analytical results for long-term stability based on highly reliable isotope dilution mass spectrometry were in the range of expanded uncertainty (k=2) for the certified values of each CRM. The concentration showed a decreasing trend in none of the target pesticides when the samples were stored at temperatures between -20 °C and -30 °C, which indicated that the target pesticides were stable for the tested long terms.
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Affiliation(s)
- Takamitsu Otake
- National Metrology Institute of Japan (NMIJ) National Institute of Advanced Industrial Science and Technology (AIST)
| | - Yoshie Aoyagi
- National Metrology Institute of Japan (NMIJ) National Institute of Advanced Industrial Science and Technology (AIST)
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54
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Ren X, Chen L, Deng L, Zhao Q, Yao D, Li X, Cong W, Zang Z, Zhao D, Zhang M, Yang S, Zhang J. Comparative transcriptomic analysis reveals the molecular mechanism underlying seedling heterosis and its relationship with hybrid contemporary seeds DNA methylation in soybean. Front Plant Sci 2024; 15:1364284. [PMID: 38444535 PMCID: PMC10913200 DOI: 10.3389/fpls.2024.1364284] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/02/2024] [Accepted: 01/31/2024] [Indexed: 03/07/2024]
Abstract
Heterosis is widely used in crop production, but phenotypic dominance and its underlying causes in soybeans, a significant grain and oil crop, remain a crucial yet unexplored issue. Here, the phenotypes and transcriptome profiles of three inbred lines and their resulting F1 seedlings were analyzed. The results suggest that F1 seedlings with superior heterosis in leaf size and biomass exhibited a more extensive recompilation in their transcriptional network and activated a greater number of genes compared to the parental lines. Furthermore, the transcriptional reprogramming observed in the four hybrid combinations was primarily non-additive, with dominant effects being more prevalent. Enrichment analysis of sets of differentially expressed genes, coupled with a weighted gene co-expression network analysis, has shown that the emergence of heterosis in seedlings can be attributed to genes related to circadian rhythms, photosynthesis, and starch synthesis. In addition, we combined DNA methylation data from previous immature seeds and observed similar recompilation patterns between DNA methylation and gene expression. We also found significant correlations between methylation levels of gene region and gene expression levels, as well as the discovery of 12 hub genes that shared or conflicted with their remodeling patterns. This suggests that DNA methylation in contemporary hybrid seeds have an impact on both the F1 seedling phenotype and gene expression to some extent. In conclusion, our study provides valuable insights into the molecular mechanisms of heterosis in soybean seedlings and its practical implications for selecting superior soybean varieties.
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Affiliation(s)
- Xiaobo Ren
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Liangyu Chen
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- Zhanjiang City Key Laboratory for Tropical Crops Genetic Improvement, South Subtropical Crops Institute, Chinese Academy of Tropical Agricultural Sciences, Zhanjiang, China
| | - Lin Deng
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Qiuzhu Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dan Yao
- College of Life Science, Jilin Agricultural University, Changchun, China
| | - Xueying Li
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Weixuan Cong
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Zhenyuan Zang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Dingyi Zhao
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Miao Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Songnan Yang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
| | - Jun Zhang
- Faculty of Agronomy, Jilin Agricultural University, Changchun, China
- National Crop Variety Approval and Characteristic Identification Station, Jilin Agricultural University, Changchun, China
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55
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Cui X, Tang M, Li L, Chang J, Yang X, Chang H, Zhou J, Liu M, Wang Y, Zhou Y, Sun F, Chen Z. Expression Patterns and Molecular Mechanisms Regulating Drought Tolerance of Soybean [ Glycine max (L.) Merr.] Conferred by Transcription Factor Gene GmNAC19. Int J Mol Sci 2024; 25:2396. [PMID: 38397076 PMCID: PMC10889163 DOI: 10.3390/ijms25042396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2024] [Revised: 02/13/2024] [Accepted: 02/14/2024] [Indexed: 02/25/2024] Open
Abstract
NAC transcription factors are commonly involved in the plant response to drought stress. A transcriptome analysis of root samples of the soybean variety 'Jiyu47' under drought stress revealed the evidently up-regulated expression of GmNAC19, consistent with the expression pattern revealed by quantitative real-time PCR analysis. The overexpression of GmNAC19 enhanced drought tolerance in Saccharomyces cerevisiae INVSc1. The seed germination percentage and root growth of transgenic Arabidopsis thaliana were improved in comparison with those of the wild type, while the transgenic soybean composite line showed improved chlorophyll content. The altered contents of physiological and biochemical indices (i.e., soluble protein, soluble sugar, proline, and malondialdehyde) related to drought stress and the activities of three antioxidant enzymes (i.e., superoxide dismutase, peroxidase, and catalase) revealed enhanced drought tolerance in both transgenic Arabidopsis and soybean. The expressions of three genes (i.e., P5CS, OAT, and P5CR) involved in proline synthesis were decreased in the transgenic soybean hairy roots, while the expression of ProDH involved in the breakdown of proline was increased. This study revealed the molecular mechanisms underlying drought tolerance enhanced by GmNAC19 via regulation of the contents of soluble protein and soluble sugar and the activities of antioxidant enzymes, providing a candidate gene for the molecular breeding of drought-tolerant crop plants.
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Affiliation(s)
- Xiyan Cui
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Minghao Tang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Lei Li
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Jiageng Chang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Xiaoqin Yang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Hongli Chang
- Shaanxi Key Laboratory for Animal Conservation, School of Life Sciences, Northwest University, Xi’an 710069, China
| | - Jiayu Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Miao Liu
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Yan Wang
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Ying Zhou
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
| | - Fengjie Sun
- Department of Biological Sciences, School of Science and Technology, Georgia Gwinnett College, Lawrenceville, GA 30043, USA
| | - Zhanyu Chen
- College of Life Sciences, Jilin Agricultural University, Changchun 130118, China; (X.C.); (Y.W.); (Y.Z.)
- College of Agronomy, Jilin Agricultural University, Changchun 130118, China
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56
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Su D, Li W, Zhang Z, Cai H, Zhang L, Sun Y, Liu X, Tian Z. Discrepancy of Growth Toxicity of Polystyrene Nanoplastics on Soybean ( Glycine max) and Mung Bean ( Vigna radiata). Toxics 2024; 12:155. [PMID: 38393250 PMCID: PMC10892715 DOI: 10.3390/toxics12020155] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/25/2023] [Revised: 02/12/2024] [Accepted: 02/15/2024] [Indexed: 02/25/2024]
Abstract
Nanoplastics, as a hot topic of novel contaminants, lack extensive concern in higher plants; especially the potential impact and mechanism of nanoplastics on legume crops remains elusive. In this study, the toxicity of polystyrene nanoplastics (PS-NPs, 200 nm) with diverse doses (control, 10, 50, 100, 200, 500 mg/L) to soybean and mung bean plants grown hydroponically for 7 d was investigated at both the macroscopic and molecular levels. The results demonstrated that the root length of both plants was markedly suppressed to varying degrees. Similarly, mineral elements (Fe, Zn) were notably decreased in soybean roots, consistent with Cu alteration in mung bean. Moreover, PS-NPs considerably elevated malondialdehyde (MDA) levels only in soybean roots. Enzyme activity data indicated mung bean exhibited significant damage only at higher doses of PS-NPs stress than soybean, implying mung bean is more resilient. Transcriptome analysis showed that PS-NPs stimulated the expression of genes associated with the antioxidant system in plant roots. Furthermore, starch and sucrose metabolism might play a key role in coping with PS-NPs to enhance soybean resistance, but the MAPK pathway was enriched in mung bean. Our findings provide valuable perspectives for an in-depth understanding of the performance of plants growing in waters contaminated by nanoplastics.
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Affiliation(s)
- Dan Su
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Wangwang Li
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Zhaowei Zhang
- State Key Laboratory of New Textile Materials and Advanced Processing Technologies, School of Bioengineering and Health, Wuhan Textile University, Wuhan 430200, China
| | - Hui Cai
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Le Zhang
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
| | - Yuanlong Sun
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
| | - Xiaoning Liu
- State Key Laboratory of Water Resources Engineering and Management, Wuhan University, Wuhan 430072, China
| | - Zhiquan Tian
- College of Chemistry and Molecular Sciences, Wuhan University, Wuhan 430072, China
- School of Ecology and Environment, Tibet University, Lhasa 850000, China
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Jia Q, Zhou M, Xiong Y, Wang J, Xu D, Zhang H, Liu X, Zhang W, Wang Q, Sun X, Chen H. Development of KASP markers assisted with soybean drought tolerance in the germination stage based on GWAS. Front Plant Sci 2024; 15:1352379. [PMID: 38425800 PMCID: PMC10902137 DOI: 10.3389/fpls.2024.1352379] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/30/2024] [Indexed: 03/02/2024]
Abstract
Soybean [Glycine max(L.)Merr.] is a leading oil-bearing crop and cultivated globally over a vast scale. The agricultural landscape in China faces a formidable challenge with drought significantly impacting soybean production. In this study, we treated a natural population of 264 Chinese soybean accessions using 15% PEG-6000 and used GR, GE, GI, RGR, RGE, RGI and ASFV as evaluation index. Using the ASFV, we screened 17 strong drought-tolerant soybean germplasm in the germination stage. Leveraging 2,597,425 high-density SNP markers, we conducted Genome-Wide Association Studies (GWAS) and identified 92 SNPs and 9 candidate genes significantly associated with drought tolerance. Furthermore, we developed two KASP markers for S14_5147797 and S18_53902767, which closely linked to drought tolerance. This research not only enriches the pool of soybean germplasm resources but also establishes a robust foundation for the molecular breeding of drought tolerance soybean varieties.
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Affiliation(s)
- Qianru Jia
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Miaomiao Zhou
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Yawen Xiong
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- College of Life Science, Nanjing Agricultural University, Nanjing, China
| | - Junyan Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Donghe Xu
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Japan
| | - Hongmei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaoqing Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qiong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xin Sun
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing, China
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58
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Jiang L, Yang X, Gao X, Yang H, Ma S, Huang S, Zhu J, Zhou H, Li X, Gu X, Zhou H, Liang Z, Yang A, Huang Y, Xiao M. Multiomics Analyses Reveal the Dual Role of Flavonoids in Pigmentation and Abiotic Stress Tolerance of Soybean Seeds. J Agric Food Chem 2024; 72:3231-3243. [PMID: 38303105 DOI: 10.1021/acs.jafc.3c08202] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/03/2024]
Abstract
The color of the seed coat has great diversity and is regarded as a biomarker of metabolic variations. Here we isolated a soybean variant (BLK) from a population of recombinant inbred lines with a black seed coat, while its sibling plants have yellow seed coats (YL). The BLK and YL plants showed no obvious differences in vegetative growth and seed weight. However, the BLK seeds had higher anthocyanins and flavonoids level and showed tolerance to various abiotic stresses including herbicide, oxidation, salt, and alkalinity during germination. Integrated metabolomic and transcriptomic analyses revealed that the upregulation of biosynthetic genes probably contributed to the overaccumulation of flavonoids in BLK seeds. The transient expression of those biosynthetic genes in soybean root hairs increased the levels of total flavonoids or anthocyanins. Our study revealed the molecular basis of flavonoid accumulation in soybean seeds, leveraging genetic engineering for both nutritious and stress-tolerant soybean germplasm.
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Affiliation(s)
- Ling Jiang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
- Yuelushan Laboratory, Changsha 410128, People's Republic of China
| | - Xiaofeng Yang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Xiewang Gao
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
- School of Life Sciences, Chinese University of Hong Kong, Hong Kong 999077, People's Republic of China
| | - Hui Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Shumei Ma
- Hunan Key Laboratory of Economic Crops Genetic Improvement and Integrated Utilization, School of Life Science, Hunan University of Science and Technology, Xiangtan 411201, People's Republic of China
| | - Shan Huang
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Jianyu Zhu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Hong Zhou
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Xiaohong Li
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Xiaoyan Gu
- Crop Research Institute, Hunan Academy of Agricultural Sciences, Changsha 410125, People's Republic of China
| | - Hongming Zhou
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Zeya Liang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Antong Yang
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
| | - Yong Huang
- Yuelushan Laboratory, Changsha 410128, People's Republic of China
- Key Laboratory of Hunan Province on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, People's Republic of China
- College of Bioscience and Biotechnology, Hunan Agricultural University, Changsha, Hunan 410128, China
| | - Mu Xiao
- Yuelushan Laboratory, Changsha 410128, People's Republic of China
- College of Agronomy, Hunan Agricultural University, Changsha 410128, People's Republic of China
- Key Laboratory of Hunan Province on Crop Epigenetic Regulation and Development, Hunan Agricultural University, Changsha 410128, People's Republic of China
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Song Z, Zhao F, Chu L, Lin H, Xiao Y, Fang Z, Wang X, Dong J, Lyu X, Yu D, Liu B, Gai J, Xu D. The GmSTF1/2-GmBBX4 negative feedback loop acts downstream of blue-light photoreceptors to regulate isoflavonoid biosynthesis in soybean. Plant Commun 2024; 5:100730. [PMID: 37817409 PMCID: PMC10873893 DOI: 10.1016/j.xplc.2023.100730] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 07/18/2023] [Accepted: 10/05/2023] [Indexed: 10/12/2023]
Abstract
Isoflavonoids, secondary metabolites derived from the phenylalanine pathway, are predominantly biosynthesized in legumes, especially soybean (Glycine max). They are not only essential for plant responses to biotic and abiotic stresses but also beneficial to human health. In this study, we report that light signaling controls isoflavonoid biosynthesis in soybean. Blue-light photoreceptors (GmCRY1s, GmCRY2s, GmPHOT1s, and GmPHOT2s) and the transcription factors GmSTF1 and GmSTF2 promote isoflavonoid accumulation, whereas the E3 ubiquitin ligase GmCOP1b negatively regulates isoflavonoid biosynthesis. GmPHOT1s and GmPHOT2s stabilize GmSTF1/2, whereas GmCOP1b promotes the degradation of these two proteins in soybean. GmSTF1/2 regulate the expression of approximately 27.9% of the genes involved in soybean isoflavonoid biosynthesis, including GmPAL2.1, GmPAL2.3, and GmUGT2. They also repress the expression of GmBBX4, a negative regulator of isoflavonoid biosynthesis in soybean. In addition, GmBBX4 physically interacts with GmSTF1 and GmSTF2 to inhibit their transcriptional activation activity toward target genes related to isoflavonoid biosynthesis. Thus, GmSTF1/2 and GmBBX4 form a negative feedback loop that acts downstream of photoreceptors in the regulation of isoflavonoid biosynthesis. Our study provides novel insights into the control of isoflavonoid biosynthesis by light signaling in soybean and will contribute to the breeding of soybean cultivars with high isoflavonoid content through genetic and metabolic engineering.
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Affiliation(s)
- Zhaoqing Song
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Fengyue Zhao
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Li Chu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Huan Lin
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Yuntao Xiao
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Zheng Fang
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Xuncheng Wang
- Beijing Key Laboratory of Environmentally Friendly Management of Fruit Diseases and Pests in North China, Institute of Plant and Environment Protection, Beijing Academy of Agriculture and Forestry Sciences, Beijing 100097, China
| | - Jie Dong
- Institute of Crop Science, College of Agriculture and Biotechnology, Zhejiang University, Hangzhou 310058, China
| | - Xiangguang Lyu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Deyue Yu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China
| | - Bin Liu
- State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Junyi Gai
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
| | - Dongqing Xu
- National Center for Soybean Improvement, State Key Laboratory of Crop Genetics & Germplasm Enhancement and Utilization, College of Agriculture, Nanjing Agricultural University, Nanjing 210095, China.
