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Yang L, Wang C, He X, Liang H, Wu Q, Sun X, Liu M, Shen P. Multi-year crop rotation and quicklime application promote stable peanut yield and high nutrient-use efficiency by regulating soil nutrient availability and bacterial/fungal community. Front Microbiol 2024; 15:1367184. [PMID: 38827150 PMCID: PMC11140132 DOI: 10.3389/fmicb.2024.1367184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/08/2024] [Accepted: 05/06/2024] [Indexed: 06/04/2024] Open
Abstract
Diversifying cultivation management, including different crop rotation patterns and soil amendment, are effective strategies for alleviating the obstacles of continuous cropping in peanut (Arachis hypogaea L.). However, the peanut yield enhancement effect and temporal changes in soil chemical properties and microbial activities in response to differential multi-year crop rotation patterns and soil amendment remain unclear. In the present study, a multi-year localization experiment with the consecutive application of five different cultivation managements (including rotation with different crops under the presence or absence of external quicklime as soil amendment) was conducted to investigate the dynamic changes in peanut nutrient uptake and yield status, soil chemical property, microbial community composition and function. Peanut continuous cropping led to a reduction in peanut yield, while green manure-peanut rotation and wheat-maize-peanut rotation increased peanut yield by 40.59 and 81.95%, respectively. A combination of quicklime application increased yield by a further 28.76 and 24.34%. Alterations in cultivation management also strongly affected the soil pH, nutrient content, and composition and function of the microbial community. The fungal community was more sensitive than the bacterial community to cultivation pattern shift. Variation in bacterial community was mainly attributed to soil organic carbon, pH and calcium content, while variation in fungal community was more closely related to soil phosphorus content. Wheat-maize-peanut rotation combined with quicklime application effectively modifies the soil acidification environment, improves the soil fertility, reshapes the composition of beneficial and harmful microbial communities, thereby improving soil health, promoting peanut development, and alleviating peanut continuous cropping obstacles. We concluded that wheat-maize-peanut rotation in combination with quicklime application was the effective practice to improve the soil fertility and change the composition of potentially beneficial and pathogenic microbial communities in the soil, which is strongly beneficial for building a healthy soil micro-ecology, promoting the growth and development of peanut, and reducing the harm caused by continuous cropping obstacles to peanut.
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Affiliation(s)
- Liyu Yang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Caibin Wang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Xinhua He
- College of Resources and Environment, Southwest University, Chongqing, China
| | - Haiyan Liang
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Qi Wu
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Xuewu Sun
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Miao Liu
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
| | - Pu Shen
- Shandong Peanut Research Institute/Key Laboratory of Peanut Biology, Genetic & Breeding, Ministry of Agriculture and Rural Affairs, Shandong Academy of Agricultural Sciences, Qingdao, Shandong, China
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Peper A, Newton CJ, Lim S, Zheng W, Brenneman T, Yang L. Functional Characterization of Core and Unique Calcite-Dissolving Bacteria Communities from Peanut Fields. PHYTOPATHOLOGY 2024; 114:1011-1019. [PMID: 38451554 DOI: 10.1094/phyto-10-23-0380-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 03/08/2024]
Abstract
Calcium deficiency is a leading cause of reduced peanut (Arachis hypogaea) seed quality and has been linked to increased disease susceptibility, specifically to soilborne fungal pathogens. Sufficient calcium at flowering time is critical to ensure proper pod development. Calcite-dissolving bacteria (CDB) isolated from farming fields can dissolve calcite (CaCO3) on plates and increase soluble calcium levels in soil. However, the phylogenetic diversity and geographic distribution of CDB is unclear. Here, we surveyed soil samples from 15 peanut-producing fields in three regions in southern Georgia, representing distinct soil compositions. We isolated CDB through differentiating media and identified 52 CDB strains. CDB abundance was not associated with any of the soil characteristics we evaluated. Three core genera, represented by 43 strains, were found in all three regions. Paenibacillus was the most common CDB found in all regions, making up 30 of the 52 identified strains. Six genera, represented by eight strains, are unique to one region. Members of the core and unique communities showed comparable solubilization indexes on plates. We conclude that a diversified phylogenetic population of CDB is present in Georgia peanut fields. Despite the phylogenetic diversity, as a population, they exhibit comparable functions in solubilizing calcite on plates.
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Affiliation(s)
- Alan Peper
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Carter J Newton
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Sheena Lim
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Wendy Zheng
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
| | - Timothy Brenneman
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
- Department of Plant Pathology, University of Georgia, Tifton, GA 31794
| | - Li Yang
- Department of Plant Pathology, University of Georgia, Athens, GA 30602
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Tian W, Zou B, Xu S, Xu Y, Zhang R, Li L, Jing Y, Wang M, Zhuang Y, Liu J, Liang C. Differences in microbial communities and potato growth in two soil types under organic cultivation. 3 Biotech 2023; 13:404. [PMID: 37982083 PMCID: PMC10656376 DOI: 10.1007/s13205-023-03832-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2022] [Accepted: 10/23/2023] [Indexed: 11/21/2023] Open
Abstract
Organic agriculture plays a positive role in promoting genetic diversity, including living organisms, plants, and cultivated crops in the soil. However, few comparative studies reported whether different soil types were suitable for organic cultivation. In this study, loam and clay-loam soils under continuous organic cultivation were analyzed. The results showed that there were no significant differences between two soil types in soil pH, bulk density, total porosity, moisture content and three soil phases. The capillary porosity and organic matter content of loam were significantly higher than those of clay-loam. Compared with clay-loam soil, the contents of total nitrogen, phosphorus, potassium, calcium, zinc and silicon in loam soil were also significantly higher. The microbial diversity was higher in loam and the dominant microbes differed between the two soils. Glycosyl transferases and carbohydrate esterases were enriched in loam, whereas glycoside hydrolases and carbohydrate-binding modules were enriched in clay loam. The potato yield in loam was significantly higher than that in clay loam. Among the tuber quality indicators, the protein content of potatoes in loam was higher than that in clay-loam, but the reducing sugar content was lower for loam than for clay-loam. In conclusion, compared with clay loam, loam was more suitable for organic cultivation of potatoes on account of the high contents of nitrogen, phosphorus, and potassium and the rich microbial community, thus promoting a high yield of tubers. This study provided a theoretical reference for the selection of soil type suitable for organic cultivation.