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Ko J, Shin T, Kang J, Baek J, Sang WG. Combining machine learning and remote sensing-integrated crop modeling for rice and soybean crop simulation. Front Plant Sci 2024; 15:1320969. [PMID: 38410726 PMCID: PMC10894942 DOI: 10.3389/fpls.2024.1320969] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/17/2023] [Accepted: 01/25/2024] [Indexed: 02/28/2024]
Abstract
Machine learning (ML) techniques offer a promising avenue for improving the integration of remote sensing data into mathematical crop models, thereby enhancing crop growth prediction accuracy. A critical variable for this integration is the leaf area index (LAI), which can be accurately assessed using proximal or remote sensing data based on plant canopies. This study aimed to (1) develop a machine learning-based method for estimating the LAI in rice and soybean crops using proximal sensing data and (2) evaluate the performance of a Remote Sensing-Integrated Crop Model (RSCM) when integrated with the ML algorithms. To achieve these objectives, we analyzed rice and soybean datasets to identify the most effective ML algorithms for modeling the relationship between LAI and vegetation indices derived from canopy reflectance measurements. Our analyses employed a variety of ML regression models, including ridge, lasso, support vector machine, random forest, and extra trees. Among these, the extra trees regression model demonstrated the best performance, achieving test scores of 0.86 and 0.89 for rice and soybean crops, respectively. This model closely replicated observed LAI values under different nitrogen treatments, achieving Nash-Sutcliffe efficiencies of 0.93 for rice and 0.97 for soybean. Our findings show that incorporating ML techniques into RSCM effectively captures seasonal LAI variations across diverse field management practices, offering significant potential for improving crop growth and productivity monitoring.
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Affiliation(s)
- Jonghan Ko
- Department of Applied Plant Science, Chonnam National University, Gwangju, Republic of Korea
| | - Taehwan Shin
- Department of Applied Plant Science, Chonnam National University, Gwangju, Republic of Korea
| | - Jiwoo Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju, Republic of Korea
| | - Jaekyeong Baek
- Crop Production and Physiology Division, National Institute of Crop Science, Wanju-gun, Jeollabuk-do, Republic of Korea
| | - Wan-Gyu Sang
- Crop Production and Physiology Division, National Institute of Crop Science, Wanju-gun, Jeollabuk-do, Republic of Korea
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Gélinas Bélanger J, Copley TR, Hoyos-Villegas V, O'Donoughue L. Dissection of the E8 locus in two early maturing Canadian soybean populations. Front Plant Sci 2024; 15:1329065. [PMID: 38390301 PMCID: PMC10881665 DOI: 10.3389/fpls.2024.1329065] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/27/2023] [Accepted: 01/15/2024] [Indexed: 02/24/2024]
Abstract
Soybean [Glycine max (L.) Merr.] is a short-day crop for which breeders want to expand the cultivation range to more northern agro-environments by introgressing alleles involved in early reproductive traits. To do so, we investigated quantitative trait loci (QTL) and expression quantitative trait loci (eQTL) regions comprised within the E8 locus, a large undeciphered region (~7.0 Mbp to 44.5 Mbp) associated with early maturity located on chromosome GM04. We used a combination of two mapping algorithms, (i) inclusive composite interval mapping (ICIM) and (ii) genome-wide composite interval mapping (GCIM), to identify major and minor regions in two soybean populations (QS15524F2:F3 and QS15544RIL) having fixed E1, E2, E3, and E4 alleles. Using this approach, we identified three main QTL regions with high logarithm of the odds (LODs), phenotypic variation explained (PVE), and additive effects for maturity and pod-filling within the E8 region: GM04:16,974,874-17,152,230 (E8-r1); GM04:35,168,111-37,664,017 (E8-r2); and GM04:41,808,599-42,376,237 (E8-r3). Using a five-step variant analysis pipeline, we identified Protein far-red elongated hypocotyl 3 (Glyma.04G124300; E8-r1), E1-like-a (Glyma.04G156400; E8-r2), Light-harvesting chlorophyll-protein complex I subunit A4 (Glyma.04G167900; E8-r3), and Cycling dof factor 3 (Glyma.04G168300; E8-r3) as the most promising candidate genes for these regions. A combinatorial eQTL mapping approach identified significant regulatory interactions for 13 expression traits (e-traits), including Glyma.04G050200 (Early flowering 3/E6 locus), with the E8-r3 region. Four other important QTL regions close to or encompassing major flowering genes were also detected on chromosomes GM07, GM08, and GM16. In GM07:5,256,305-5,404,971, a missense polymorphism was detected in the candidate gene Glyma.07G058200 (Protein suppressor of PHYA-105). These findings demonstrate that the locus known as E8 is regulated by at least three distinct genomic regions, all of which comprise major flowering genes.
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Affiliation(s)
- Jérôme Gélinas Bélanger
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
- Department of Plant Science, McGill University, Montréal, QC, Canada
| | - Tanya Rose Copley
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
| | | | - Louise O'Donoughue
- Centre de recherche sur les grains (CÉROM) Inc., St-Mathieu-de-Beloeil, QC, Canada
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Hu XY, Hua ZW, Yao LG, Du L, Niu QH, Li YY, Yan L, Chen ZJ, Zhang H. [Effects of Combined Stress of High Density Polyethylene Microplastics and Chlorimuron-ethyl on Soybean Growth and Rhizosphere Bacterial Community]. Huan Jing Ke Xue 2024; 45:1161-1172. [PMID: 38471953 DOI: 10.13227/j.hjkx.202304023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Subscribe] [Scholar Register] [Indexed: 03/14/2024]
Abstract
With the vigorous development of agriculture in China, plastic mulch film and pesticides are widely used in agricultural production. However, the accumulation of microplastics (formed by the degradation of plastic mulch film) and pesticides in soil has also caused many environmental problems. At present, the environmental biological effects of microplastics or pesticides have been reported, but there are few studies on the combined effects on crop growth and the rhizosphere soil bacterial community. Therefore, in this study, the high density polyethylene microplastics (HDPE, 500 mesh) were designed to be co-treated with sulfonylurea herbicide chlorimuron-ethyl to study their effects on soybean growth. In addition, the effects of the combined stress of HDPE and chlorimuron-ethyl on soybean rhizosphere soil bacterial community diversity, structure composition, microbial community network, and soil function were investigated using high-throughput sequencing technology, interaction network, and PICRUSt2 function analysis to clarify the combined toxicity of HDPE and chlorimuron-ethyl to soybean. The results showed that the half-life of chlorimuron-ethyl in soil was prolonged by the 1% HDPE treatment (from 11.5 d to 14.3 d), and the combined stress of HDPE and chlorimuron-ethyl had more obvious inhibition effects on soybean growth than that of the single pollutant or control. The HiSeq 2 500 sequencing showed that the rhizosphere bacterial community of soybean was composed of 20 phyla and 312 genera under combined stress, the number of phyla and genera was significantly less than that of the control and single pollutant treatment, and the relative abundances of bacteria with potential biological control and plant growth-promoting characteristics (such as Nocardioides and Sphingomonas) were reduced. Alpha diversity analysis showed that the combined stress significantly reduced the richness and diversity of the soybean rhizosphere bacterial community, and Beta diversity analysis showed that the combined stress significantly changed the structure of the bacterial community. The dominant flora of the rhizosphere bacterial community were regulated, and the abundances of secondary functional layers such as amino acid metabolism, energy metabolism, and lipid metabolism were reduced under combined stress by the analysis of LEfSe and PICRUSt2. It was inferred from the network analysis that the combined stress of HDPE and chlorimuron-ethyl reduced the total number of connections and network density of soil bacteria, simplified the network structure, and changed the important flora species to maintain the stability of the network. The results above indicated that the combined stress of HDPE and chlorimuron-ethyl significantly affected the growth of soybean and changed the rhizosphere bacterial community structure, soil function, and network structure. Compared with that of the single pollutant treatment, the potential risk of combined stress was greater. The results of this study can provide guidance for evaluating the ecological risks of polyethylene microplastics and chlorimuron-ethyl and for the remediation of contaminated soil.
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Affiliation(s)
- Xiao-Yue Hu
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of SouthNorth Water Diversion of Henan Province, Nanyang Normal University, Nanyang 473061, China
| | - Zi-Wei Hua
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of SouthNorth Water Diversion of Henan Province, Nanyang Normal University, Nanyang 473061, China
| | - Lun-Guang Yao
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of SouthNorth Water Diversion of Henan Province, Nanyang Normal University, Nanyang 473061, China
| | - Li Du
- School of Water Resources and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Qiu-Hong Niu
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of SouthNorth Water Diversion of Henan Province, Nanyang Normal University, Nanyang 473061, China
| | - Yu-Ying Li
- School of Water Resources and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Lu Yan
- School of Water Resources and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Zhao-Jin Chen
- School of Water Resources and Environmental Engineering, Nanyang Normal University, Nanyang 473061, China
| | - Hao Zhang
- School of Life Science and Agricultural Engineering, Research Center of Henan Provincial Agricultural Biomass Resource Engineering and Technology, Henan Province Artemisiae argyi Development and Utilization Engineering Technology Research Center, Innovation Center of Water Security for Water Source Region of Mid-Route Project of SouthNorth Water Diversion of Henan Province, Nanyang Normal University, Nanyang 473061, China
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Coffman L, Mejia HD, Alicea Y, Mustafa R, Ahmad W, Crawford K, Khan AL. Microbiome structure variation and soybean's defense responses during flooding stress and elevated CO 2. Front Plant Sci 2024; 14:1295674. [PMID: 38389716 PMCID: PMC10882081 DOI: 10.3389/fpls.2023.1295674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/17/2023] [Accepted: 12/27/2023] [Indexed: 02/24/2024]
Abstract
Introduction With current trends in global climate change, both flooding episodes and higher levels of CO2 have been key factors to impact plant growth and stress tolerance. Very little is known about how both factors can influence the microbiome diversity and function, especially in tolerant soybean cultivars. This work aims to (i) elucidate the impact of flooding stress and increased levels of CO2 on the plant defenses and (ii) understand the microbiome diversity during flooding stress and elevated CO2 (eCO2). Methods We used next-generation sequencing and bioinformatic methods to show the impact of natural flooding and eCO2 on the microbiome architecture of soybean plants' below- (soil) and above-ground organs (root and shoot). We used high throughput rhizospheric extra-cellular enzymes and molecular analysis of plant defense-related genes to understand microbial diversity in plant responses during eCO2 and flooding. Results Results revealed that bacterial and fungal diversity was substantially higher in combined flooding and eCO2 treatments than in non-flooding control. Microbial diversity was soil>root>shoot in response to flooding and eCO2. We found that sole treatment of eCO2 and flooding had significant abundances of Chitinophaga, Clostridium, and Bacillus. Whereas the combination of flooding and eCO2 conditions showed a significant abundance of Trichoderma and Gibberella. Rhizospheric extra-cellular enzyme activities were significantly higher in eCO2 than flooding or its combination with eCO2. Plant defense responses were significantly regulated by the oxidative stress enzyme activities and gene expression of Elongation factor 1 and Alcohol dehydrogenase 2 in floodings and eCO2 treatments in soybean plant root or shoot parts. Conclusion This work suggests that climatic-induced changes in eCO2 and submergence can reshape microbiome structure and host defenses, essential in plant breeding and developing stress-tolerant crops. This work can help in identifying core-microbiome species that are unique to flooding stress environments and increasing eCO2.
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Affiliation(s)
- Lauryn Coffman
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Hector D Mejia
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Yelinska Alicea
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Raneem Mustafa
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Waqar Ahmad
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
| | - Kerri Crawford
- Department of Biological Sciences and Chemistry, College of Natural Science and Mathematics, University of Houston, Houston, TX, United States
| | - Abdul Latif Khan
- Department of Engineering Technology, Cullen College of Engineering, University of Houston, Sugar Land, TX, United States
- Department of Biological Sciences and Chemistry, College of Natural Science and Mathematics, University of Houston, Houston, TX, United States
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Ma T, Zhang Y, Li Y, Zhao Y, Attiogbe KB, Fan X, Fan W, Sun J, Luo Y, Yu X, Ji W, Cheng X, Wu X. The Resistance of Soybean Variety Heinong 84 to Apple Latent Spherical Virus Is Controlled by Two Genetic Loci. Int J Mol Sci 2024; 25:2034. [PMID: 38396711 PMCID: PMC10889123 DOI: 10.3390/ijms25042034] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Revised: 02/01/2024] [Accepted: 02/03/2024] [Indexed: 02/25/2024] Open
Abstract
Apple latent spherical virus (ALSV) is widely used as a virus-induced gene silencing (VIGS) vector for function genome study. However, the application of ALSV to soybeans is limited by the resistance of many varieties. In this study, the genetic locus linked to the resistance of a resistant soybean variety Heinong 84 was mapped by high-throughput sequencing-based bulk segregation analysis (HTS-BSA) using a hybrid population crossed from Heinong 84 and a susceptible variety, Zhonghuang 13. The results showed that the resistance of Heinong 84 to ALSV is controlled by two genetic loci located on chromosomes 2 and 11, respectively. Cleaved amplified polymorphic sequence (CAPS) markers were developed for identification and genotyping. Inheritance and biochemical analyses suggest that the resistance locus on chromosome 2 plays a dominant dose-dependent role, while the other locus contributes a secondary role in resisting ALSV. The resistance locus on chromosome 2 might encode a protein that can directly inhibit viral proliferation, while the secondary resistance locus on chromosome 11 may encode a host factor required for viral proliferation. Together, these data reveal novel insights on the resistance mechanism of Heinong 84 to ALSV, which will benefit the application of ALSV as a VIGS vector.
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Affiliation(s)
- Tingshuai Ma
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Ying Zhang
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Yong Li
- College of Life Science, Northeast Agricultural University, Harbin 150030, China;
| | - Yu Zhao
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Kekely Bruno Attiogbe
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Xinyue Fan
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Wenqian Fan
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Jiaxing Sun
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Yalou Luo
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Xinwei Yu
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Weiqin Ji
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Xiaofei Cheng
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
| | - Xiaoyun Wu
- College of Plant Protection, Northeast Agricultural University, Harbin 150030, China; (T.M.); (Y.Z.); (Y.Z.); (K.B.A.); (X.F.); (W.F.); (Y.L.); (X.Y.); (W.J.)
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Wang J, Zhou M, Zhang H, Liu X, Zhang W, Wang Q, Jia Q, Xu D, Chen H, Su C. A genome-wide association analysis for salt tolerance during the soybean germination stage and development of KASP markers. Front Plant Sci 2024; 15:1352465. [PMID: 38384759 PMCID: PMC10879362 DOI: 10.3389/fpls.2024.1352465] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/08/2023] [Accepted: 01/12/2024] [Indexed: 02/23/2024]
Abstract
Salt stress poses a significant challenge to crop productivity, and understanding the genetic basis of salt tolerance is paramount for breeding resilient soybean varieties. In this study, a soybean natural population was evaluated for salt tolerance during the germination stage, focusing on key germination traits, including germination rate (GR), germination energy (GE), and germination index (GI). It was seen that under salt stress, obvious inhibitions were found on these traits, with GR, GE, and GI diminishing by 32% to 54% when compared to normal conditions. These traits displayed a coefficient of variation (31.81% to 50.6%) and a substantial generalized heritability (63.87% to 86.48%). Through GWAS, a total of 1841 significant single-nucleotide polymorphisms (SNPs) were identified to be associated with these traits, distributed across chromosome 2, 5, 6, and 20. Leveraging these significant association loci, 12 candidate genes were identified to be associated with essential functions in coordinating cellular responses, regulating osmotic stress, mitigating oxidative stress, clearing reactive oxygen species (ROS), and facilitating heavy metal ion transport - all of which are pivotal for plant development and stress tolerance. To validate the candidate genes, quantitative real-time polymerase chain reaction (qRT-PCR) analysis was conducted, revealing three highly expressed genes (Glyma.02G067700, Glyma.02G068900, and Glyma.02G070000) that play pivotal roles in plant growth, development, and osmoregulation. In addition, based on these SNPs related with salt tolerance, KASP (Kompetitive Allele-Specific PCR)markers were successfully designed to genotype soybean accessions. These findings provide insight into the genetic base of soybean salt tolerance and candidate genes for enhancing soybean breeding programs in this study.