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Affiliation(s)
- Wei Tian
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Benge Zou
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Shujing Xu
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Yinghao Xu
- Shandong Luyuan Weipin Agricultural High-Tech Co., Ltd., Laiyang, 265211 China
| | - Ruifeng Zhang
- Shandong Luyuan Weipin Agricultural High-Tech Co., Ltd., Laiyang, 265211 China
| | - Li Li
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Yali Jing
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Mengzhen Wang
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Yingyu Zhuang
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
| | - Jianlong Liu
- College of Horticulture, Qingdao Agricultural University, Qingdao, 266109 China
| | - Chenglin Liang
- Haidu College, Qingdao Agricultural University, Laiyang, 265200 China
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Fan S, Yang S, Li G, Wan S. Genome-Wide Identification and Characterization of CDPK Gene Family in Cultivated Peanut ( Arachis hypogaea L.) Reveal Their Potential Roles in Response to Ca Deficiency. Cells 2023; 12:2676. [PMID: 38067104 PMCID: PMC10705679 DOI: 10.3390/cells12232676] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2023] [Revised: 11/13/2023] [Accepted: 11/17/2023] [Indexed: 12/18/2023] Open
Abstract
This study identified 45 calcium-dependent protein kinase (CDPK) genes in cultivated peanut (Arachis hypogaea L.), which are integral in plant growth, development, and stress responses. These genes, classified into four subgroups based on phylogenetic relationships, are unevenly distributed across all twenty peanut chromosomes. The analysis of the genetic structure of AhCDPKs revealed significant similarity within subgroups, with their expansion primarily driven by whole-genome duplications. The upstream promoter sequences of AhCDPK genes contained 46 cis-acting regulatory elements, associated with various plant responses. Additionally, 13 microRNAs were identified that target 21 AhCDPK genes, suggesting potential post-transcriptional regulation. AhCDPK proteins interacted with respiratory burst oxidase homologs, suggesting their involvement in redox signaling. Gene ontology and KEGG enrichment analyses affirmed AhCDPK genes' roles in calcium ion binding, protein kinase activity, and environmental adaptation. RNA-seq data revealed diverse expression patterns under different stress conditions. Importantly, 26 AhCDPK genes were significantly induced when exposed to Ca deficiency during the pod stage. During the seedling stage, four AhCDPKs (AhCDPK2/-25/-28/-45) in roots peaked after three hours, suggesting early signaling roles in pod Ca nutrition. These findings provide insights into the roles of CDPK genes in plant development and stress responses, offering potential candidates for predicting calcium levels in peanut seeds.
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Affiliation(s)
| | | | - Guowei Li
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan 250100, China; (S.F.); (S.Y.)
| | - Shubo Wan
- Institute of Crop Germplasm Resources, Shandong Academy of Agricultural Sciences, Ji’nan 250100, China; (S.F.); (S.Y.)
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Tang K, Li L, Zhang B, Zhang W, Zeng N, Zhang H, Liu D, Luo Z. Gene co-expression network analysis identifies hub genes associated with different tolerance under calcium deficiency in two peanut cultivars. BMC Genomics 2023; 24:421. [PMID: 37501179 PMCID: PMC10373417 DOI: 10.1186/s12864-023-09436-9] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 06/08/2023] [Indexed: 07/29/2023] Open
Abstract
BACKGROUND Peanut is an economically-important oilseed crop and needs a large amount of calcium for its normal growth and development. Calcium deficiency usually leads to embryo abortion and subsequent abnormal pod development. Different tolerance to calcium deficiency has been observed between different cultivars, especially between large and small-seed cultivars. RESULTS In order to figure out different molecular mechanisms in defensive responses between two cultivars, we treated a sensitive (large-seed) and a tolerant (small-seed) cultivar with different calcium levels. The transcriptome analysis identified a total of 58 and 61 differentially expressed genes (DEGs) within small-seed and large-seed peanut groups under different calcium treatments, and these DEGs were entirely covered by gene modules obtained via weighted gene co-expression network analysis (WGCNA). KEGG enrichment analysis showed that the blue-module genes in the large-seed cultivar were mainly enriched in plant-pathogen attack, phenolic metabolism and MAPK signaling pathway, while the green-module genes in the small-seed cultivar were mainly enriched in lipid metabolism including glycerolipid and glycerophospholipid metabolisms. By integrating DEGs with WGCNA, a total of eight hub-DEGs were finally identified, suggesting that the large-seed cultivar concentrated more on plant defensive responses and antioxidant activities under calcium deficiency, while the small-seed cultivar mainly focused on maintaining membrane features to enable normal photosynthesis and signal transduction. CONCLUSION The identified hub genes might give a clue for future gene validation and molecular breeding to improve peanut survivability under calcium deficiency.
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Affiliation(s)
- Kang Tang
- College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Lin Li
- College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
- Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
- Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Bowen Zhang
- College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Wei Zhang
- College of Plant Protection, Hunan Agricultural University, No.1 Nongda Road, Changsha, 410128, Hunan, China
| | - Ningbo Zeng
- College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
- Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China
- Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China
| | - Hao Zhang
- College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
- Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
- Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
| | - Dengwang Liu
- College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
- Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
- Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
| | - Zinan Luo
- College of Agriculture, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
- Arid Land Crop Research Institute, Hunan Agricultural University, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
- Hunan Peanut Engineering & Technology Research Center, No. 1 Nongda Road, Changsha, 410128, Hunan, China.
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Zhang W, Zhang BW, Deng JF, Li L, Yi TY, Hong YY. The resistance of peanut to soil-borne pathogens improved by rhizosphere probiotics under calcium treatment. BMC Microbiol 2021; 21:299. [PMID: 34715786 PMCID: PMC8555263 DOI: 10.1186/s12866-021-02355-3] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/05/2021] [Accepted: 10/13/2021] [Indexed: 11/26/2022] Open
Abstract
Background Peanut (Arachis hypogaea L.) is an important oil and economic crop. Calcium modulates plants in response to abiotic stresses and improves plant resistance to pathogens. Enrichment of beneficial microorganisms in the rhizosphere is associated with plant disease resistance and soil development. The purpose of this study was to analyze the differences in peanut rhizosphere microbial community structure between the calcium treatment and the control during two growth stages and to explain why calcium application could improve the resistance of peanuts to soil-borne pathogens. Results The 16S rDNA amplicon sequencing of rhizosphere microbiome showed that calcium application significantly enriched Serratia marcescens and other three dominant strains at the seedling stage. At the pod filling stage, ten dominant stains such as Sphingomonas changbaiensis and Novosphingobium panipatense were enriched by calcium. Serratia marcescens aseptic fermentation filtrate was mixed with PDA medium and inoculated with the main soil-borne pathogens in the seedling stage, which could inhibit the growth of Fusarium solani and Aspergillus flavus. The aseptic fermentation filtrate of Novosphingobium panipatense was mixed with PDA medium and inoculated with the main soil-borne pathogens in the pod filling stage, which could inhibit the growth of Sclerotium rolfsii and Leptosphaerulina arachidicola. Conclusions Calcium application increases the resistance of peanuts to soil-borne pathogens by enriching them with specific dominant bacteria. Supplementary Information The online version contains supplementary material available at 10.1186/s12866-021-02355-3.
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Affiliation(s)
- Wei Zhang
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Bo-Wen Zhang
- Research Centre for Hunan Peanut Engineering Technology, College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Jie-Fu Deng
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China
| | - Lin Li
- Research Centre for Hunan Peanut Engineering Technology, College of Agriculture, Hunan Agricultural University, Changsha, China
| | - Tu-Yong Yi
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China.
| | - Yan-Yun Hong
- Hunan Provincial Key Laboratory for Biology and Control of Plant Pests, College of Plant Protection, Hunan Agricultural University, Changsha, China.
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Fang T, Bai Y, Huang W, Wu Y, Yuan Z, Luan X, Liu X, Sun L. Identification of Potential Gene Regulatory Pathways Affecting the Ratio of Four-Seed Pod in Soybean. Front Genet 2021; 12:717770. [PMID: 34539747 PMCID: PMC8440838 DOI: 10.3389/fgene.2021.717770] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/23/2021] [Accepted: 08/05/2021] [Indexed: 12/13/2022] Open
Abstract
The number of four-seed pods is one of the most important agronomic traits affected by gene and environment that can potentially improve soybean (Glycine max) yield. However, the gene regulatory network that affects the ratio of four-seed pod (the ratio of the number of four-seed pods to the total number of pods in each individual plant) is yet unclear. Here, we performed bulked segregant RNA sequencing (BSR-seq) on a series of recombinant inbred lines (RILs) derived from hybrid progenies between Heinong 48 (HN48), a cultivar with a high ratio of four-seed pod, and Henong 64 (HN64), a cultivar with a low ratio of four-seed pod. Two tissues, flower bud and young pod, at two different growth stages, R1 and R3, were analyzed under the ratios of four-seed pod at less than 10% and greater than 30%, respectively. To identify the potential gene regulation pathways associated with the ratio of soybean four-seed pod, we performed differentially expressed analysis on the four bulked groups. A differentially expressed gene (DEG) encoding a photosystem II 5-kDa protein had the function of participating in the energy conversion of photosynthesis. In addition, 79 common DEGs were identified at different developmental stages and under different ratios of four-seed pod. Among them, four genes encoding calcium-binding proteins and a WRKY transcription factor were enriched in the plant-pathogen interaction pathway, and they showed a high level of expression in roots. Moreover, 10 DEGs were identified in the reported quantitative trait locus (QTL) interval of four-seed pod, and two of them were significantly enriched in the pentose and glucuronate interconversion pathway. These findings provide basic insights into the understanding of the underlying gene regulatory network affected by specific environment and lay the foundation for identifying the targets that affect the ratio of four-seed pod in soybean.