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Affiliation(s)
- Junyan Wang
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Miaomiao Zhou
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Hongmei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Xiaoqing Liu
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Wei Zhang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qiong Wang
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Qianru Jia
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
| | - Donghe Xu
- Japan International Research Center for Agricultural Sciences (JIRCAS), Tsukuba, Ibaraki, Japan
| | - Huatao Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing, China
- Zhongshan Biological Breeding Laboratory (ZSBBL), Nanjing, China
| | - Chengfu Su
- College of Agronomy, Qingdao Agricultural University, Qingdao, China
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Ding C, Alghabari F, Rauf M, Zhao T, Javed MM, Alshamrani R, Ghazy AH, Al-Doss AA, Khalid T, Yang SH, Shah ZH. Optimization of soybean physiochemical, agronomic, and genetic responses under varying regimes of day and night temperatures. Front Plant Sci 2024; 14:1332414. [PMID: 38379774 PMCID: PMC10876898 DOI: 10.3389/fpls.2023.1332414] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/02/2023] [Accepted: 12/29/2023] [Indexed: 02/22/2024]
Abstract
Soybean is an important oilseed crop worldwide; however, it has a high sensitivity to temperature variation, particularly at the vegetative stage to the pod-filling stage. Temperature change affects physiochemical and genetic traits regulating the soybean agronomic yield. In this regard, the current study aimed to comparatively evaluate the effects of varying regimes of day and night temperatures (T1 = 20°C/12°C, T2 = 25°C/17°C, T3 = 30°C/22°C, T4 = 35°C/27°C, and T5 = 40°C/32°C) on physiological (chlorophyll, photosynthesis, stomatal conductance, transpiration, and membrane damage) biochemical (proline and antioxidant enzymes), genetic (GmDNJ1, GmDREB1G;1, GmHSF-34, GmPYL21, GmPIF4b, GmPIP1;6, GmGBP1, GmHsp90A2, GmTIP2;6, and GmEF8), and agronomic traits (pods per plant, seeds per plant, pod weight per plant, and seed yield per plant) of soybean cultivars (Swat-84 and NARC-1). The experiment was performed in soil plant atmosphere research (SPAR) units using two factorial arrangements with cultivars as one factor and temperature treatments as another factor. A significant increase in physiological, biochemical, and agronomic traits with increased gene expression was observed in both soybean cultivars at T4 (35°C/27°C) as compared to below and above regimes of temperatures. Additionally, it was established by correlation, principal component analysis (PCA), and heatmap analysis that the nature of soybean cultivars and the type of temperature treatments have a significant impact on the paired association of agronomic and biochemical traits, which in turn affects agronomic productivity. Furthermore, at corresponding temperature regimes, the expression of the genes matched the expression of physiochemical traits. The current study has demonstrated through extensive physiochemical, genetic, and biochemical analyses that the ideal day and night temperature for soybeans is T4 (35°C/27°C), with a small variation having a significant impact on productivity from the vegetative stage to the grain-filling stage.
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Affiliation(s)
- Chuanbo Ding
- College of Traditional Chinese Medicine, Jilin Agriculture Science and Technology College, Jilin, China
| | - Fahad Alghabari
- Department of Plant Breeding and Genetics, Pir Mehr Ali Shah, Arid Agriculture University, Rawalpindi, Pakistan
| | - Muhammad Rauf
- Department of Plant Breeding and Genetics, Pir Mehr Ali Shah, Arid Agriculture University, Rawalpindi, Pakistan
| | - Ting Zhao
- College of Traditional Chinese Medicine, Jilin Agriculture Science and Technology College, Jilin, China
| | - Muhammad Matloob Javed
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Rahma Alshamrani
- College of Traditional Chinese Medicine, Jilin Agriculture Science and Technology College, Jilin, China
| | - Abdel-Halim Ghazy
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Abdullah A. Al-Doss
- Department of Plant Production, College of Food and Agriculture Science, King Saud University, Riyadh, Saudi Arabia
| | - Taimoor Khalid
- Department of Plant Breeding and Genetics, Pir Mehr Ali Shah, Arid Agriculture University, Rawalpindi, Pakistan
| | - Seung Hwan Yang
- Department of Biotechnology, Chonnam National University, Yeosu, Republic of Korea
| | - Zahid Hussain Shah
- Department of Plant Breeding and Genetics, Pir Mehr Ali Shah, Arid Agriculture University, Rawalpindi, Pakistan
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Petrović K, Orzali L, Krsmanović S, Valente MT, Tolimir M, Pavlov J, Riccioni L. Genetic diversity and pathogenicity of the Fusarium species complex on soybean in Serbia. Plant Dis 2024. [PMID: 38311795 DOI: 10.1094/pdis-11-23-2450-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 02/06/2024]
Abstract
Using morphological and cultural characteristics for identification, 36 Fusarium isolates were recovered from diseased roots, stems, and seeds of soybean from several localities throughout Vojvodina Province, Serbia, were identified as Fusarium spp. Based on molecular characterization, 12 Fusarium species were identified: F. acuminatum, F. avenaceum, F. commune, F. equiseti, F. graminearum, F. incarnatum, F. oxysporum, F. proliferatum, F. solani, F. sporotrichioides, F. subglutinans, and F. tricinctum. The EF-1α based-phylogeny grouped the isolates into 12 well-supported clades, but the polymorphisms among sequences in some clades suggested the use of the species complex concept: (1) FIESC - F. incarnatum and F. equiseti; (2) FOSC - F. oxysporum; (3) FSSC - F. solani; and (4) FAATSC - F. acuminatum, F. avenaceum and F. tricinctum. Pathogenicity tests showed that the most aggressive species causing soybean seed rot were F. sporotrichioides, F. graminearum, FIESC, and F. avenaceum. Furthermore, F. subglutinans, FSSC, and F. proliferatum, showed a high percentage of pathogenicity on soybean seeds (80-100%), while variability in pathogenicity occurred within isolates of F. tricinctum species has occurred variability in the virulence of different isolates. FOSC, F. commune and F. acuminatum had the lowest pathogenicity degree. To our knowledge, this is the first study of the characterization of Fusarium complex species on soybean in Serbia. This study provides valuable information about the structure composition of Fusarium complex species and pathogenicity that will be used in further research on soybean resistance to Fusarium-based diseases.
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Affiliation(s)
- Kristina Petrović
- Maize Research Institute Zemun Polje, 229787, Belgrade, Serbia
- BioSense Institute, 622259, Novi Sad, Vojvodina, Serbia;
| | - Laura Orzali
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, 462014, Centro di ricerca per la patologia vegetale, Rome, Italy;
| | | | - Maria Teresa Valente
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, 462014, Centro di ricerca per la patologia vegetale, Rome, Italy;
| | - Miodrag Tolimir
- Maize Research Institute Zemun Polje, 229787, Belgrade, Serbia;
| | - Jovan Pavlov
- Maize Research Institute Zemun Polje, 229787, Belgrade, Serbia;
| | - Luca Riccioni
- Consiglio per la ricerca in agricoltura e l'analisi dell'economia agraria, 462014, Centro di ricerca per la patologia vegetale, Rome, Italy;
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Li Y, Ye H, Vuong TD, Zhou L, Do TD, Satish Chhapekar S, Zhao W, Li B, Jin T, Gu J, Li C, Chen Y, Li Y, Wang ZY, Nguyen HT. A novel natural variation in the promoter of GmCHX1 regulates conditional gene expression to improve salt tolerance in soybean. J Exp Bot 2024; 75:1051-1062. [PMID: 37864556 PMCID: PMC10837011 DOI: 10.1093/jxb/erad404] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 10/20/2023] [Indexed: 10/23/2023]
Abstract
Identification and characterization of soybean germplasm and gene(s)/allele(s) for salt tolerance is an effective way to develop improved varieties for saline soils. Previous studies identified GmCHX1 (Glyma03g32900) as a major salt tolerance gene in soybean, and two main functional variations were found in the promoter region (148/150 bp insertion) and the third exon with a retrotransposon insertion (3.78 kb). In the current study, we identified four salt-tolerant soybean lines, including PI 483460B (Glycine soja), carrying the previously identified salt-sensitive variations at GmCHX1, suggesting new gene(s) or new functional allele(s) of GmCHX1 in these soybean lines. Subsequently, we conducted quantitative trait locus (QTL) mapping in a recombinant-inbred line population (Williams 82 (salt-sensitive) × PI 483460B) to identify the new salt tolerance loci/alleles. A new locus, qSalt_Gm18, was mapped on chromosome 18 associated with leaf scorch score. Another major QTL, qSalt_Gm03, was identified to be associated with chlorophyll content ratio and leaf scorch score in the same chromosomal region of GmCHX1 on chromosome 3. Novel variations in a STRE (stress response element) cis-element in the promoter region of GmCHX1 were found to regulate the salt-inducible expression of the gene in these four newly identified salt-tolerant lines including PI 483460B. This new allele of GmCHX1 with salt-inducible expression pattern provides an energy cost efficient (conditional gene expression) strategy to protect soybean yield in saline soils without yield penalty under non-stress conditions. Our results suggest that there might be no other major salt tolerance locus similar to GmCHX1 in soybean germplasm, and further improvement of salt tolerance in soybean may rely on gene-editing techniques instead of looking for natural variations.
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Affiliation(s)
- Yang Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Heng Ye
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Tri D Vuong
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Lijuan Zhou
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | - Tuyen D Do
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
| | | | - Wenqian Zhao
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Bin Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Ting Jin
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Jinbao Gu
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Cong Li
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yanhang Chen
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Yan Li
- National Key Laboratory of Crop Genetics and Germplasm Enhancement, National Center for Soybean Improvement, Key Laboratory for Biology and Genetic Improvement of Soybean (General, Ministry of Agriculture), Jiangsu Collaborative Innovation Center for Modern Crop Production, Nanjing Agricultural University, Nanjing, 210095, China
| | - Zhen-Yu Wang
- Institute of Nanfan & Seed Industry, Guangdong Academy of Science, Guangzhou, 510316, China
| | - Henry T Nguyen
- Division of Plant Science and Technology, University of Missouri, Columbia, MO 65211, USA
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Yan D, Huang L, Mei Z, Bao H, Xie Y, Yang C, Gao X. Untargeted metabolomics revealed the effect of soybean metabolites on poly(γ-glutamic acid) production in fermented natto and its metabolic pathway. J Sci Food Agric 2024; 104:1298-1307. [PMID: 37782527 DOI: 10.1002/jsfa.13011] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/25/2023] [Revised: 09/17/2023] [Accepted: 10/02/2023] [Indexed: 10/03/2023]
Abstract
BACKGROUND Natto mucus is mainly composed of poly(γ-glutamic acid) (γ-PGA), which affects the sensory quality of natto and has some effective functional activities. The soybean metabolites that cause different γ-PGA contents in different fermented natto are unclear. RESULTS In this study, we use untargeted metabolomics to analyze the metabolites of high-production γ-PGA natto and low-production γ-PGA natto and their fermented substrate soybean. A total of 257 main significantly different metabolites with the same trend among the three comparison groups were screened, of which 114 were downregulated and 143 were upregulated. Through the enrichment of metabolic pathways, the metabolic pathways with significant differences were purine metabolism, nucleotide metabolism, fructose and mannose metabolism, anthocyanin biosynthesis, isoflavonoid biosynthesis and the pentose phosphate pathway. CONCLUSION For 114 downregulated main significantly different metabolites with the same trend among the three comparison groups, Bacillus subtilis (natto) may directly decompose them to synthesize γ-PGA. Adding downregulated substances before fermentation or cultivating soybean varieties with the goal of high production of such substances has a great effect on the production of γ-PGA by natto fermentation. The enrichment analysis results showed the main pathways affecting the production of γ-PGA by Bacillus subtilis (natto) using soybean metabolites, which provides a theoretical basis for the production of γ-PGA by soybean and promotes the diversification of natto products. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Delin Yan
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Lei Huang
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Zhiqing Mei
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Han Bao
- College of Food Engineering, Beibu Gulf University, Qinzhou, China
| | - Yaman Xie
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
| | - Cunyi Yang
- Guangdong Provincial Key Laboratory of Molecular Plant Breeding, College of Agriculture, South China Agricultural University, Guangzhou, China
| | - Xiangyang Gao
- Guangdong Provincial Key Laboratory of Nutraceuticals and Functional Foods, College of Food Science, South China Agricultural University, Guangzhou, China
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Mengistu A, Read QD, Sykes V, Kelly H, Kharel T, Bellaloui N. Cover Crop and Crop Rotation Effects on Tissue and Soil Population Dynamics of Macrophomina phaseolina and Yield Under No-Till System. Plant Dis 2024; 108:302-310. [PMID: 37773328 DOI: 10.1094/pdis-03-23-0443-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/01/2023]
Abstract
The effects of crop rotation and winter cover crops on soybean yield and colony-forming (CFU) units of Macrophomina phaseolina, the causal agent of charcoal rot (CR), are poorly understood. A field trial was conducted from 2011 to 2015 to evaluate (i) the impact of crop rotation consisting of soybean (Glycine max [L.] Merr.) following cotton (Gossypium hirsutum L.), soybean following corn (Zea mays L.), and soybean following soybean over a 2-year rotation and its interaction with cover crop and (ii) the impact of different cover crops on a continuous soybean crop over a 5-year period. This trial was conducted in a field with 10 subsequent years of cover crop and rotation treatments. Cover crops consisted of winter wheat (Triticum aestivum L.) and Austrian winter pea (Pisum sativum L. subsp. sativum var. arvense), hairy vetch (Vicia villosa Roth), and a fallow treatment was evaluated with and without poultry litter application (bio-cover). Tissue CFU of M. phaseolina varied significantly between crop rotation treatments: plots where soybean was grown following cotton had significantly greater tissue CFU than plots following soybean. Poultry litter and hairy vetch cover cropping caused increased tissue CFU, though this effect differed by year and crop rotation treatment. Soil CFU in 2015 was substantially lower compared with 2011. However, under some crop rotation sequences, plots in the fallow treatment had significantly greater soil CFU than plots where hairy vetch and wheat was grown as a cover crop. Yield was greater in 2015 compared with 2011. There was a significant interaction of the previous crop in the rotation with year, and greater yield was observed in plots planted following cotton in the rotation in 2015 but not in 2011. The result from the continuous soybean planted over 5 years showed that there were no significant overall effects of any of the cover crop treatments nor was there interaction between cover crop treatment and year on yield. The lack of significant interaction between crop rotation and cover crop and the absence of significant differences between cover crop treatments in continuous soybean planting suggest that cover crop recommendations for midsouthern soybean growers may need to be independent of crop rotation and be based on long-term crop needs.
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Affiliation(s)
- Alemu Mengistu
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Jackson, TN 38301
| | - Quentin D Read
- Southeast Area Statistician, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Raleigh, NC 27606
| | - Virginia Sykes
- Department of Plant Sciences, University of Tennessee, Knoxville, TN 37996
| | - Heather Kelly
- Entomology and Plant Pathology, University of Tennessee, Jackson, TN 38301
| | - Tulsi Kharel
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Stoneville, MS 38776-0350
| | - Nacer Bellaloui
- Crop Genetics Research Unit, United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Stoneville, MS 38776-0350
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71
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Zhang X, Chen JX, Lian WT, Zhou HW, He Y, Li XX, Liao H. Molecular module GmPTF1a/b-GmNPLa regulates rhizobia infection and nodule formation in soybean. New Phytol 2024; 241:1813-1828. [PMID: 38062896 DOI: 10.1111/nph.19462] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/21/2023] [Accepted: 11/08/2023] [Indexed: 01/26/2024]
Abstract
Nodulation begins with the initiation of infection threads (ITs) in root hairs. Though mutual recognition and early symbiotic signaling cascades in legumes are well understood, molecular mechanisms underlying bacterial infection processes and successive nodule organogenesis remain largely unexplored. We functionally investigated a novel pectate lyase enzyme, GmNPLa, and its transcriptional regulator GmPTF1a/b in soybean (Glycine max), where their regulatory roles in IT development and nodule formation were elucidated through investigation of gene expression patterns, bioinformatics analysis, biochemical verification of genetic interactions, and observation of phenotypic impacts in transgenic soybean plants. GmNPLa was specifically induced by rhizobium inoculation in root hairs. Manipulation of GmNPLa produced remarkable effects on IT and nodule formation. GmPTF1a/b displayed similar expression patterns as GmNPLa, and manipulation of GmPTF1a/b also severely influenced nodulation traits. LI soybeans with low nodulation phenotypes were nearly restored to HI nodulation level by complementation of GmNPLa and/or GmPTF1a. Further genetic and biochemical analysis demonstrated that GmPTF1a can bind to the E-box motif to activate transcription of GmNPLa, and thereby facilitate nodulation. Taken together, our findings potentially reveal novel mediation of cell wall gene expression involving the basic helix-loop-helix transcription factor GmPTF1a/b acts as a key early regulator of nodulation in soybean.