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Affiliation(s)
- Ting Fang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory for Crop Genetic Improvement and College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yiwei Bai
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory for Crop Genetic Improvement and College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Wenxuan Huang
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory for Crop Genetic Improvement and College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Yueying Wu
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory for Crop Genetic Improvement and College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Zhihui Yuan
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory for Crop Genetic Improvement and College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
| | - Xiaoyan Luan
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, China
| | - Xinlei Liu
- Institute of Soybean Research, Heilongjiang Provincial Academy of Agricultural Sciences, Harbin, China
| | - Lianjun Sun
- State Key Laboratory of Agrobiotechnology, Beijing Key Laboratory for Crop Genetic Improvement and College of Agronomy and Biotechnology, China Agricultural University, Beijing, China
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Hamza M, Abbas M, Abd Elrahman A, Helal M, Shahba M. Conventional versus Nano Calcium Forms on Peanut Production under Sandy Soil Conditions. AGRICULTURE 2021; 11:767. [DOI: 10.3390/agriculture11080767] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 09/01/2023]
Abstract
Abiotic stresses in sandy soil, which include saline water, saline soil, and lack of nutrients, affect the productivity and quality traits of peanuts (Arachis hypogaea L). Elemental calcium (Ca2+) is necessary for the proper development of peanut pods. This work aimed at comparing conventional Ca and nano-Ca form effects on peanut production and quality traits. Two randomized complete block field experiments were conducted in the 2015 and 2016 seasons. Treatments were control, gypsum plus calcium nitrate Ca(NO3)2, Ca(NO3)2, and chelated calcium, as well as 100, 75, 50, 25, and 12.5% of Ca(NO3)2 doses in a nano form. The results indicated that the treatment of gypsum plus conventional CaNO3 achieved the highest yield and best quality traits, followed by the Ca(NO3)2 and 100% nano Ca(NO3)2 treatments. The treatments of the control, gypsum, and 12.5% nano Ca(NO3)2 had the lowest effect on peanut performance. The conventional treatment of gypsum plus Ca(NO3)2 resulted in the greatest seed yield (1.6 ton ha−1), oil yield (700.3 kg ha−1), and protein yield (380.1 kg ha−1). Peanuts may benefit from Ca2+ better by using gypsum as the soil application and calcium nitrate as the foliar application to prevent disorders of Ca2+ deficiency under sandy soil conditions.
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Canaveze Y, Scudeler EL, Rodrigues Machado S. Neem secretory cells: developmental cytology and indications of cell autotoxicity. PROTOPLASMA 2021; 258:415-429. [PMID: 33140195 DOI: 10.1007/s00709-020-01580-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/22/2020] [Accepted: 10/28/2020] [Indexed: 06/11/2023]
Abstract
The neem tree (Azadirachta indica A.Juss.) contains a range of biologically active compounds-mainly triterpenoids produced in single secretory cells, which are distributed among all plant parts. Neem secretions are toxic to animal cells, triggering autolytic mechanisms that culminate in cell disruption. However, little is known about the self-toxicity of these secretions to the cells that produce them. We carried out an anatomical, histochemical, and ultrastructural investigation of neem's single secretory cells in the shoot apex and in young leaves. We evaluated the morphological changes as possible evidences of stress reactions to their own secretions. The subcellular apparatus involved in synthesis and compartmentation was consistent with hydrophilic and lipophilic secretions. Polymorphic plastids devoid of thylakoids and abundant smooth endoplasmic reticulum in the later stages of differentiation are comparable with previous reports on neem cotyledons with regard to terpenoid synthesis. However, secretions were compartmentalized within autophagic vacuoles and periplasmic spaces instead of in terpenoid vesicles. Cellular swelling, increased vesiculation, dilatation of endoplasmic reticulum cisternae, mitochondrial hypertrophy in the cristolysis process, autolytic vacuoles, and vacuolar degeneration culminating in protoplast autolysis are all consistent with early indications of autotoxicity. The signaling stress reaction mechanism was expressed as cytoplasmic deposits of calcium salt and by the expression of a 70-kDa heat-shock protein. The morphological and histochemical changes in the secreting cells are comparable with those described in animal cells exposed to neem oil. Our data provide evidence of cell damage and signaling reactions linked to these cells' own secretions before autolysis.
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Affiliation(s)
- Yve Canaveze
- IBB - Institute of Biosciences of Botucatu, Laboratory of Plant Anatomy, UNESP - São Paulo State University, PO Box 510, Botucatu, São Paulo State, 18618-970, Brazil
| | - Elton Luiz Scudeler
- IBB - Institute of Biosciences of Botucatu, Laboratory of Insects, UNESP - São Paulo State University, PO Box 510, Botucatu, São Paulo State, 18618-970, Brazil
| | - Silvia Rodrigues Machado
- IBB - Institute of Biosciences of Botucatu, Laboratory of Plant Anatomy, UNESP - São Paulo State University, PO Box 510, Botucatu, São Paulo State, 18618-970, Brazil.
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Transcriptome of peanut kernel and shell reveals the mechanism of calcium on peanut pod development. Sci Rep 2020; 10:15723. [PMID: 32973268 PMCID: PMC7518428 DOI: 10.1038/s41598-020-72893-9] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2020] [Accepted: 08/20/2020] [Indexed: 11/24/2022] Open
Abstract
Calcium is not only a nutrient necessary for plant growth but also a ubiquitous central element of different signaling pathways. Ca2+ deficiency in soil may cause embryo abortion, which can eventually lead to abnormal development of peanut pods during the harvest season. To further study the mechanisms by which Ca2+ affects the shells and kernels of peanuts, transcriptome sequencing was used to explore the genes differentially expressed in shells and kernels during the early stage of peanut pod development between Ca2+ sufficient and deficient treatments. In this study, 38,894 expressed genes were detected. RNA-seq based gene expression profiling showed a large number of genes at the transcriptional level that changed significantly in shells and kernels between the Ca2+ sufficient and deficient treatments, respectively. Genes encoding key proteins involved in Ca2+ signal transduction, hormones, development, ion transport, and nutrition absorption changed significantly. Meanwhile, in the early stage of pod development, calcium first promoted nutrient absorption and development of shells, which has less effect on the formation of seed kernels. These results provide useful information for understanding the relationship between Ca2+ absorption and pod development.
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Gong L, Han S, Yuan M, Ma X, Hagan A, He G. Transcriptomic analyses reveal the expression and regulation of genes associated with resistance to early leaf spot in peanut. BMC Res Notes 2020; 13:381. [PMID: 32782019 PMCID: PMC7418390 DOI: 10.1186/s13104-020-05225-9] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 08/05/2020] [Indexed: 12/04/2022] Open
Abstract
Objective Early leaf spot (ELS) caused by Cercospora arachidicola (Hori) is a serious foliar disease in peanut worldwide, which causes considerable reduction of yield. Identification of resistance genes is important for both conventional and molecular breeding. Few resistance genes have been identified and the mechanism of defense responses to this pathogen remains unknown. Results We detected several genes involved in disease resistance to ELS through transcriptome analysis. Using RNA-seq technology, one hundred thirty-three differentially expressed genes (DEGs) were identified between resistant and susceptible lines. Among these DEGs, coiled coil-nucleotide binding-leucine rich repeat (NLR) type resistance genes were identified as duplicated R genes on the chromosome B2. Peanut phytoalexin deficient 4 (PAD4) regulator of effector-triggered immunity mediated by NLR resistance proteins and polyphenol oxidase (PPO) genes play important roles in early leaf spot resistance. Our study provides the useful information on plant response to C. arachidicola infection in peanut. The results suggest that a few major genes and several factors mediate the resistance to ELS disease, showing the characteristics of quantitative trait in defense responses.
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Affiliation(s)
- Limin Gong
- Tuskegee University, Tuskegee, AL, 36088, USA
| | - Suoyi Han
- Henan Academy of Agricultural Sciences, Zhengzhou, 450002, China
| | - Mei Yuan
- Shandong Peanut Research Institute, Qingdao, 266000, China
| | - Xingli Ma
- Henan Agricultural University, Zhengzhou, 450002, China
| | | | - Guohao He
- Tuskegee University, Tuskegee, AL, 36088, USA.
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12
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Zhang X, Yao Y, Li X, Zhang L, Fan S. Transcriptomic analysis identifies novel genes and pathways for salt stress responses in Suaeda salsa leaves. Sci Rep 2020; 10:4236. [PMID: 32144380 PMCID: PMC7060309 DOI: 10.1038/s41598-020-61204-x] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2019] [Accepted: 02/24/2020] [Indexed: 02/07/2023] Open
Abstract
Salinity is a critical abiotic stress, which significantly impacts the agricultural yield worldwide. Identification of the molecular mechanisms underlying the salt tolerance in euhalophyte Suaeda salsa is conducive to the development of salt-resistant crops. In the present study, high-throughput RNA sequencing was performed after S. salsa leaves were exposed to 300 mM NaCl for 7 days, and 7,753 unigenes were identified as differently expressed genes (DEGs) in S. salsa, including 3,638 increased and 4,115 decreased unigenes. Moreover, hundreds of pathways were predicted to participate in salt stress response in S. salsa by Gene Ontology (GO), MapMan and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses, including ion transport and sequestration as well as photoprotection of photosystem (PS) II. The GO enrichment analysis indicated that genes related to ion transport, reactive oxygen species (ROS) scavenging and transcriptional factors were highly expressed upon NaCl treatment. The excessive Na+ and Cl- ions were supposed to be absorbed into the vacuole for ion sequestration and balance adjustment by potassium transporters (such as KEA3) with high expressions. Moreover, we predicted that mutiple candidate genes associated with photosynthesis (such as PSB33 and ABA4), ROS (such as TAU9 and PHI8) and transcriptional regulation (HB-7 and MYB78) pathways could mitigate salt stress-caused damage in S. salsa.
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Affiliation(s)
- Xuejie Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Yan Yao
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Xiaotong Li
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Luoyan Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China.
| | - Shoujin Fan
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China.
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13
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Sun H, Sun X, Wang H, Ma X. Advances in salt tolerance molecular mechanism in tobacco plants. Hereditas 2020; 157:5. [PMID: 32093781 PMCID: PMC7041081 DOI: 10.1186/s41065-020-00118-0] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2019] [Accepted: 02/18/2020] [Indexed: 02/01/2023] Open
Abstract
Tobacco, an economic crop and important model plant, has received more progress in salt tolerance with the aid of transgenic technique. Salt stress has become a key research field in abiotic stress. The study of tobacco promotes the understanding about the important adjustment for survival in high salinity environments, including cellular ion transport, osmotic regulation, antioxidation, signal transduction and expression regulation, and protection of cells from stress damage. Genes, which response to salt, have been studied using targeted transgenic technologies in tobacco plants to investigate the molecular mechanisms. The transgenic tobacco plants exhibited higher seed germination and survival rates, better root and shoot growth under salt stress treatments. Transgenic approach could be the promising option for enhancing tobacco production under saline condition. This review highlighted the salt tolerance molecular mechanisms of tobacco.
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Affiliation(s)
- Haiji Sun
- School of Life Science, Shandong Normal University, Jinan, 250014 China
| | - Xiaowen Sun
- School of Life Science, Shandong Normal University, Jinan, 250014 China
| | - Hui Wang
- School of Life Science, Shandong Normal University, Jinan, 250014 China
| | - Xiaoli Ma
- Central laboratory, Jinan Central Hospital Affiliated to Shandong University, Jinan, 250013 China
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14
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Shao Q, Liu X, Su T, Ma C, Wang P. New Insights Into the Role of Seed Oil Body Proteins in Metabolism and Plant Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1568. [PMID: 31921234 PMCID: PMC6914826 DOI: 10.3389/fpls.2019.01568] [Citation(s) in RCA: 44] [Impact Index Per Article: 8.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/25/2019] [Accepted: 11/08/2019] [Indexed: 05/10/2023]
Abstract
Oil bodies (OBs) are ubiquitous dynamic organelles found in plant seeds. They have attracted increasing attention recently because of their important roles in plant physiology. First, the neutral lipids stored within these organelles serve as an initial, essential source of energy and carbon for seed germination and post-germinative growth of the seedlings. Secondly, they are involved in many other cellular processes such as stress responses, lipid metabolism, organ development, and hormone signaling. The biological functions of seed OBs are dependent on structural proteins, principally oleosins, caleosins, and steroleosins, which are embedded in the OB phospholipid monolayer. Oleosin and caleosin proteins are specific to plants and mainly act as OB structural proteins and are important for the biogenesis, stability, and dynamics of the organelle; whereas steroleosin proteins are also present in mammals and play an important role in steroid hormone metabolism and signaling. Significant progress using new genetic, biochemical, and imaging technologies has uncovered the roles of these proteins. Here, we review recent work on the structural or metabolic roles of these proteins in OB biogenesis, stabilization and degradation, lipid homeostasis and mobilization, hormone signal transduction, stress defenses, and various aspects of plant growth and development.