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Affiliation(s)
- Xiao Zhang
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Jia-Xin Chen
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Wen-Ting Lian
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hui-Wen Zhou
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Ying He
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Xin-Xin Li
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
| | - Hong Liao
- Root Biology Center, College of Resources and Environment, Fujian Agriculture and Forestry University, Fuzhou, 350002, China
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72
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Santos TLB, Baldin ELL, Lima APS, Santana AS, Santos MC, Silveira BRR, Bueno NM, Cabral IR, Soares MCE, Pinheiro AM, Lourenção AL. Intraspecific and interspecific interaction and fitness cost of stink bugs Euschistus heros, Diceraeus melacanthus, and Piezodorus guildinii in soybean. Pest Manag Sci 2024; 80:661-668. [PMID: 37752087 DOI: 10.1002/ps.7794] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 08/16/2023] [Accepted: 09/27/2023] [Indexed: 09/28/2023]
Abstract
BACKGROUND The most common pentatomid species in soybean crops are Euschistus heros (F.), Piezodorus guildinii (W.), and Diceraeus melacanthus (D.), causing a significant reduction in yield. It is known that these stink bugs inhabit the reproductive structures of soybeans simultaneously; however, there are few studies addressing their intraguild interactions, as well as aspects of possible competition between them in plants. Thus, the interspecific and intraspecific interactions of these stink bugs were evaluated in laboratory and field conditions, throughout the duration of the instars and adulthood, including longevity, mortality, and the number of eggs per female. RESULTS Euschistus heros had a higher competitive capacity in the interaction with D. melacanthus and P. guildinii, negatively interfering in the abundance or development (duration of instar, fertility, and mortality) of these stink bugs in soybean crops. This interference may act on the natural balance of these insect pests. Mortality of adults in interactions containing E. heros as a competitor or not showed that this species was not affected by the other species under field conditions. In the scenario where D. melacanthus was evaluated, it was observed that the presence of other species caused higher mortality in D. melacanthus. Additionally, higher P. guildiniii mortality was observed in interspecific interactions. CONCLUSION Our results suggest that E. heros has a greater competitive ability in the soybean crop, followed by D. melacanthus and P. guildinii. Therefore, the results found justified the greater abundance of E. heros and helped to explain the increasing occurrence of D. melacanthus in soybean crops, contributing to new directions for understanding the interaction of the soybean stink bug complex. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Thais L Braga Santos
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | - Edson L Lopes Baldin
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | - Ana P Santana Lima
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | - Alisson S Santana
- Department of Entomology, University of Nebraska, North Platte, NE, USA
| | - Maria C Santos
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | | | - Nadia M Bueno
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | - Isabella R Cabral
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | - Muriel C Emanoeli Soares
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | - Aline M Pinheiro
- Department of Crop Protection, School of Agriculture, São Paulo State University, Botucatu, Brazil
| | - André L Lourenção
- Department of Entomology and Acarology, College of Agriculture, University of São Paulo, São Paulo, Brazil
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Song J, Liu Y, Cai W, Zhou S, Fan X, Hu H, Ren L, Xue Y. Unregulated GmAGL82 due to Phosphorus Deficiency Positively Regulates Root Nodule Growth in Soybean. Int J Mol Sci 2024; 25:1802. [PMID: 38339080 PMCID: PMC10855635 DOI: 10.3390/ijms25031802] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2023] [Revised: 01/28/2024] [Accepted: 01/30/2024] [Indexed: 02/12/2024] Open
Abstract
Nitrogen fixation, occurring through the symbiotic relationship between legumes and rhizobia in root nodules, is crucial in sustainable agriculture. Nodulation and soybean production are influenced by low levels of phosphorus stress. In this study, we discovered a MADS transcription factor, GmAGL82, which is preferentially expressed in nodules and displays significantly increased expression under conditions of phosphate (Pi) deficiency. The overexpression of GmAGL82 in composite transgenic plants resulted in an increased number of nodules, higher fresh weight, and enhanced soluble Pi concentration, which subsequently increased the nitrogen content, phosphorus content, and overall growth of soybean plants. Additionally, transcriptome analysis revealed that the overexpression of GmAGL82 significantly upregulated the expression of genes associated with nodule growth, such as GmENOD100, GmHSP17.1, GmHSP17.9, GmSPX5, and GmPIN9d. Based on these findings, we concluded that GmAGL82 likely participates in the phosphorus signaling pathway and positively regulates nodulation in soybeans. The findings of this research may lay the theoretical groundwork for further studies and candidate gene resources for the genetic improvement of nutrient-efficient soybean varieties in acidic soils.
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Affiliation(s)
- Jia Song
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
| | - Ying Liu
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Wangxiao Cai
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China; (W.C.); (S.Z.); (X.F.)
| | - Silin Zhou
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China; (W.C.); (S.Z.); (X.F.)
| | - Xi Fan
- College of Chemistry and Environment, Guangdong Ocean University, Zhanjiang 524088, China; (W.C.); (S.Z.); (X.F.)
| | - Hanqiao Hu
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Lei Ren
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
| | - Yingbin Xue
- College of Coastal Agricultural Science, Guangdong Ocean University, Zhanjiang 524088, China; (J.S.); (Y.L.); (H.H.)
- South China Branch of National Saline-Alkali Tolerant Rice Technology Innovation Center, Zhanjiang 524088, China
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74
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Yu X, Fu X, Yang Q, Jin H, Zhu L, Yuan F. Genetic and Phenotypic Characterization of Soybean Landraces Collected from the Zhejiang Province in China. Plants (Basel) 2024; 13:353. [PMID: 38337886 PMCID: PMC10856940 DOI: 10.3390/plants13030353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/16/2023] [Revised: 01/12/2024] [Accepted: 01/19/2024] [Indexed: 02/12/2024]
Abstract
The soybean is an important feed, industrial raw material, and food crop in the world due to its rich components. There is a long history of soybean cultivation with different types and rich resources in the Zhejiang province of China. It is important to understand genetic diversity as well as phenotypic variation for soybean breeding. The objective of this study was to analyze both genetic and phenotypic characteristics of the 78 soybean landraces collected, and to explore a potential advantage of germplasm resources for further application. These 78 autumn-type soybean landraces have been propagated, identified, and evaluated in both 2021 and 2022. There were agronomic, quality, and genetic variations according to the comprehensive analyses. There was a good consistency between seed size and seed coat color. There were significant differences of seed protein, fat, and sugar contents based upon the seed coat color. These soybean landraces were genotyped using 42 simple sequence repeat markers and then clustered into two groups. The two groups had a consistency with the seed coat color. This study gave us a combined understanding of both the phenotypic variation and the genetic diversity of the soybean landraces. Therefore, the reasonable crossing between different soybean types is highly recommended.
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Affiliation(s)
- Xiaomin Yu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Xujun Fu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Qinghua Yang
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Hangxia Jin
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Longming Zhu
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
| | - Fengjie Yuan
- Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China; (X.F.); (Q.Y.); (H.J.); (L.Z.)
- Xianghu Laboratory, Hangzhou 311231, China
- Key Laboratory of Information Traceability for Agricultural Products, Ministry of Agriculture and Rural Affairs of China, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
- Key Laboratory of Digital Upland Crops of Zhejiang Province, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, China
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75
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Zhang Y, Bhat JA, Zhang Y, Yang S. Understanding the Molecular Regulatory Networks of Seed Size in Soybean. Int J Mol Sci 2024; 25:1441. [PMID: 38338719 PMCID: PMC10855573 DOI: 10.3390/ijms25031441] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2023] [Revised: 01/22/2024] [Accepted: 01/23/2024] [Indexed: 02/12/2024] Open
Abstract
Soybean being a major cash crop provides half of the vegetable oil and a quarter of the plant proteins to the global population. Seed size traits are the most important agronomic traits determining the soybean yield. These are complex traits governed by polygenes with low heritability as well as are highly influenced by the environment as well as by genotype x environment interactions. Although, extensive efforts have been made to unravel the genetic basis and molecular mechanism of seed size in soybean. But most of these efforts were majorly limited to QTL identification, and only a few genes for seed size were isolated and their molecular mechanism was elucidated. Hence, elucidating the detailed molecular regulatory networks controlling seed size in soybeans has been an important area of research in soybeans from the past decades. This paper describes the current progress of genetic architecture, molecular mechanisms, and regulatory networks for seed sizes of soybeans. Additionally, the main problems and bottlenecks/challenges soybean researchers currently face in seed size research are also discussed. This review summarizes the comprehensive and systematic information to the soybean researchers regarding the molecular understanding of seed size in soybeans and will help future research work on seed size in soybeans.
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Affiliation(s)
- Ye Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (Y.Z.); (Y.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | | | - Yaohua Zhang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (Y.Z.); (Y.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
| | - Suxin Yang
- Key Laboratory of Soybean Molecular Design Breeding, State Key Laboratory of Black Soils Conservation and Utilization, Northeast Institute of Geography and Agroecology, Chinese Academy of Sciences, Changchun 130102, China; (Y.Z.); (Y.Z.)
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing 101408, China
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76
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Clayton EJ, Islam NS, Pannunzio K, Kuflu K, Sirjani R, Kohalmi SE, Dhaubhadel S. Soybean AROGENATE DEHYDRATASES (GmADTs): involvement in the cytosolic isoflavonoid metabolon or trans-organelle continuity? Front Plant Sci 2024; 15:1307489. [PMID: 38322824 PMCID: PMC10845154 DOI: 10.3389/fpls.2024.1307489] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/04/2023] [Accepted: 01/03/2024] [Indexed: 02/08/2024]
Abstract
Soybean (Glycine max) produces a class of phenylalanine (Phe) derived specialized metabolites, isoflavonoids. Isoflavonoids are unique to legumes and are involved in defense responses in planta, and they are also necessary for nodule formation with nitrogen-fixing bacteria. Since Phe is a precursor of isoflavonoids, it stands to reason that the synthesis of Phe is coordinated with isoflavonoid production. Two putative AROGENATE DEHYDRATASE (ADT) isoforms were previously co-purified with the soybean isoflavonoid metabolon anchor ISOFLAVONE SYNTHASE2 (GmIFS2), however the GmADT family had not been characterized. Here, we present the identification of the nine member GmADT family. We determined that the GmADTs share sequences required for enzymatic activity and allosteric regulation with other characterized plant ADTs. Furthermore, the GmADTs are differentially expressed, and multiple members have dual substrate specificity, also acting as PREPHENATE DEHYDRATASES. All GmADT isoforms were detected in the stromules of chloroplasts, and they all interact with GmIFS2 in the cytosol. In addition, GmADT12A interacts with multiple other isoflavonoid metabolon members. These data substantiate the involvement of GmADT isoforms in the isoflavonoid metabolon.
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Affiliation(s)
- Emily J. Clayton
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Nishat S. Islam
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Kelsey Pannunzio
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Kuflom Kuflu
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
| | - Ramtin Sirjani
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Susanne E. Kohalmi
- Department of Biology, University of Western Ontario, London, ON, Canada
| | - Sangeeta Dhaubhadel
- London Research and Development Centre, Agriculture and Agri-Food Canada, London, ON, Canada
- Department of Biology, University of Western Ontario, London, ON, Canada
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77
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Zhang Z, Zhang Z, Shan M, Amjad Z, Xue J, Zhang Z, Wang J, Guo Y. Genome-Wide Studies of FH Family Members in Soybean ( Glycine max) and Their Responses under Abiotic Stresses. Plants (Basel) 2024; 13:276. [PMID: 38256829 PMCID: PMC10820127 DOI: 10.3390/plants13020276] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/05/2023] [Revised: 01/10/2024] [Accepted: 01/15/2024] [Indexed: 01/24/2024]
Abstract
Formins or formin homology 2 (FH2) proteins, evolutionarily conserved multi-domain proteins in eukaryotes, serve as pivotal actin organizers, orchestrating the structure and dynamics of the actin cytoskeleton. However, a comprehensive investigation into the formin family and their plausible involvement in abiotic stress remains undocumented in soybean (Glycine max). In the current study, 34 soybean FH (GmFH)family members were discerned, their genomic distribution spanning the twenty chromosomes in a non-uniform pattern. Evolutionary analysis of the FH gene family across plant species delineated five discernible groups (Group I to V) and displayed a closer evolutionary relationship within Glycine soja, Glycine max, and Arabidopsis thaliana. Analysis of the gene structure of GmFH unveiled variable sequence lengths and substantial diversity in conserved motifs. Structural prediction in the promoter regions of GmFH gene suggested a large set of cis-acting elements associated with hormone signaling, plant growth and development, and stress responses. The investigation of the syntenic relationship revealed a greater convergence of GmFH genes with dicots, indicating a close evolutionary affinity. Transcriptome data unveiled distinctive expression patterns of several GmFH genes across diverse plant tissues and developmental stages, underscoring a spatiotemporal regulatory framework governing the transcriptional dynamics of GmFH gene. Gene expression and qRT-PCR analysis identified many GmFH genes with a dynamic pattern in response to abiotic stresses, revealing their potential roles in regulating plant stress adaptation. Additionally, protein interaction analysis highlighted an intricate web of interactions among diverse GmFH proteins. These findings collectively underscore a novel biological function of GmFH proteins in facilitating stress adaptation in soybeans.
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Affiliation(s)
- Zhenbiao Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zhongqi Zhang
- Heze Academy of Agricultural Sciences, Heze 274000, China
| | - Muhammad Shan
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zarmeena Amjad
- SINO_PAK Joint Research Laboratory, Institute of Plant Breeding and Biotechnology, MNS University of Agriculture, Multan 60000, Pakistan
| | - Jin Xue
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Zenglin Zhang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Jie Wang
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
| | - Yongfeng Guo
- Tobacco Research Institute, Chinese Academy of Agricultural Sciences, Qingdao 266101, China
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78
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Li M, Zhang P, Guo Z, Zhao W, Li Y, Yi T, Cao W, Gao L, Tian CF, Chen Q, Ren F, Rui Y, White JC, Lynch I. Dynamic Transformation of Nano-MoS 2 in a Soil-Plant System Empowers Its Multifunctionality on Soybean Growth. Environ Sci Technol 2024; 58:1211-1222. [PMID: 38173352 PMCID: PMC10795185 DOI: 10.1021/acs.est.3c09004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/30/2023] [Revised: 12/20/2023] [Accepted: 12/21/2023] [Indexed: 01/05/2024]
Abstract
Molybdenum disulfide (nano-MoS2) nanomaterials have shown great potential for biomedical and catalytic applications due to their unique enzyme-mimicking properties. However, their potential agricultural applications have been largely unexplored. A key factor prior to the application of nano-MoS2 in agriculture is understanding its behavior in a complex soil-plant system, particularly in terms of its transformation. Here, we investigate the distribution and transformation of two types of nano-MoS2 (MoS2 nanoparticles and MoS2 nanosheets) in a soil-soybean system through a combination of synchrotron radiation-based X-ray absorption near-edge spectroscopy (XANES) and single-particle inductively coupled plasma mass spectrometry (SP-ICP-MS). We found that MoS2 nanoparticles (NPs) transform dynamically in soil and plant tissues, releasing molybdenum (Mo) and sulfur (S) that can be incorporated gradually into the key enzymes involved in nitrogen metabolism and the antioxidant system, while the rest remain intact and act as nanozymes. Notably, there is 247.9 mg/kg of organic Mo in the nodule, while there is only 49.9 mg/kg of MoS2 NPs. This study demonstrates that it is the transformation that leads to the multifunctionality of MoS2, which can improve the biological nitrogen fixation (BNF) and growth. Therefore, MoS2 NPs enable a 30% increase in yield compared to the traditional molybdenum fertilizer (Na2MoO4). Excessive transformation of MoS2 nanosheets (NS) leads to the overaccumulation of Mo and sulfate in the plant, which damages the nodule function and yield. The study highlights the importance of understanding the transformation of nanomaterials for agricultural applications in future studies.