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Affiliation(s)
| | | | | | - Changle Ma
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
| | - Pingping Wang
- Shandong Provincial Key Laboratory of Plant Stress, College of Life Sciences, Shandong Normal University, Jinan, China
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15
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Cui L, Guo F, Zhang J, Yang S, Meng J, Geng Y, Li X, Wan S. Synergy of arbuscular mycorrhizal symbiosis and exogenous Ca 2+ benefits peanut (Arachis hypogaea L.) growth through the shared hormone and flavonoid pathway. Sci Rep 2019; 9:16281. [PMID: 31700111 PMCID: PMC6838158 DOI: 10.1038/s41598-019-52630-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/13/2018] [Accepted: 10/14/2019] [Indexed: 12/23/2022] Open
Abstract
Peanut yield is severely affected by exchangeable calcium ion (Ca2+) deficiency in the soil. Arbuscular mycorrhizal (AM) symbiosis increases the absorption of Ca2+ for host plants. Here, we analyzed the physiological and transcriptional changes in the roots of Arachis hypogaea L. colonized by Funneliformis mosseae under Ca2+-deficient and -sufficient conditions. The results showed that exogenous Ca2+ application increased arbuscular mycorrhizal fungi (AMF) colonization, plant dry weight, and Ca content of AM plants. Simultaneously, transcriptome analysis showed that Ca2+ application further induced 74.5% of differentially expressed gene transcripts in roots of AM peanut seedlings. These genes are involved in AM symbiosis development, hormone biosynthesis and signal transduction, and carotenoid and flavonoid biosynthesis. The transcripts of AM-specific marker genes in AM plants with Ca2+ deprivation were further up-regulated by Ca2+ application. Gibberellic acid (GA3) and flavonoid contents were higher in roots of AM- and Ca2+-treated plants, but salicylic acid (SA) and carotenoid contents specifically increased in roots of the AM plants. Thus, these results suggest that the synergy of AM symbiosis and Ca2+ improves plant growth due to the shared GA- and flavonoid-mediated pathway, whereas SA and carotenoid biosynthesis in peanut roots are specific to AM symbiosis.
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Affiliation(s)
- Li Cui
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China
| | - Feng Guo
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China
| | - Jialei Zhang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China
| | - Sha Yang
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China
| | - JingJing Meng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China
| | - Yun Geng
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China
| | - Xinguo Li
- Biotechnology Research Center, Shandong Academy of Agricultural Sciences, Jinan, 250100, China.
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China.
- College of Life Sciences, Shandong Normal University, Jinan, 250014, China.
| | - Shubo Wan
- Scientific Observing and Experimental Station of Crop Cultivation in East China, Ministry of Agriculture, Jinan, 250100, China.
- Shandong Academy of Agricultural Sciences and Key Laboratory of Crop Genetic Improvement and Ecological Physiology of Shandong Province, Jinan, 250100, China.
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16
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Zhang L, Zhang X, Fan S, Zhang Z. Identification of modules and hub genes associated with platinum-based chemotherapy resistance and treatment response in ovarian cancer by weighted gene co-expression network analysis. Medicine (Baltimore) 2019; 98:e17803. [PMID: 31689861 PMCID: PMC6946301 DOI: 10.1097/md.0000000000017803] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/14/2019] [Revised: 08/23/2019] [Accepted: 10/04/2019] [Indexed: 12/23/2022] Open
Abstract
High-grade serous ovarian carcinoma (HGSOC) is the most prevalent and malignant ovarian tumor.To identify co-expression modules and hub genes correlated with platinum-based chemotherapy resistant and sensitive HGSOC, we performed weighted gene co-expression network analysis (WGCNA) on microarray data of HGSOC with 12 resistant samples and 16 sensitive samples of GSE51373 dataset.A total of 5122 genes were included in WGCNA, and 16 modules were identified. Module-trait analysis identified that the module salmon (cor = 0.50), magenta (cor = 0.49), and black (cor = 0.45) were discovered associated with chemotherapy resistant, and the significance for these platinum-resistant modules were validated in the GSE63885 dataset. Given that the black module was validated to be the most related one, hub genes of this module, alcohol dehydrogenase 1B, cadherin 11, and vestigial like family member 3were revealed to be expressional related with platinum resistance, and could serve as prognostic markers for ovarian cancer.Our analysis might provide insight for molecular mechanisms of platinum-based chemotherapy resistance and treatment response in ovarian cancer.
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Affiliation(s)
- Luoyan Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University
| | - Xuejie Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University
| | - Shoujin Fan
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University
| | - Zhen Zhang
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong First Medical University & Shandong Academy of Medical Sciences, Jinan, Shandong, China
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17
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Kumar R, Pandey MK, Roychoudhry S, Nayyar H, Kepinski S, Varshney RK. Peg Biology: Deciphering the Molecular Regulations Involved During Peanut Peg Development. FRONTIERS IN PLANT SCIENCE 2019; 10:1289. [PMID: 31681383 PMCID: PMC6813228 DOI: 10.3389/fpls.2019.01289] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/10/2019] [Accepted: 09/17/2019] [Indexed: 05/07/2023]
Abstract
Peanut or groundnut is one of the most important legume crops with high protein and oil content. The high nutritional qualities of peanut and its multiple usage have made it an indispensable component of our daily life, in both confectionary and therapeutic food industries. Given the socio-economic significance of peanut, understanding its developmental biology is important in providing a molecular framework to support breeding activities. In peanut, the formation and directional growth of a specialized reproductive organ called a peg, or gynophore, is especially relevant in genetic improvement. Several studies have indicated that peanut yield can be improved by improving reproductive traits including peg development. Therefore, we aim to identify unifying principles for the genetic control, underpinning molecular and physiological basis of peg development for devising appropriate strategy for peg improvement. This review discusses the current understanding of the molecular aspects of peanut peg development citing several studies explaining the key mechanisms. Deciphering and integrating recent transcriptomic, proteomic, and miRNA-regulomic studies provide a new perspective for understanding the regulatory events of peg development that participate in pod formation and thus control yield.
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Affiliation(s)
- Rakesh Kumar
- Center of Excellence in Genomics and Systems Biology, International Crops Research, Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | - Manish K. Pandey
- Center of Excellence in Genomics and Systems Biology, International Crops Research, Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
| | | | - Harsh Nayyar
- Department of Botany, Panjab University, Chandigarh, India
| | - Stefan Kepinski
- Centre for Plant Sciences, University of Leeds, Leeds, United Kingdom
| | - Rajeev K. Varshney
- Center of Excellence in Genomics and Systems Biology, International Crops Research, Institute for the Semi-Arid Tropics (ICRISAT), Hyderabad, India
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18
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Transcriptome Analysis of Elm (Ulmus pumila) Fruit to Identify Phytonutrients Associated Genes and Pathways. FORESTS 2019. [DOI: 10.3390/f10090738] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
Abstract
Plant fruit is an important source of natural active phytonutrients that are profitable for human health. Elm (Ulmus pumila) fruit is considered as natural plant food in China that is rich in nutrients. In the present study, high-throughput RNA sequencing was performed in U. pumila edible fruits and leaves and 11,386 unigenes were filtered as dysregulated genes in fruit samples, including 5231 up- and 6155 downregulated genes. Hundreds of pathways were predicted to participate in seed development and phytonutrient biosynthesis in U. pumila by GO, MapMan, and KEGG enrichment analysis, including “seed maturation”, “glycine, serine, and threonine metabolism” and “phenylpropanoid biosynthesis”. ABA-mediated glucose response-related ethylene-activated signaling pathway (e.g., ABI4) were supposed to associate with elm fruit development; unsaturated fatty acids pathway (e.g., ACX2 and SAD) were predicted to participate in determination of fatty acid composition in elm fruit; flavonoid and coumarins biosynthesis (e.g., CYP98A3 and CCoAOMT1) were demonstrated to correlate with the bioactivity of elm fruits in human cancer and inflammation resistance. To provide more information about fruit developmental status, the qRT-PCR analysis for key genes of “phenylpropanoid biosynthesis” and “alpha-Linolenic acid metabolism” were conducted in samples of young fruits, ripe fruit, old fruit, and leaves. Two biosynthetic pathways for unsaturated fatty acid and Jasmonic acid (JA) were deduced to be involved in fruit development in U. pumila and the phenylpropanoid glycoside, syringin, was speculated to accumulate in the early development stages of elm fruit. Our transcriptome data supports molecular clues for seed development and biologically active substances in elm fruits.
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19
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Sun X, Han G, Meng Z, Lin L, Sui N. Roles of malic enzymes in plant development and stress responses. PLANT SIGNALING & BEHAVIOR 2019; 14:e1644596. [PMID: 31322479 PMCID: PMC6768271 DOI: 10.1080/15592324.2019.1644596] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Revised: 06/30/2019] [Accepted: 07/02/2019] [Indexed: 05/12/2023]
Abstract
Malic enzyme (ME) comprises a family of proteins with multiple isoforms located in different compartments of eukaryotic cells. It is a key enzyme regulating malic acid metabolism and can catalyze the reversible reaction of oxidative decarboxylation of malic acid. And it is also one of the important enzymes in plant metabolism and is involved in multiple metabolic processes. ME is widely present in plants and mainly discovered in cytoplasmic stroma, mitochondria, chloroplasts. It is involved in plant growth, development, and stress response. Plants are stressed by various environmental factors such as drought, high salt, and high temperature during plant growth, and the mechanisms of plant response to various environmental stresses are synergistic. Numerous studies have shown that ME participates in the process of coping with the above environmental factors by increasing water use efficiency, improving photosynthesis of plants, providing reducing power, and so on. In this review, we discuss the important role of ME in plant development and plant stress response, and prospects for its application. It provides a theoretical basis for the future use of ME gene for molecular resistance breeding.
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Affiliation(s)
- Xi Sun
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, PR China
| | - Guoliang Han
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, PR China
| | - Zhe Meng
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, PR China
| | - Lin Lin
- Water Research Institute of Shandong Province, Jinan, PR China
| | - Na Sui
- Shandong Provincial Key Laboratory of Plant Stress, College of life Sciences, Shandong Normal University, Jinan, PR China
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20
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Zhang L, Tan Y, Fan S, Zhang X, Zhang Z. Phylostratigraphic analysis of gene co-expression network reveals the evolution of functional modules for ovarian cancer. Sci Rep 2019; 9:2623. [PMID: 30796309 PMCID: PMC6384884 DOI: 10.1038/s41598-019-40023-9] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/29/2018] [Accepted: 01/23/2019] [Indexed: 01/06/2023] Open
Abstract
Ovarian cancer (OV) is an extremely lethal disease. However, the evolutionary machineries of OV are still largely unknown. Here, we used a method that combines phylostratigraphy information with gene co-expression networks to extensively study the evolutionary compositions of OV. The present co-expression network construction yielded 18,549 nodes and 114,985 edges based on 307 OV expression samples obtained from the Genome Data Analysis Centers database. A total of 20 modules were identified as OV related clusters. The human genome sequences were divided into 19 phylostrata (PS), the majority (67.45%) of OV genes was already present in the eukaryotic ancestor. There were two strong peaks of the emergence of OV genes screened by hypergeometric test: the evolution of the multicellular metazoan organisms (PS5 and PS6, P value = 0.002) and the emergence of bony fish (PS11 and PS12, P value = 0.009). Hence, the origin of OV is far earlier than its emergence. The integrated analysis of the topology of OV modules and the phylogenetic data revealed an evolutionary pattern of OV in human, namely, OV modules have arisen step by step during the evolution of the respective lineages. New genes have evolved and become locked into a pathway, where more and more biological pathways are fixed into OV modules by recruiting new genes during human evolution.