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Affiliation(s)
- Mingshu Li
- Department
of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- College
of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
- China
CDC Key Laboratory of Environment and Population Health, National
Institute of Environmental Health, Chinese
Center for Disease Control and Prevention, Beijing 100021, China
| | - Peng Zhang
- Department
of Environmental Science and Engineering, University of Science and Technology of China, Hefei 230026, China
- School
of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Zhiling Guo
- School
of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
| | - Weichen Zhao
- State
Key Laboratory of Environmental Chemistry and Ecotoxicology, Research
Center for Eco-Environmental Sciences, Chinese
Academy of Sciences, Beijing 100085, China
| | - Yuanbo Li
- College
of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Tianjing Yi
- College
of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Weidong Cao
- Institute
of Agricultural Resources and Regional Planning, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Li Gao
- State
Key Laboratory for Biology of Plant Disease and Insect Pests, Institute
of Plant Protection, Chinese Academy of
Agricultural Sciences, Beijing 100193, China
| | - Chang Fu Tian
- State
Key Laboratory of Agrobiotechnology, College of Biological Sciences, China Agricultural University, Beijing 100193, China
| | - Qing Chen
- College
of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Fazheng Ren
- Key
Laboratory of Precision Nutrition and Food Quality, China Agricultural University, Beijing 100083, China
| | - Yukui Rui
- College
of Resources and Environmental Sciences, China Agricultural University, Beijing 100193, China
| | - Jason C. White
- The
Connecticut Agricultural Experiment Station, New Haven, Connecticut 06504, United States
| | - Iseult Lynch
- School
of Geography, Earth and Environmental Sciences, University of Birmingham, Edgbaston, Birmingham B15 2TT, U.K.
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79
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Kang BH, Chowdhury S, Kang SH, Shin SY, Lee WH, Lee HS, Ha BK. Transcriptome Profiling of a Soybean Mutant with Salt Tolerance Induced by Gamma-ray Irradiation. Plants (Basel) 2024; 13:254. [PMID: 38256807 PMCID: PMC10818854 DOI: 10.3390/plants13020254] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/28/2023] [Revised: 12/21/2023] [Accepted: 01/11/2024] [Indexed: 01/24/2024]
Abstract
Salt stress is a significant abiotic stress that reduces crop yield and quality globally. In this study, we utilized RNA sequencing (RNA-Seq) to identify differentially expressed genes (DEGs) in response to salt stress induced by gamma-ray irradiation in a salt-tolerant soybean mutant. The total RNA library samples were obtained from the salt-sensitive soybean cultivar Kwangan and the salt-tolerant mutant KA-1285. Samples were taken at three time points (0, 24, and 72 h) from two tissues (leaves and roots) under 200 mM NaCl. A total of 967,719,358 clean reads were generated using the Illumina NovaSeq 6000 platform, and 94.48% of these reads were mapped to 56,044 gene models of the soybean reference genome (Glycine_max_Wm82.a2.v1). The DEGs with expression values were compared at each time point within each tissue between the two soybeans. As a result, 296 DEGs were identified in the leaves, while 170 DEGs were identified in the roots. In the case of the leaves, eight DEGs were related to the phenylpropanoid biosynthesis pathway; however, in the roots, Glyma.03G171700 within GmSalt3, a major QTL associated with salt tolerance in soybean plants, was differentially expressed. Overall, these differences may explain the mechanisms through which mutants exhibit enhanced tolerance to salt stress, and they may provide a basic understanding of salt tolerance in soybean plants.
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Affiliation(s)
- Byeong Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Sreeparna Chowdhury
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
| | - Se-Hee Kang
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Seo-Young Shin
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Won-Ho Lee
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
| | - Hyeon-Seok Lee
- National Institute of Crop Science, RDA, Wanju 55365, Republic of Korea
| | - Bo-Keun Ha
- Department of Applied Plant Science, Chonnam National University, Gwangju 61186, Republic of Korea; (B.H.K.); (S.C.); (S.-H.K.); (S.-Y.S.); (W.-H.L.)
- BK21 Interdisciplinary Program in IT-Bio Convergence System, Chonnam National University, Gwangju 61186, Republic of Korea
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80
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Sharma D, Lande AG, Sameni D, Yadav DN, Kapila R, Kapila S. Comparative evaluation of milk proteins and oil-seed-cake-derived proteins extracted by chemical and biological methods for obesity management. J Sci Food Agric 2024; 104:315-327. [PMID: 37592881 DOI: 10.1002/jsfa.12920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/11/2023] [Revised: 08/04/2023] [Accepted: 08/18/2023] [Indexed: 08/19/2023]
Abstract
BACKGROUND In light of the exponential rise in global population, there is a critical requirement to reduce food waste on a global scale. According to studies, agricultural wastes such as oil-seed cakes offer great nutritional value. Acid precipitation (A) and alkaline extraction methods (traditional methods) were used to extract protein from oil-seed cakes; however, both procedures are linked to decreased protein quality and quantity, which prompted the development of a novel strategy known as the biological/microbial/probiotic (B) method. Therefore, the present study aimed to highlight the optimal way of protein extraction from oil-seed cakes and the effect of extraction methods on protein efficacy against obesity. The outcomes were also compared with milk proteins. RESULTS In vitro study provided evidence that proteins from both sources (plant and milk) suppressed adipogenesis and stimulated adipolysis in 3T3L-1 cells. For the in vivo study, mice were fed with different protein extracts: soya protein preparation (SPP), ground protein preparation (GPP), whey protein (WP) and casein protein (CP) containing 40% of their calories as fat. Body weight decreased significantly in all the rats except CP-fed rats. Body mass index, atherogenic index, plasma triglyceride and very-low-density lipoprotein cholesterol level decreased significantly in all the groups in comparison to the model group (high-fat-diet group), but the decrease was more pronounced in plant proteins than milk proteins. In hepatocytes, the expression of fasting-induced adipose factor, carnitine palmitoyltransferase I and peroxisome proliferator-activated receptor α genes was increased significantly in SPP-fed groups. Adiponectin gene expression was upregulated significantly in visceral fat tissue in groups fed SPP-B, GPP-A and CP, whereas leptin gene was downregulated significantly in all groups except SPP-A. CONCLUSION This study demonstrates that SPP-B showed the most effective anti-obesity property, followed by WP. Additionally, we found that the biological precipitation approach produced better outcomes for plant proteins isolated from oil-seed cakes than the acid precipitation method. © 2023 Society of Chemical Industry.
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Affiliation(s)
- Diksha Sharma
- Animal Biochemistry Division, ICAR National Dairy Research Institute, Karnal, 132001, India
| | - Abhijit Gajanan Lande
- Animal Biochemistry Division, ICAR National Dairy Research Institute, Karnal, 132001, India
| | - Deepika Sameni
- Animal Biochemistry Division, ICAR National Dairy Research Institute, Karnal, 132001, India
| | | | - Rajeev Kapila
- Animal Biochemistry Division, ICAR National Dairy Research Institute, Karnal, 132001, India
| | - Suman Kapila
- Animal Biochemistry Division, ICAR National Dairy Research Institute, Karnal, 132001, India
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81
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Tran DT, Mitchum MG, Zhang S, Wallace JG, Li Z. Soybean microbiome composition and the impact of host plant resistance. Front Plant Sci 2024; 14:1326882. [PMID: 38288404 PMCID: PMC10822979 DOI: 10.3389/fpls.2023.1326882] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/24/2023] [Accepted: 12/14/2023] [Indexed: 01/31/2024]
Abstract
Microbial communities play an important role in the growth and development of plants, including plant immunity and the decomposition of complex substances into absorbable nutrients. Hence, utilizing beneficial microbes becomes a promising strategy for the optimization of plant growth. The objective of this research was to explore the root bacterial profile across different soybean genotypes and the change in the microbial community under soybean cyst nematode (SCN) infection in greenhouse conditions using 16S rRNA sequencing. Soybean genotypes with soybean cyst nematode (SCN) susceptible and resistant phenotypes were grown under field and greenhouse conditions. Bulked soil, rhizosphere, and root samples were collected from each replicate. Sequencing of the bacterial 16S gene indicated that the bacterial profile of soybean root and soil samples partially overlapped but also contained different communities. The bacterial phyla Proteobacteria, Actinobacteria, and Bacteroidetes dominate the soybean root-enriched microbiota. The structure of bacteria was significantly affected by sample year (field) or time point (greenhouse). In addition, the host genotype had a small but significant effect on the diversity of the root microbiome under SCN pressure in the greenhouse test. These differences may potentially represent beneficial bacteria or secondary effects related to SCN resistance.
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Affiliation(s)
- Dung T. Tran
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Melissa G. Mitchum
- Department of Plant Pathology, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Shuzhen Zhang
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
- Soybean Research Institute, Northeast Agricultural University, Harbin, China
| | - Jason G. Wallace
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
| | - Zenglu Li
- Department of Crop and Soil Sciences, and Institute of Plant Breeding, Genetics and Genomics, University of Georgia, Athens, GA, United States
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82
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Li J, Zhang W, Zhou H, Yu C, Li Q. Weed detection in soybean fields using improved YOLOv7 and evaluating herbicide reduction efficacy. Front Plant Sci 2024; 14:1284338. [PMID: 38273952 PMCID: PMC10808379 DOI: 10.3389/fpls.2023.1284338] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Accepted: 12/19/2023] [Indexed: 01/27/2024]
Abstract
With the increasing environmental awareness and the demand for sustainable agriculture, herbicide reduction has become an important goal. Accurate and efficient weed detection in soybean fields is the key to test the effectiveness of herbicide application, but current technologies and methods still have some problems in terms of accuracy and efficiency, such as relying on manual detection and poor adaptability to some complex environments. Therefore, in this study, weeding experiments in soybean fields with reduced herbicide application, including four levels, were carried out, and an unmanned aerial vehicle (UAV) was utilized to obtain field images. We proposed a weed detection model-YOLOv7-FWeed-based on improved YOLOv7, adopted F-ReLU as the activation function of the convolution module, and added the MaxPool multihead self-attention (M-MHSA) module to enhance the recognition accuracy of weeds. We continuously monitored changes in soybean leaf area and dry matter weight after herbicide reduction as a reflection of soybean growth at optimal herbicide application levels. The results showed that the herbicide application level of electrostatic spraying + 10% reduction could be used for weeding in soybean fields, and YOLOv7-FWeed was higher than YOLOv7 and YOLOv7-enhanced in all the evaluation indexes. The precision of the model was 0.9496, the recall was 0.9125, the F1 was 0.9307, and the mAP was 0.9662. The results of continuous monitoring of soybean leaf area and dry matter weight showed that herbicide reduction could effectively control weed growth and would not hinder soybean growth. This study can provide a more accurate, efficient, and intelligent solution for weed detection in soybean fields, thus promoting herbicide reduction and providing guidance for exploring efficient herbicide application techniques.
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Affiliation(s)
- Jinyang Li
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Wei Zhang
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
- Key Laboratory of Soybean Mechanization Production, Ministry of Agriculture and Rural Affairs, Daqing, China
| | - Hong Zhou
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Chuntao Yu
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
| | - Qingda Li
- College of Engineering, Heilongjiang Bayi Agricultural University, Daqing, China
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83
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Dai D, Huang L, Zhang X, Zhang S, Yuan Y, Wu G, Hou Y, Yuan X, Chen X, Xue C. Identification of a Branch Number Locus in Soybean Using BSA-Seq and GWAS Approaches. Int J Mol Sci 2024; 25:873. [PMID: 38255945 PMCID: PMC10815202 DOI: 10.3390/ijms25020873] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 01/04/2024] [Accepted: 01/05/2024] [Indexed: 01/24/2024] Open
Abstract
The determination of the soybean branch number plays a pivotal role in plant morphogenesis and yield components. This polygenic trait is subject to environmental influences, and despite its significance, the genetic mechanisms governing the soybean branching number remain incompletely understood. To unravel these mechanisms, we conducted a comprehensive investigation employing a genome-wide association study (GWAS) and bulked sample analysis (BSA). The GWAS revealed 18 SNPs associated with the soybean branch number, among which qGBN3 on chromosome 2 emerged as a consistently detected locus across two years, utilizing different models. In parallel, a BSA was executed using an F2 population derived from contrasting cultivars, Wandou35 (low branching number) and Ruidou1 (high branching number). The BSA results pinpointed a significant quantitative trait locus (QTL), designated as qBBN1, located on chromosome 2 by four distinct methods. Importantly, both the GWAS and BSA methods concurred in co-locating qGBN3 and qBBN1. In the co-located region, 15 candidate genes were identified. Through gene annotation and RT-qPCR analysis, we predicted that Glyma.02G125200 and Glyma.02G125600 are candidate genes regulating the soybean branch number. These findings significantly enhance our comprehension of the genetic intricacies regulating the branch number in soybeans, offering promising candidate genes and materials for subsequent investigations aimed at augmenting the soybean yield. This research represents a crucial step toward unlocking the full potential of soybean cultivation through targeted genetic interventions.
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Affiliation(s)
| | | | | | | | | | | | | | | | - Xin Chen
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China (S.Z.); (Y.Y.); (Y.H.)
| | - Chenchen Xue
- Institute of Industrial Crops, Jiangsu Academy of Agricultural Sciences, Nanjing 210014, China (S.Z.); (Y.Y.); (Y.H.)
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84
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Bissonnette KM, Barizon J, Adee EA, Ames KA, Becker TM, Biggs M, Bradley C, Brown MT, Byamukama E, Chilvers MI, Faske TR, Harbach CJ, Jackson-Ziems TA, Kandel YR, Kleczewski NM, Koehler AM, Markell SG, Mueller DS, Sjarpe D, Smith DL, Telenko DEP, Tenuta A. Management of soybean cyst nematode and sudden death syndrome with nematode-protectant seed treatments across multiple environments in soybean. Plant Dis 2024. [PMID: 38199961 DOI: 10.1094/pdis-02-23-0292-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/12/2024]
Abstract
As soybean (Glycine max) production continues to expand in the U.S. and Canada, so do pathogens and pests which directly threaten soybean yield potential and economic returns for farmers. One such pathogen is the soybean cyst nematode (SCN; Heterodera glycines). SCN has traditionally been managed using SCN-resistant cultivars and rotation with non-host crops, but the interaction of SCN with sudden death syndrome (SDS; caused by Fusarium virguliforme) in the field makes management more difficult. Nematode-protectant seed treatments have become options for SCN and SDS management. The objectives of this study were to evaluate nematode-protectant seed treatments for their effects on: (i) early and full season SCN reproduction, (ii) foliar symptoms and root-rot caused by SDS, and (iii) soybean yield across environments accounting for the above factors. Using a standard protocol, field trials were implemented in 13 U.S. States and 1 Canadian Province from 2019 to 2021 constituting 51 site-years. Six nematode-protectant seed treatment products were compared to a fungicide + insecticide base treatment and a non-treated check. Initial (at soybean planting) and final (at soybean harvest) SCN egg populations were enumerated and SCN females were extracted from roots and counted at 30 to 35 days post-planting. Foliar disease index (FDX) and root rot caused by the SDS pathogen were evaluated, and yield data were collected for each plot. No seed treatment offered significant nematode control versus the non-treated check for in-season and full season nematode response, no matter the initial SCN population or FDX level. Of all treatments, ILEVO (fluopyram) and Saltro (pydiflumetofen) provided more consistent increases in yield over the non-treated check in a broader range of SCN environments, even when FDX level was high.