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Affiliation(s)
- Luoyan Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Yi Tan
- Qilu Cell Therapy Technology Co., Ltd, Jinan, 250000, Shandong, China
| | - Shoujin Fan
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Xuejie Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, Jinan, 250014, Shandong, China
| | - Zhen Zhang
- Laboratory for Molecular Immunology, Institute of Basic Medicine, Shandong Academy of Medical Sciences, Jinan, 250062, Shandong, China.
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21
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Wang N, Qian Z, Luo M, Fan S, Zhang X, Zhang L. Identification of Salt Stress Responding Genes Using Transcriptome Analysis in Green Alga Chlamydomonas reinhardtii. Int J Mol Sci 2018; 19:E3359. [PMID: 30373210 PMCID: PMC6274750 DOI: 10.3390/ijms19113359] [Citation(s) in RCA: 45] [Impact Index Per Article: 7.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2018] [Revised: 10/24/2018] [Accepted: 10/24/2018] [Indexed: 12/20/2022] Open
Abstract
Salinity is one of the most important abiotic stresses threatening plant growth and agricultural productivity worldwide. In green alga Chlamydomonas reinhardtii, physiological evidence indicates that saline stress increases intracellular peroxide levels and inhibits photosynthetic-electron flow. However, understanding the genetic underpinnings of salt-responding traits in plantae remains a daunting challenge. In this study, the transcriptome analysis of short-term acclimation to salt stress (200 mM NaCl for 24 h) was performed in C. reinhardtii. A total of 10,635 unigenes were identified as being differently expressed by RNA-seq, including 5920 up- and 4715 down-regulated unigenes. A series of molecular cues were screened for salt stress response, including maintaining the lipid homeostasis by regulating phosphatidic acid, acetate being used as an alternative source of energy for solving impairment of photosynthesis, and enhancement of glycolysis metabolism to decrease the carbohydrate accumulation in cells. Our results may help understand the molecular and genetic underpinnings of salt stress responses in green alga C. reinhardtii.
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Affiliation(s)
- Ning Wang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Jinan 250014, China.
| | - Zhixin Qian
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Jinan 250014, China.
| | - Manwei Luo
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Jinan 250014, China.
| | - Shoujin Fan
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Jinan 250014, China.
| | - Xuejie Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Jinan 250014, China.
| | - Luoyan Zhang
- Key Lab of Plant Stress Research, College of Life Science, Shandong Normal University, No. 88 Wenhuadong Road, Jinan 250014, China.
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22
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Hui WK, Wang Y, Chen XY, Zayed MZ, Wu GJ. Analysis of Transcriptional Responses of the Inflorescence Meristems in Jatropha curcas Following Gibberellin Treatment. Int J Mol Sci 2018; 19:ijms19020432. [PMID: 29389867 PMCID: PMC5855654 DOI: 10.3390/ijms19020432] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2017] [Revised: 01/16/2018] [Accepted: 01/25/2018] [Indexed: 12/25/2022] Open
Abstract
Jatropha curcas L. seeds an oilseed plant with great potential for biodiesel production. However, low seed yield, which was limited by its lower female flowers, was a major drawback for its utilization. Our previous study found that the flower number and female-to-male ratio were increased by gibberellin treatment. Here, we compared the transcriptomic profiles of inflorescence meristem at different time points after gibberellic acid A3 (GA3) treatment. The present study showed that 951 differentially expressed genes were obtained in response to gibberellin treatment, compared with control samples. The 6-h time point was an important phase in the response to exogenous gibberellin. Furthermore, the plant endogenous gibberellin, auxin, ethylene, abscisic acid, and brassinolide-signaling transduction pathways were repressed, whereas the genes associated with cytokinin and jasmonic acid signaling were upregulated for 24-h time point following GA3 treatment. In addition, the floral meristem determinacy genes (JcLFY, JcSOC1) and floral organ identity genes (JcAP3, JcPI, JcSEP1-3) were significantly upregulated, but their negative regulator (JcSVP) was downregulated after GA3 treatment. Moreover, the effects of phytohormone, which was induced by exogenous plant growth regulator, mainly acted on the female floral differentiation process. To the best of our knowledge, this data is the first comprehensive analysis of the underlying transcriptional response mechanism of floral differentiation following GA3 treatment in J. curcas, which helps in engineering high-yielding varieties of Jatropha.
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Affiliation(s)
- Wen-Kai Hui
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China.
| | - Yi Wang
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
| | - Xiao-Yang Chen
- National Engineering Laboratory for Forest Tree Breeding, College of Biological Science and Technology, Beijing Forestry University, Beijing 100083, China.
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
| | - Mohamed Zaky Zayed
- State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China.
- Forestry and Wood Technology Department, Faculty of Agriculture (EL-Shatby), Alexandria University, Alexandria 21527, Egypt.
| | - Guo-Jiang Wu
- Key Laboratory of Plant Resources Conservation and Sustainable Utilization, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China.
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