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Affiliation(s)
- Kaitlyn M Bissonnette
- Cotton Inc, 2296, Cary, North Carolina, United States
- University of Missouri, 14716, Division of Plant Science and Technology, Columbia, Missouri, United States;
| | - Jefferson Barizon
- University of Missouri, 14716, Division of Plant Science and Technology, Columbia, Missouri, United States;
| | - Eric A Adee
- Kansas State University, Kansas River Valley Experiment Field, Agronomy, 6347 NW 17th St., Topeka, Kansas, United States, 66618;
| | - Keith A Ames
- University of Illinois, Crop Sciences, Urbana, Illinois, United States;
| | - Talon M Becker
- University of Illinois Urbana-Champaign, 14589, Department of Crop Science, Urbana, Illinois, United States;
| | - Meghan Biggs
- University of Missouri, 14716, Division of Plant Science and Technology, Columbia, Missouri, United States;
| | - Carl Bradley
- University of Kentucky, Plant Pathology, UKREC, 1205 Hopkinsville St., PO Box 469, Princeton, Kentucky, United States, 42445;
| | - Mariama T Brown
- Purdue Univeristy, Botany and Plant Pathology, 3171 Pheasant Run Drive Apt 112, lafayette, Indiana, United States, 47909;
| | - Emmanuel Byamukama
- USDA, 1097, Division of Plant Systems-Protection, Washington, District of Columbia, United States;
| | - Martin I Chilvers
- Michigan State University, Plant Soil and Microbial Sciences, 578 Wilson Road, 104 CIPS bldg, East Lansing, Michigan, United States, 48824;
| | - Travis R Faske
- University of Arkansas, Department of Plant Pathology, Lonoke Extension Center, 2001 Hwy 70 E., Lonoke, Arkansas, United States, 72086;
| | - Chelsea J Harbach
- Iowa State University, 1177, Plant Pathology and Microbiology, Ames, Iowa, United States;
| | - Tamra A Jackson-Ziems
- Univ. of Nebraska, Dept. of Plant Pathology, 406 Plant Sciences Hall, Lincoln, Nebraska, United States, 68583
- 85056 506th AveEwing, Nebraska, United States, 68735;
| | - Yuba Raj Kandel
- Iowa State University , Plant Pathology and Microbiology, 351 Bessey Hall, Department of Plant Pathology and Microbiology, Iowa State University, Ames, Iowa, United States, 50011
- 2310 Mortensen PKWYUnit # 16Ames, Iowa, United States, 5014;
| | - Nathan Michael Kleczewski
- University of Illinois, Crop Sciences, 065 National Soybean Research Building, Champaign, United States, 61820;
| | - Alyssa M Koehler
- University of Delaware, 5972, Plant and Soil Sciences , 16483 County Seat Hwy, Georgetown, Delaware, United States, 19947;
| | - Samuel G Markell
- North Dakota State Universtiy, Plant Pathology, NDSU Dept 7660, Box 6050, Fargo, North Dakota, United States, 58108-6050;
| | - Daren S Mueller
- Iowa State University, Plant Pathology, 351 Bessey Hall, Ames, Iowa, United States, 50011;
| | - Daniel Sjarpe
- University of Missouri, 14716, Division of Plant Science and Technology, Columbia, Missouri, United States;
| | - Damon L Smith
- University of Wisconsin, Plant Pathology, 1630 Linden Drive, Madison, Wisconsin, United States, 53706;
| | - Darcy E P Telenko
- Purdue Univeristy, Botany and Plant Pathology, 914 W. State Street, West Lafayette, Indiana, United States, 47907;
| | - Albert Tenuta
- Ontario Ministry of Agriculture, Food, and Rural Affairs, P.O. Box 400, 120 Main St. East, Ridgetown, Ontario, Canada, N0P2C0
- Canada;
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85
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Biová J, Kaňovská I, Chan YO, Immadi MS, Joshi T, Bilyeu K, Škrabišová M. Natural and artificial selection of multiple alleles revealed through genomic analyses. Front Genet 2024; 14:1320652. [PMID: 38259621 PMCID: PMC10801239 DOI: 10.3389/fgene.2023.1320652] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/17/2023] [Indexed: 01/24/2024] Open
Abstract
Genome-to-phenome research in agriculture aims to improve crops through in silico predictions. Genome-wide association study (GWAS) is potent in identifying genomic loci that underlie important traits. As a statistical method, increasing the sample quantity, data quality, or diversity of the GWAS dataset positively impacts GWAS power. For more precise breeding, concrete candidate genes with exact functional variants must be discovered. Many post-GWAS methods have been developed to narrow down the associated genomic regions and, ideally, to predict candidate genes and causative mutations (CMs). Historical natural selection and breeding-related artificial selection both act to change the frequencies of different alleles of genes that control phenotypes. With higher diversity and more extensive GWAS datasets, there is an increased chance of multiple alleles with independent CMs in a single causal gene. This can be caused by the presence of samples from geographically isolated regions that arose during natural or artificial selection. This simple fact is a complicating factor in GWAS-driven discoveries. Currently, none of the existing association methods address this issue and need to identify multiple alleles and, more specifically, the actual CMs. Therefore, we developed a tool that computes a score for a combination of variant positions in a single candidate gene and, based on the highest score, identifies the best number and combination of CMs. The tool is publicly available as a Python package on GitHub, and we further created a web-based Multiple Alleles discovery (MADis) tool that supports soybean and is hosted in SoyKB (https://soykb.org/SoybeanMADisTool/). We tested and validated the algorithm and presented the utilization of MADis in a pod pigmentation L1 gene case study with multiple CMs from natural or artificial selection. Finally, we identified a candidate gene for the pod color L2 locus and predicted the existence of multiple alleles that potentially cause loss of pod pigmentation. In this work, we show how a genomic analysis can be employed to explore the natural and artificial selection of multiple alleles and, thus, improve and accelerate crop breeding in agriculture.
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Affiliation(s)
- Jana Biová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Ivana Kaňovská
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
| | - Yen On Chan
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
| | - Manish Sridhar Immadi
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
| | - Trupti Joshi
- MU Institute for Data Science and Informatics, University of Missouri-Columbia, Columbia, MO, United States
- Christopher S. Bond Life Sciences Center, University of Missouri-Columbia, Columbia, MO, United States
- Department of Electrical Engineering and Computer Science, University of Missouri-Columbia, Columbia, MO, United States
- Department of Biomedical Informatics, Biostatistics and Medical Epidemiology, University of Missouri-Columbia, Columbia, MO, United States
| | - Kristin Bilyeu
- United States Department of Agriculture-Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO, United States
| | - Mária Škrabišová
- Department of Biochemistry, Faculty of Science, Palacký University in Olomouc, Olomouc, Czechia
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86
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McCabe CE, Lincoln LM, O’Rourke JA, Graham MA. Virus induced gene silencing confirms oligogenic inheritance of brown stem rot resistance in soybean. Front Plant Sci 2024; 14:1292605. [PMID: 38259908 PMCID: PMC10801082 DOI: 10.3389/fpls.2023.1292605] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/11/2023] [Accepted: 12/11/2023] [Indexed: 01/24/2024]
Abstract
Brown Stem Rot (BSR), caused by the soil borne fungal pathogen Phialophora gregata, can reduce soybean yields by as much as 38%. Previous allelism studies identified three Resistant to brown stem Rot genes (Rbs1, Rbs2, and Rbs3), all mapping to large, overlapping regions on soybean chromosome 16. However, recent fine-mapping and genome wide association studies (GWAS) suggest Rbs1, Rbs2, and Rbs3 are alleles of a single Rbs locus. To address this conflict, we characterized the Rbs locus using the Williams82 reference genome (Wm82.a4.v1). We identified 120 Receptor-Like Proteins (RLPs), with hallmarks of disease resistance receptor-like proteins (RLPs), which formed five distinct clusters. We developed virus induced gene silencing (VIGS) constructs to target each of the clusters, hypothesizing that silencing the correct RLP cluster would result in a loss of resistance phenotype. The VIGS constructs were tested against P. gregata resistant genotypes L78-4094 (Rbs1), PI 437833 (Rbs2), or PI 437970 (Rbs3), infected with P. gregata or mock infected. No loss of resistance phenotype was observed. We then developed VIGS constructs targeting two RLP clusters with a single construct. Construct B1a/B2 silenced P. gregata resistance in L78-4094, confirming at least two genes confer Rbs1-mediated resistance to P. gregata. Failure of B1a/B2 to silence resistance in PI 437833 and PI 437970 suggests additional genes confer BSR resistance in these lines. To identify differentially expressed genes (DEGs) responding to silencing, we conducted RNA-seq of leaf, stem and root samples from B1a/B2 and empty vector control plants infected with P. gregata or mock infected. B1a/B2 silencing induced DEGs associated with cell wall biogenesis, lipid oxidation, the unfolded protein response and iron homeostasis and repressed numerous DEGs involved in defense and defense signaling. These findings will improve integration of Rbs resistance into elite germplasm and provide novel insights into fungal disease resistance.
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Affiliation(s)
- Chantal E. McCabe
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Lori M. Lincoln
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
| | - Jamie A. O’Rourke
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
| | - Michelle A. Graham
- United States Department of Agriculture, Agricultural Research Service (USDA-ARS), Corn Insects and Crop Genetics Research Unit, Ames, IA, United States
- Department of Agronomy, Iowa State University, Ames, IA, United States
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87
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Niu M, Tian K, Chen Q, Yang C, Zhang M, Sun S, Wang X. A multi-trait GWAS-based genetic association network controlling soybean architecture and seed traits. Front Plant Sci 2024; 14:1302359. [PMID: 38259929 PMCID: PMC10801003 DOI: 10.3389/fpls.2023.1302359] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2023] [Accepted: 12/18/2023] [Indexed: 01/24/2024]
Abstract
Ideal plant architecture is essential for enhancing crop yields. Ideal soybean (Glycine max) architecture encompasses an appropriate plant height, increased node number, moderate seed weight, and compact architecture with smaller branch angles for growth under high-density planting. However, the functional genes regulating plant architecture are far not fully understood in soybean. In this study, we investigated the genetic basis of 12 agronomic traits in a panel of 496 soybean accessions with a wide geographical distribution in China. Analysis of phenotypic changes in 148 historical elite soybean varieties indicated that seed-related traits have mainly been improved over the past 60 years, with targeting plant architecture traits having the potential to further improve yields in future soybean breeding programs. In a genome-wide association study (GWAS) of 12 traits, we detected 169 significantly associated loci, of which 61 overlapped with previously reported loci and 108 new loci. By integrating the GWAS loci for different traits, we constructed a genetic association network and identified 90 loci that were associated with a single trait and 79 loci with pleiotropic effects. Of these 79 loci, 7 hub-nodes were strongly linked to at least three related agronomic traits. qHub_5, containing the previously characterized Determinate 1 (Dt1) locus, was associated not only with plant height and node number (as determined previously), but also with internode length and pod range. Furthermore, we identified qHub_7, which controls three branch angle-related traits; the candidate genes in this locus may be beneficial for breeding soybean with compact architecture. These findings provide insights into the genetic relationships among 12 important agronomic traits in soybean. In addition, these studies uncover valuable loci for further functional gene studies and will facilitate molecular design breeding of soybean architecture.
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Affiliation(s)
- Mengrou Niu
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
| | - Kewei Tian
- Center of Integrative Biology, College of Life Science and Technology, Huazhong Agricultural University, Wuhan, Hubei, China
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
| | - Qiang Chen
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Chunyan Yang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Mengchen Zhang
- Institute of Cereal and Oil Crops, Hebei Academy of Agriculture and Forestry Sciences/Hebei Laboratory of Crop Genetics and Breeding, Shijiazhuang, Hebei, China
| | - Shiyong Sun
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
| | - Xuelu Wang
- Sanya Institute of Henan University, Henan University, Sanya, Hainan, China
- State Key Laboratory of Crop Stress Adaptation and Improvement, School of Life Science, Henan University, Zhengzhou, China
- The Academy for Advanced Interdisciplinary Studies, Henan University, Zhengzhou, China
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88
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Wang Y, Zhang X, Yan Y, Niu T, Zhang M, Fan C, Liang W, Shu Y, Guo C, Guo D, Bi Y. GmABCG5, an ATP-binding cassette G transporter gene, is involved in the iron deficiency response in soybean. Front Plant Sci 2024; 14:1289801. [PMID: 38250443 PMCID: PMC10796643 DOI: 10.3389/fpls.2023.1289801] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/06/2023] [Accepted: 11/24/2023] [Indexed: 01/23/2024]
Abstract
Iron deficiency is a major nutritional problem causing iron deficiency chlorosis (IDC) and yield reduction in soybean, one of the most important crops. The ATP-binding cassette G subfamily plays a crucial role in substance transportation in plants. In this study, we cloned the GmABCG5 gene from soybean and verified its role in Fe homeostasis. Analysis showed that GmABCG5 belongs to the ABCG subfamily and is subcellularly localized at the cell membrane. From high to low, GmABCG5 expression was found in the stem, root, and leaf of young soybean seedlings, and the order of expression was flower, pod, seed stem, root, and leaf in mature soybean plants. The GUS assay and qRT-PCR results showed that the GmABCG5 expression was significantly induced by iron deficiency in the leaf. We obtained the GmABCG5 overexpressed and inhibitory expressed soybean hairy root complexes. Overexpression of GmABCG5 promoted, and inhibition of GmABCG5 retarded the growth of soybean hairy roots, independent of nutrient iron conditions, confirming the growth-promotion function of GmABCG5. Iron deficiency has a negative effect on the growth of soybean complexes, which was more obvious in the GmABCG5 inhibition complexes. The chlorophyll content was increased in the GmABCG5 overexpression complexes and decreased in the GmABCG5 inhibition complexes. Iron deficiency treatment widened the gap in the chlorophyll contents. FCR activity was induced by iron deficiency and showed an extraordinary increase in the GmABCG5 overexpression complexes, accompanied by the greatest Fe accumulation. Antioxidant capacity was enhanced when GmABCG5 was overexpressed and reduced when GmABCG5 was inhibited under iron deficiency. These results showed that the response mechanism to iron deficiency is more actively mobilized in GmABCG5 overexpression seedlings. Our results indicated that GmABCG5 could improve the plant's tolerance to iron deficiency, suggesting that GmABCG5 might have the function of Fe mobilization, redistribution, and/or secretion of Fe substances in plants. The findings provide new insights into the ABCG subfamily genes in the regulation of iron homeostasis in plants.
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Affiliation(s)
- Yu Wang
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Xuemeng Zhang
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Yuhan Yan
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Tingting Niu
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Miao Zhang
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Chao Fan
- Institute of Crops Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Wenwei Liang
- Institute of Crops Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
| | - Yongjun Shu
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Changhong Guo
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Donglin Guo
- Heilongjiang Provincial Key Laboratory of Molecular Cell Genetics and Genetic Breeding, College of Life Science and Technology, Harbin Normal University, Harbin, China
| | - Yingdong Bi
- Institute of Crops Tillage and Cultivation, Heilongjiang Academy of Agricultural Sciences, Harbin, China
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89
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Sun T, Li Z, Wang Z, Liu Y, Zhu Z, Zhao Y, Xie W, Cui S, Chen G, Yang W, Zhang Z, Zhang F. Monitoring of Nitrogen Concentration in Soybean Leaves at Multiple Spatial Vertical Scales Based on Spectral Parameters. Plants (Basel) 2024; 13:140. [PMID: 38202447 PMCID: PMC10780363 DOI: 10.3390/plants13010140] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/12/2023] [Revised: 12/28/2023] [Accepted: 01/01/2024] [Indexed: 01/12/2024]
Abstract
Nitrogen is a fundamental component for building amino acids and proteins, playing a crucial role in the growth and development of plants. Leaf nitrogen concentration (LNC) serves as a key indicator for assessing plant growth and development. Monitoring LNC provides insights into the absorption and utilization of nitrogen from the soil, offering valuable information for rational nutrient management. This, in turn, contributes to optimizing nutrient supply, enhancing crop yields, and minimizing adverse environmental impacts. Efficient and non-destructive estimation of crop LNC is of paramount importance for on-field crop management. Spectral technology, with its advantages of repeatability and high-throughput observations, provides a feasible method for obtaining LNC data. This study explores the responsiveness of spectral parameters to soybean LNC at different vertical scales, aiming to refine nitrogen management in soybeans. This research collected hyperspectral reflectance data and LNC data from different leaf layers of soybeans. Three types of spectral parameters, nitrogen-sensitive empirical spectral indices, randomly combined dual-band spectral indices, and "three-edge" parameters, were calculated. Four optimal spectral index selection strategies were constructed based on the correlation coefficients between the spectral parameters and LNC for each leaf layer. These strategies included empirical spectral index combinations (Combination 1), randomly combined dual-band spectral index combinations (Combination 2), "three-edge" parameter combinations (Combination 3), and a mixed combination (Combination 4). Subsequently, these four combinations were used as input variables to build LNC estimation models for soybeans at different vertical scales using partial least squares regression (PLSR), random forest (RF), and a backpropagation neural network (BPNN). The results demonstrated that the correlation coefficients between the LNC and spectral parameters reached the highest values in the upper soybean leaves, with most parameters showing significant correlations with the LNC (p < 0.05). Notably, the reciprocal difference index (VI6) exhibited the highest correlation with the upper-layer LNC at 0.732, with a wavelength combination of 841 nm and 842 nm. In constructing the LNC estimation models for soybeans at different leaf layers, the accuracy of the models gradually improved with the increasing height of the soybean plants. The upper layer exhibited the best estimation performance, with a validation set coefficient of determination (R2) that was higher by 9.9% to 16.0% compared to other layers. RF demonstrated the highest accuracy in estimating the upper-layer LNC, with a validation set R2 higher by 6.2% to 8.8% compared to other models. The RMSE was lower by 2.1% to 7.0%, and the MRE was lower by 4.7% to 5.6% compared to other models. Among different input combinations, Combination 4 achieved the highest accuracy, with a validation set R2 higher by 2.3% to 13.7%. In conclusion, by employing Combination 4 as the input, the RF model achieved the optimal estimation results for the upper-layer LNC, with a validation set R2 of 0.856, RMSE of 0.551, and MRE of 10.405%. The findings of this study provide technical support for remote sensing monitoring of soybean LNCs at different spatial scales.
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Affiliation(s)
- Tao Sun
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Zhijun Li
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Zhangkai Wang
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Yuchen Liu
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Zhiheng Zhu
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Yizheng Zhao
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Weihao Xie
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Shihao Cui
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Guofu Chen
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Wanli Yang
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Zhitao Zhang
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
| | - Fucang Zhang
- Key Laboratory of Agricultural Soil and Water Engineering in Arid and Semiarid Areas of Ministry of Education, Northwest A&F University, Xianyang 712100, China; (T.S.); (Z.W.); (Y.L.); (Z.Z.); (Y.Z.); (W.X.); (S.C.); (G.C.); (W.Y.); (Z.Z.); (F.Z.)
- Institute of Water-Saving Agriculture in Arid Areas of China, Northwest A&F University, Xianyang 712100, China
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90
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Petzel EA, Acharya S, Titgemeyer EC, Bailey EA, Brake DW. Effects of heating soybeans on postruminal amino acid bioavailability, performance, and ruminal fermentation in lactating cows. J Anim Sci 2024; 102:skae084. [PMID: 38520315 PMCID: PMC11044706 DOI: 10.1093/jas/skae084] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2023] [Accepted: 03/21/2024] [Indexed: 03/25/2024] Open
Abstract
Soybeans can provide ruminally degradable protein, lipid, and metabolizable amino acid (AA) to lactating dairy cows; however, soy-based trypsin inhibitors can limit protein digestion in nonruminants. Eight ruminally cannulated lactating Holstein cows were used to evaluate the impacts of soy-based trypsin inhibitors on nutrient disappearance, lactation, and plasma AA bioavailability. Treatments were abomasal infusion of 0 or 400 g/d casein or a crystalline AA analog of casein with unroasted or roasted soybeans fed at 10% dry matter (DM). Data were analyzed using the MIXED procedure of SAS. Measures of digestion were determined from fecal output determined with acid detergent insoluble ash and urine output determined from measures of urine creatinine. Neither soybean processing (P ≥ 0.20) nor the source of abomasal infusion (P ≥ 0.60) impacted nutrient digestibility. Ruminal ammonia, isobutyrate, and isovalerate were increased (P ≤ 0.01) among cattle consuming unroasted soybeans. Source of infusion did not affect (P ≥ 0.38) ruminal volatile fatty acids or nitrogen metabolism. Ruminal N metabolism was largely unaffected by soybean processing although microbial N efficiency was greater (P < 0.01) among cows fed unroasted soybeans. DM intake and energy-corrected milk were greater (P < 0.01) in cows fed roasted compared to unroasted soybeans. The proportion of fat, protein, lactose, and solids not fat (SNF) in milk did not differ between soybean processing or postruminal AA source, but fat, protein, lactose, and SNF yield was greater (P ≤ 0.01) when cows were fed roasted soybeans because milk yields were greater when cows were fed roasted vs. unroasted soybeans. As expected, infusion of casein or its crystalline AA analog increased plasma essential AA and milk urea nitrogen concentration. The rate of increase in essential AA concentration in plasma was 2.9× greater for casein than for crystalline AA. These data seem to indicate that soy-based trypsin inhibitors have no impacts on postruminal AA bioavailability when fed to cows and that metabolizable protein from casein is greater than from crystalline AA.
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Affiliation(s)
- Emily A Petzel
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA
| | - Subash Acharya
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA
| | - Evan C Titgemeyer
- Department of Animal Science and Industry, Kansas State University, Manhattan, KS, USA
| | - Eric A Bailey
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA
| | - Derek W Brake
- Division of Animal Science, University of Missouri, Columbia, MO 65211, USA
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91
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Wu G, Guan K, Ainsworth EA, Martin DG, Kimm H, Yang X. Solar-induced chlorophyll fluorescence captures the effects of elevated ozone on canopy structure and acceleration of senescence in soybean. J Exp Bot 2024; 75:350-363. [PMID: 37702411 DOI: 10.1093/jxb/erad356] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/14/2023] [Accepted: 09/11/2023] [Indexed: 09/14/2023]
Abstract
Solar-induced chlorophyll fluorescence (SIF) provides an opportunity to rapidly and non-destructively investigate how plants respond to stress. Here, we explored the potential of SIF to detect the effects of elevated O3 on soybean in the field where soybean was subjected to ambient and elevated O3 throughout the growing season in 2021. Exposure to elevated O3 resulted in a significant decrease in canopy SIF at 760 nm (SIF760), with a larger decrease in the late growing season (36%) compared with the middle growing season (13%). Elevated O3 significantly decreased the fraction of absorbed photosynthetically active radiation by 8-15% in the middle growing season and by 35% in the late growing stage. SIF760 escape ratio (fesc) was significantly increased under elevated O3 by 5-12% in the late growth stage due to a decrease of leaf chlorophyll content and leaf area index. Fluorescence yield of the canopy was reduced by 5-11% in the late growing season depending on the fesc estimation method, during which leaf maximum carboxylation rate and maximum electron transport were significantly reduced by 29% and 20% under elevated O3. These results demonstrated that SIF could capture the elevated O3 effect on canopy structure and acceleration of senescence in soybean and provide empirical support for using SIF for soybean stress detection and phenotyping.
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Affiliation(s)
- Genghong Wu
- Agroecosystem Sustainability Center, Institute for Sustainability, Energy, and Environment, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumers, and Environmental Sciences, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
- Institute of Bio- and Geosciences, IBG-2: Plant Sciences, Forschungszentrum Jülich GmbH, Jülich 52425, Germany
| | - Kaiyu Guan
- Agroecosystem Sustainability Center, Institute for Sustainability, Energy, and Environment, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumers, and Environmental Sciences, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
- National Center for Supercomputing Applications, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
| | - Elizabeth A Ainsworth
- Agroecosystem Sustainability Center, Institute for Sustainability, Energy, and Environment, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
- Department of Plant Biology, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
- USDA-ARS, Global Change and Photosynthesis Research Unit, Urbana, IL 61801, USA
| | - Duncan G Martin
- Department of Plant Biology, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
| | - Hyungsuk Kimm
- Department of Natural Resources and Environmental Sciences, College of Agricultural, Consumers, and Environmental Sciences, University of Illinois Urbana Champaign, Urbana, IL 61801, USA
- Research Institute of Agriculture and Life Sciences, Seoul National University, Seoul 08826, South Korea
| | - Xi Yang
- Department of Environmental Sciences, University of Virginia, Charlottesville, VA 22903, USA
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92
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Nakashima K, Yuhazu M, Mikuriya S, Kasai M, Abe J, Taneda A, Kanazawa A. Frequency of cytosine methylation in the adjacent regions of soybean retrotransposon SORE-1 depends on chromosomal location. Genome 2024; 67:1-12. [PMID: 37746933 DOI: 10.1139/gen-2023-0044] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 09/26/2023]
Abstract
Mobilization of transposable elements (TEs) is suppressed by epigenetic mechanisms involving cytosine methylation. However, few studies have focused on clarifying relationships between epigenetic influences of TEs on the adjacent DNA regions and time after insertion of TEs into the genome and/or their chromosomal location. Here we addressed these issues using soybean retrotransposon SORE-1. We analyzed SORE-1, inserted in exon 1 of the GmphyA2 gene, one of the newest insertions in this family so far identified. Cytosine methylation was detected in this element but was barely present in the adjacent regions. These results were correlated, respectively, with the presence and absence of the production of short interfering RNAs. Cytosine methylation profiles of 74 SORE-1 elements in the Williams 82 reference genome indicated that methylation frequency in the adjacent regions of SORE-1 was profoundly higher in pericentromeric regions than in euchromatic chromosome arms and was only weakly correlated with the length of time after insertion into the genome. Notably, the higher level of methylation in the 5' adjacent regions of SORE-1 coincided with the presence of repetitive elements in pericentromeric regions. Together, these results suggest that epigenetic influence of SORE-1 on the adjacent regions is influenced by its location on the chromosome.
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Affiliation(s)
- Kenta Nakashima
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Mashiro Yuhazu
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Shun Mikuriya
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Megumi Kasai
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Jun Abe
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
| | - Akito Taneda
- Graduate School of Science and Technology, Hirosaki University, Hirosaki, Aomori 036-8561, Japan
| | - Akira Kanazawa
- Research Faculty of Agriculture, Hokkaido University, Sapporo 060-8589, Japan
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93
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Wang Z, Han Q, Ji H. GmRj2/Rfg1 control of soybean-rhizobium-soil compatibility. Trends Plant Sci 2024; 29:7-9. [PMID: 37838520 DOI: 10.1016/j.tplants.2023.10.006] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/08/2023] [Revised: 10/01/2023] [Accepted: 10/03/2023] [Indexed: 10/16/2023]
Abstract
Coordinated evolution and mutual adaptation of soybean-rhizobium-soil (SRS) are crucial for soybean distribution, but the genetic mechanism involved had remained unclear. In a recent study, Li et al. identified a natural variant of the GmRj2/Rfg1 gene that affected the ability of soybean to adapt to distinct soil types by controlling soybean-rhizobium interaction, thus unravelling the mystery of SRS compatibility.
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Affiliation(s)
- Zhijuan Wang
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China
| | - Qin Han
- Oil Crops Research Institute, Chinese Academy of Agricultural Sciences, Wuhan 430061, China; Laboratory of Risk Assessment for Oilseeds Products (Wuhan), Ministry of Agriculture, Wuhan 430061, China
| | - Hongtao Ji
- National Key Laboratory of Crop Genetic Improvement, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China.
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94
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Chen J, Xu H, Liu Q, Ke M, Zhang Z, Wang X, Gao Z, Wu R, Yuan Q, Qian C, Huang L, Chen J, Han Q, Guan Y, Yu X, Huang X, Chen X. Shoot-to-root communication via GmUVR8-GmSTF3 photosignaling and flavonoid biosynthesis fine-tunes soybean nodulation under UV-B light. New Phytol 2024; 241:209-226. [PMID: 37881032 DOI: 10.1111/nph.19353] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/16/2023] [Accepted: 09/29/2023] [Indexed: 10/27/2023]
Abstract
Legume nodulation requires light perception by plant shoots and precise long-distance communication between shoot and root. Recent studies have revealed that TGACG-motif binding factors (GmSTFs) integrate light signals to promote root nodulation; however, the regulatory mechanisms underlying nodule formation in changing light conditions remain elusive. Here, we applied genetic engineering, metabolite measurement, and transcriptional analysis to study soybean (Glycine max) nodules. We clarify a fine-tuning mechanism in response to ultraviolet B (UV-B) irradiation and rhizobia infection, involving GmUVR8-dependent UV-B perception and GmSTF3/4-GmMYB12-GmCHS-mediated (iso)flavonoid biosynthesis for soybean nodule formation. GmUVR8 receptor-perceived UV-B signal triggered R2R3-MYB transcription factors GmMYB12-dependent flavonoid biosynthesis separately in shoot and root. In shoot, UV-B-triggered flavonoid biosynthesis relied on GmUVR8a, b, c receptor-dependent activation of GmMYB12L-GmCHS8 (chalcone synthase) module. In root, UV-B signaling distinctly promotes the accumulation of the isoflavones, daidzein, and its derivative coumestrol, via GmMYB12B2-GmCHS9 module, resulting in hypernodulation. The mobile transcription factors, GmSTF3/4, bind to cis-regulatory elements in the GmMYB12L, GmMYB12B2, and GmCHS9 promoters, to coordinate UV-B light perception in shoot and (iso)flavonoid biosynthesis in root. Our findings establish a novel shoot-to-root communication module involved in soybean nodulation and reveal an adaptive strategy employed by soybean roots in response to UV-B light.
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Affiliation(s)
- Jiansheng Chen
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Huifang Xu
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qiulin Liu
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Meiyu Ke
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhongqin Zhang
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- College of Agricultural Science, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xu Wang
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Zhen Gao
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Ruimei Wu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qiao Yuan
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Chongzhen Qian
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Laimei Huang
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Jiaomei Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Qingqing Han
- College of Life Science and Fujian Provincial Key Laboratory of Haixia Applied Plant Systems Biology, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Yuefeng Guan
- School of Life Sciences, Guangzhou University, Guangzhou, 510006, China
| | - Xiaomin Yu
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
| | - Xi Huang
- State Key Laboratory of Cellular Stress Biology, School of Life Sciences, Xiamen University, Xiamen, 361102, China
| | - Xu Chen
- Haixia Institute of Science and Technology, Horticultural Plant Biology and Metabolomics Center, Fujian Agriculture and Forestry University, Fuzhou, 350002, Fujian, China
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95
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Ahn G, Ban YJ, Shin GI, Jeong SY, Park KH, Kim WY, Cha JY. Ethylene enhances transcriptions of asparagine biosynthetic genes in soybean (Glycine max L. Merr) leaves. Plant Signal Behav 2023; 18:2287883. [PMID: 38019725 PMCID: PMC10761183 DOI: 10.1080/15592324.2023.2287883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/12/2023] [Accepted: 11/19/2023] [Indexed: 12/01/2023]
Abstract
Soybean, a vital protein-rich crop, offers bioactivity that can mitigate various chronic human diseases. Nonetheless, soybean breeding poses a challenge due to the negative correlation between enhanced protein levels and overall productivity. Our previous studies demonstrated that applying gaseous phytohormone, ethylene, to soybean leaves significantly boosts the accumulation of free amino acids, particularly asparagine (Asn). Current studies also revealed that ethylene application to soybeans significantly enhanced both essential and non-essential amino acid contents in leaves and stems. Asn plays a crucial role in ammonia detoxification and reducing fatigue. However, the molecular evidence supporting this phenomenon remains elusive. This study explores the molecular mechanisms behind enhanced Asn accumulation in ethylene-treated soybean leaves. Transcriptional analysis revealed that ethylene treatments to soybean leaves enhance the transcriptional levels of key genes involved in Asn biosynthesis, such as aspartate aminotransferase (AspAT) and Asn synthetase (ASN), which aligns with our previous observations of elevated Asn levels. These findings shed light on the role of ethylene in upregulating Asn biosynthetic genes, subsequently enhancing Asn concentrations. This molecular insight into amino acid metabolism regulation provides valuable knowledge for the metabolic farming of crops, especially in elevating nutraceutical ingredients with non-genetic modification (GM) approach for improved protein content.
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Affiliation(s)
- Gyeongik Ahn
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Yeong Jun Ban
- Herbal Medicine Resources Research Center, Korea Institute of Oriental Medicine, Naju, Republic of Korea
| | - Gyeong-Im Shin
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Song Yi Jeong
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Ki Hun Park
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Woe-Yeon Kim
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
| | - Joon-Yung Cha
- Division of Applied Life Science (BK21four), IALS, RILS, and PBRRC, Gyeongsang National University, Jinju, Republic of Korea
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96
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Guan RX, Guo XY, Qu Y, Zhang ZW, Bao LG, Ye RY, Chang RZ, Qiu LJ. Salt Tolerance in Soybeans: Focus on Screening Methods and Genetics. Plants (Basel) 2023; 13:97. [PMID: 38202405 PMCID: PMC10780708 DOI: 10.3390/plants13010097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Revised: 12/25/2023] [Accepted: 12/25/2023] [Indexed: 01/12/2024]
Abstract
Salinity greatly affects the production of soybeans in arid and semi-arid lands around the world. The responses of soybeans to salt stress at germination, emergence, and other seedling stages have been evaluated in multitudes of studies over the past decades. Considerable salt-tolerant accessions have been identified. The association between salt tolerance responses during early and later growth stages may not be as significant as expected. Genetic analysis has confirmed that salt tolerance is distinctly tied to specific soybean developmental stages. Our understanding of salt tolerance mechanisms in soybeans is increasing due to the identification of key salt tolerance genes. In this review, we focus on the methods of soybean salt tolerance screening, progress in forward genetics, potential mechanisms involved in salt tolerance, and the importance of translating laboratory findings into field experiments via marker-assisted pyramiding or genetic engineering approaches, and ultimately developing salt-tolerant soybean varieties that produce high and stable yields. Progress has been made in the past decades, and new technologies will help mine novel salt tolerance genes and translate the mechanism of salt tolerance into new varieties via effective routes.
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Affiliation(s)
- Rong-Xia Guan
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Lab of Soybean Biology, Ministry of Agriculture, State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.-Y.G.); (Z.-W.Z.); (R.-Z.C.)
| | - Xiao-Yang Guo
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Lab of Soybean Biology, Ministry of Agriculture, State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.-Y.G.); (Z.-W.Z.); (R.-Z.C.)
| | - Yue Qu
- Australian Research Council Centre of Excellence in Plant Energy Biology, School of Agriculture, Food and Wine, Waite Research Institute, University of Adelaide, Glen Osmond, SA 5064, Australia;
| | - Zheng-Wei Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Lab of Soybean Biology, Ministry of Agriculture, State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.-Y.G.); (Z.-W.Z.); (R.-Z.C.)
| | - Li-Gao Bao
- Agriculture and Animal Husbandry Technology Promotion Center of Inner Mongolia Autonomous Region, Hohhot 010018, China;
| | - Rui-Yun Ye
- The Economic Development Center of China State Farm, Beijing 100122, China;
| | - Ru-Zhen Chang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Lab of Soybean Biology, Ministry of Agriculture, State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.-Y.G.); (Z.-W.Z.); (R.-Z.C.)
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), Key Lab of Soybean Biology, Ministry of Agriculture, State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; (X.-Y.G.); (Z.-W.Z.); (R.-Z.C.)
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97
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Ye MY, Lan HJ, Liu JZ. GmCBP60b Plays Both Positive and Negative Roles in Plant Immunity. Int J Mol Sci 2023; 25:378. [PMID: 38203547 PMCID: PMC10778643 DOI: 10.3390/ijms25010378] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/29/2023] [Revised: 12/20/2023] [Accepted: 12/22/2023] [Indexed: 01/12/2024] Open
Abstract
CBP60b (CALMODULIN-BINDING PROTEIN 60b) is a member of the CBP60 transcription factor family. In Arabidopsis, AtCBP60b not only regulates growth and development but also activates the transcriptions in immune responses. So far, CBP60b has only been studied extensively in the model plant Arabidopsis and rarely in crops. In this study, Bean pod mottle virus (BPMV)-mediated gene silencing (BPMV-VIGS) was used to silence GmCBP60b.1/2 in soybean plants. The silencing of GmCBP60b.1/2 resulted in typical autoimmunity, such as dwarfism and enhanced resistance to both Soybean mosaic virus (SMV) and Pseudomonas syringae pv. glycinea (Psg). To further understand the roles of GmCBP60b in immunity and circumvent the recalcitrance of soybean transformation, we generated transgenic tobacco lines that overexpress GmCBP60b.1. The overexpression of GmCBP60b.1 also resulted in autoimmunity, including spontaneous cell death on the leaves, highly induced expression of PATHOGENESIS-RELATED (PR) genes, significantly elevated accumulation of defense hormone salicylic acid (SA), and significantly enhanced resistance to Pst DC3000 (Pseudomonas syrangae pv. tomato DC3000). The transient coexpression of a luciferase reporter gene driven by the promoter of soybean SYSTEMIC ACQUIRED RESISTANCE DEFICIENT 1 (GmSARD1) (ProGmSARD1::LUC), together with GmCBP60b.1 driven by the 35S promoter, led to the activation of the LUC reporter gene, suggesting that GmCBP60b.1 could bind to the core (A/T)AATT motifs within the promoter region of GmSARD1 and, thus, activate the expression of the LUC reporter. Taken together, our results indicate that GmCBP60b.1/2 play both positive and negative regulatory roles in immune responses. These results also suggest that the function of CBP60b is conserved across plant species.
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Affiliation(s)
- Mei-Yan Ye
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (M.-Y.Y.); (H.-J.L.)
| | - Hu-Jiao Lan
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (M.-Y.Y.); (H.-J.L.)
| | - Jian-Zhong Liu
- College of Life Sciences, Zhejiang Normal University, Jinhua 321004, China; (M.-Y.Y.); (H.-J.L.)
- Zhejiang Provincial Key Laboratory of Biotechnology on Specialty Economic Plants, Zhejiang Normal University, Jinhua 321004, China
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98
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Hamilton R, Jacobs JL, McCoy AG, Kelly HM, Bradley C, Malvick D, Rojas JA, Chilvers MI. Multistate sensitivity monitoring of Fusarium virguliforme to the SDHI fungicides fluopyram and pydiflumetofen in the United States. Plant Dis 2023. [PMID: 38127633 DOI: 10.1094/pdis-11-23-2465-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/23/2023]
Abstract
Sudden death syndrome (SDS), caused by Fusarium virguliforme, is an important yield-limiting disease of soybean (Glycine max). From 1996 to 2022, cumulative yield losses attributed to SDS in North America totaled over 25 million metric tons, valued at over $7.8 billion USD. Seed treatments are widely used to manage SDS by reducing early season soybean root infection by F. virguliforme. Fluopyram (SDHI - FRAC 7), a fungicide seed treatment for SDS management, has been registered for use on soybean in the U.S. since 2014. A baseline sensitivity study conducted in 2014 evaluated 130 F. virguliforme isolates collected from five U.S. states to fluopyram in a mycelial growth inhibition assay and reported a mean EC50 of 3.35 mg/L. This baseline study provided the foundation for the objectives of this research: to detect any statistically significant change in fluopyram sensitivity over time and geographical regions within the U.S. and to investigate sensitivity to the fungicide pydiflumetofen. We repeated fluopyram sensitivity testing on a panel of 80 historical F. virguliforme isolates collected from 2006-2013 (76 of which were used in the baseline study) and conducted testing on 123 contemporary isolates collected from 2016-2022 from eleven U.S. states. This study estimated a mean absolute EC50 of 3.95 mg/L in isolates collected from 2006-2013 and a mean absolute EC50 of 4.19 mg/L in those collected in 2016-2022. There was no significant change in fluopyram sensitivity (P = 0.1) identified between the historical and contemporary isolates. A subset of 23 isolates, tested against pydiflumetofen under the same conditions, estimated an mean absolute EC50 of 0.11 mg/L. Moderate correlation was detected between fluopyram and pydiflumetofen sensitivity estimates (R = 0.53, P < 0.001). These findings enable future fluopyram and pydiflumetofen resistance monitoring and inform current soybean SDS management strategies in a regional and national context.
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Affiliation(s)
- Ryan Hamilton
- Michigan State University, 3078, Plant, Soil and Microbial Sciences, 578 Wilson Rd, CIPS 104, East Lansing, Michigan, United States, 48824
- Michigan State University;
| | - Janette L Jacobs
- Michigan State University, Plant, Soil and Microbial Sciences, 578 Wilson Road, 104 CIPS, 48824, Michigan, United States, 48824;
| | - Austin Glenn McCoy
- Michigan State University, Plant Soil and Microbial Sciences, 578 Wilson Road, Rm. 104, East Lansing, Michigan, United States, 48824;
| | - Heather M Kelly
- University of, TennesseeEntomology & Plant Pathology, 605 Airways Blvd., 605 Airways Blvd., Jackson, Tennessee, United States, 38301;
| | - Carl Bradley
- University of Kentucky, Plant Pathology, UKREC, 1205 Hopkinsville St., PO Box 469, Princeton, Kentucky, United States, 42445;
| | - Dean Malvick
- University of Minnesota, Plant Pathology, 1991 Upper Buford Circle, 495 Borlaug Hall, St. Paul, United States, 55108;
| | - J Alejandro Rojas
- Michigan State University, 3078, Plant, Soil and Microbial Sciences, 1066 Bogue Street, PSSB 260, East Lansing, Michigan, United States, 48824-1312;
| | - Martin I Chilvers
- Michigan State University, Plant Soil and Microbial Sciences, 578 Wilson Road, 104 CIPS bldg, East Lansing, Michigan, United States, 48824;
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99
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Souza R, Rouf Mian MA, Vaughn JN, Li Z. Introgression of a Danbaekkong high-protein allele across different genetic backgrounds in soybean. Front Plant Sci 2023; 14:1308731. [PMID: 38173927 PMCID: PMC10761420 DOI: 10.3389/fpls.2023.1308731] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/07/2023] [Accepted: 11/28/2023] [Indexed: 01/05/2024]
Abstract
Soybean meal is a major component of livestock feed due to its high content and quality of protein. Understanding the genetic control of protein is essential to develop new cultivars with improved meal protein. Previously, a genomic region on chromosome 20 significantly associated with elevated protein content was identified in the cultivar Danbaekkong. The present research aimed to introgress the Danbaekkong high-protein allele into elite lines with different genetic backgrounds by developing and deploying robust DNA markers. A multiparent population consisting of 10 F5-derived populations with a total of 1,115 recombinant inbred lines (RILs) was developed using "Benning HP" as the donor parent of the Danbaekkong high-protein allele. A new functional marker targeting the 321-bp insertion in the gene Glyma.20g085100 was developed and used to track the Danbaekkong high-protein allele across the different populations and enable assessment of its effect and stability. Across all populations, the high-protein allele consistently increased the content, with an increase of 3.3% in seed protein. A total of 103 RILs were selected from the multiparent population for yield testing in five environments to assess the impact of the high-protein allele on yield and to enable the selection of new breeding lines with high protein and high yield. The results indicated that the high-protein allele impacts yield negatively in general; however, it is possible to select high-yielding lines with high protein content. An analysis of inheritance of the Chr 20 high-protein allele in Danbaekkong indicated that it originated from a Glycine soja line (PI 163453) and is the same as other G. soja lines studied. A survey of the distribution of the allele across 79 G. soja accessions and 35 Glycine max ancestors of North American soybean cultivars showed that the high-protein allele is present in all G. soja lines evaluated but not in any of the 35 North American soybean ancestors. These results demonstrate that G. soja accessions are a valuable source of favorable alleles for improvement of protein composition.
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Affiliation(s)
- Renan Souza
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
| | - M. A. Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Raleigh, NC, United States
| | - Justin N. Vaughn
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
- Genomics and Bioinformatics Research Unit, United States Department of Agriculture - Agricultural Research Service (USDA-ARS), Athens, GA, United States
| | - Zenglu Li
- Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States
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100
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Zhang J, Liu S, Liu CB, Zhang M, Fu XQ, Wang YL, Song T, Chao ZF, Han ML, Tian Z, Chao DY. Natural variants of molybdate transporters contribute to yield traits of soybean by affecting auxin synthesis. Curr Biol 2023; 33:5355-5367.e5. [PMID: 37995699 DOI: 10.1016/j.cub.2023.10.072] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/27/2023] [Revised: 10/10/2023] [Accepted: 10/31/2023] [Indexed: 11/25/2023]
Abstract
Soybean (Glycine max) is a crop with high demand for molybdenum (Mo) and typically requires Mo fertilization to achieve maximum yield potential. However, the genetic basis underlying the natural variation of Mo concentration in soybean and its impact on soybean agronomic performance is still poorly understood. Here, we performed a genome-wide association study (GWAS) to identify GmMOT1.1 and GmMOT1.2 that drive the natural variation of soybean Mo concentration and confer agronomic traits by affecting auxin synthesis. The soybean population exhibits five haplotypes of the two genes, with the haplotype 5 demonstrating the highest expression of GmMOT1.1 and GmMOT1.2, as well as the highest transport activities of their proteins. Further studies showed that GmMOT1.1 and GmMOT1.2 improve soybean yield, especially when cultivated in acidic or slightly acidic soil. Surprisingly, these two genes contribute to soybean growth by enhancing the activity of indole-3-acetaldehyde (IAAld) aldehyde oxidase (AO), leading to increased indole-3-acetic acid (IAA) synthesis, rather than being involved in symbiotic nitrogen fixation or nitrogen assimilation. Furthermore, the geographical distribution of five haplotypes in China and their correlation with soil pH suggest the potential significance of GmMOT1.1 and GmMOT1.2 in soybean breeding strategies.
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Affiliation(s)
- Jing Zhang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Shulin Liu
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Chu-Bin Liu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Min Zhang
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China
| | - Xue-Qin Fu
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Ya-Ling Wang
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Tao Song
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China; University of Chinese Academy of Sciences, Beijing 100049, China
| | - Zhen-Fei Chao
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Mei-Ling Han
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China
| | - Zhixi Tian
- University of Chinese Academy of Sciences, Beijing 100049, China; State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovation Academy for Seed Design, Chinese Academy of Sciences, Beijing 100101, China.
| | - Dai-Yin Chao
- National Key Laboratory of Plant Molecular Genetics, Shanghai Center for Plant Stress Biology, CAS Center for Excellence in Molecular Plant Sciences, Chinese Academy of Sciences, Shanghai 200032, China.
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