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Mikwa EO, Wittkop B, Windpassinger SM, Weber SE, Ehrhardt D, Snowdon RJ. Early exposure to phosphorus starvation induces genetically determined responses in Sorghum bicolor roots. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:220. [PMID: 39259361 PMCID: PMC11390786 DOI: 10.1007/s00122-024-04728-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/19/2024] [Accepted: 07/27/2024] [Indexed: 09/13/2024]
Abstract
KEY MESSAGE We identified novel physiological and genetic responses to phosphorus starvation in sorghum diversity lines that augment current knowledge of breeding for climate-smart crops in Europe. Phosphorus (P) deficiency and finite P reserves for fertilizer production pose a threat to future global crop production. Understanding root system architecture (RSA) plasticity is central to breeding for P-efficient crops. Sorghum is regarded as a P-efficient and climate-smart crop with strong adaptability to different climatic regions of the world. Here we investigated early genetic responses of sorghum RSA to P deficiency in order to identified genotypes with interesting root phenotypes and responses under low P. A diverse set of sorghum lines (n = 285) was genotyped using DarTSeq generating 12,472 quality genome wide single-nucleotide polymorphisms. Root phenotyping was conducted in a paper-based hydroponic rhizotron system under controlled greenhouse conditions with low and optimal P nutrition, using 16 RSA traits to describe genetic and phenotypic variability at two time points. Genotypic and phenotypic P-response variations were observed for multiple root traits at 21 and 42 days after germination with high broad sense heritability (0.38-0.76). The classification of traits revealed four distinct sorghum RSA types, with genotypes clustering separately under both low and optimal P conditions, suggesting genetic control of root responses to P availability. Association studies identified quantitative trait loci in chromosomes Sb02, Sb03, Sb04, Sb06 and Sb09 linked with genes potentially involved in P transport and stress responses. The genetic dissection of key factors underlying RSA responses to P deficiency could enable early identification of P-efficient sorghum genotypes. Genotypes with interesting RSA traits for low P environments will be incorporated into current sorghum breeding programs for later growth stages and field-based evaluations.
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Affiliation(s)
- Erick O Mikwa
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany.
| | - Benjamin Wittkop
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | | | - Sven E Weber
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Dorit Ehrhardt
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
| | - Rod J Snowdon
- Department of Plant Breeding, Justus Liebig University, Giessen, Germany
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Qu J, Liu G, Zheng H, Wang X, Zhang H, Gou X, Xu S, Xue J. Deciphering the Genetic Basis of Kernel Composition in a Maize Association Panel. JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY 2024; 72:20182-20193. [PMID: 39196892 DOI: 10.1021/acs.jafc.4c04683] [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: 08/30/2024]
Abstract
The primary objective in contemporary maize breeding is to pursue high quality alongside high yield. Deciphering the genetic basis of natural variation in starch, protein, oil, and fiber contents is essential for manipulating kernel composition, thereby enhancing the kernel quality and meeting growing demands. Here, we identified 12 to 88 statistically significant loci associated with kernel composition traits through a genome-wide association study (GWAS) using a panel of 212 diverse inbred lines. A regional association study pinpointed numerous causal candidate genes at these loci. Coexpression and protein-protein interaction network analyses of candidate genes revealed several causal genes directly or indirectly involved in the metabolic processes related to kernel composition traits. Subsequent mutant experiment revealed that nonsense mutations in ZmTIFY12 affect starch, protein, and fiber content, whereas nonsense mutations in ZmTT12 affect starch, protein, and oil content. These findings provide valuable guidance for improving kernel quality in maize breeding efforts.
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Affiliation(s)
- Jianzhou Qu
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Gengyu Liu
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Hongyun Zheng
- College of Agronomy, Shenyang Agricultural University, Shenyang, Liaoning 110866, China
| | - Xiaoyue Wang
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Hao Zhang
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Xiaonan Gou
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Shutu Xu
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jiquan Xue
- The Key Laboratory of Maize Biology and Genetic Breeding in Arid Area of Northwest Region, Yangling, Shaanxi 712100, China
- Maize Engineering & Technology Research Centre, College of Agronomy, Northwest A&F University, Yangling, Shaanxi 712100, China
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Massman C, Rivedal HM, Dorman SJ, Tanner KC, Fredrickson C, Temple TN, Fisk S, Helgerson L, Hayes PM. Yellow Dwarf Virus Resistance in Barley: Phenotyping, Remote Imagery, and Virus-Vector Characterization. PHYTOPATHOLOGY 2024:PHYTO10230394KC. [PMID: 38916923 DOI: 10.1094/phyto-10-23-0394-kc] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/26/2024]
Abstract
Yellow dwarf viruses (YDVs) spread by aphids are some of the most economically important barley (Hordeum vulgare) virus-vector complexes worldwide. Detection and control of these viruses are critical components in the production of barley, wheat, and numerous other grasses of agricultural importance. Genetic control of plant diseases is often preferable to chemical control to reduce the environmental and economic cost of foliar insecticides. Accordingly, the objectives of this work were to (i) screen a barley population for resistance to YDVs under natural infection using phenotypic assessment of disease symptoms, (ii) implement drone imagery to further assess resistance and test its utility as a disease screening tool, (iii) identify the prevailing virus and vector types in the experimental environment, and (iv) perform a genome-wide association study to identify genomic regions associated with measured traits. Significant genetic differences were found in a population of 192 barley inbred lines regarding their YDV symptom severity, and symptoms were moderately to highly correlated with grain yield. The YDV severity measured with aerial imaging was highly correlated with on-the-ground estimates (r = 0.65). Three aphid species vectoring three YDV species were identified with no apparent genotypic influence on their distribution. A quantitative trait locus impacting YDV resistance was detected on chromosome 2H, albeit undetected using aerial imaging. However, quantitative trait loci for canopy cover and mean normalized difference vegetation index were successfully mapped using the drone. This work provides a framework for utilizing drone imagery in future resistance breeding efforts for YDVs in cereals and grasses, as well as in other virus-vector disease complexes.
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Affiliation(s)
- Chris Massman
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Hannah M Rivedal
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| | - Seth J Dorman
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| | - K Christy Tanner
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Chance Fredrickson
- Department of Botany and Plant Pathology, Oregon State University, Corvallis, OR 97331
| | - Todd N Temple
- U.S. Department of Agriculture-Agricultural Research Service, Forage Seed and Cereal Research Unit, Corvallis, OR 97331
| | - Scott Fisk
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Laura Helgerson
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
| | - Patrick M Hayes
- Department of Crop and Soil Science, Oregon State University, Corvallis, OR 97331
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Ganguly S, Nimitha K, Saha S, Sinha Mahapatra N, Bhattacharya K, Kundu R, Ganguly S, Sen P, Saha AK, Purkayastha S, Bhattacharyya PK, Biswas T, Bhattacharyya S. Identification and analysis of low light responsive yield enhancing QTLs in rice. Sci Rep 2024; 14:21011. [PMID: 39251768 PMCID: PMC11385566 DOI: 10.1038/s41598-024-71593-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/17/2024] [Accepted: 08/29/2024] [Indexed: 09/11/2024] Open
Abstract
Rice is one of the major food crops grown globally. However, during the wet season, rice suffers significant yield loss due to reduced light intensity caused by overcast clouds when the light intensity is only around 450-500 µmol/m2/s, compared to 1400-1800 µmol/m2/s in summer. This reduction in light intensity leads to a decrease in seed yield, mainly by limiting tiller or panicle numbers. Yield and its attributing parameters were recorded in one hundred thirty RILs for four consecutive wet seasons in ambient light (AL) and low light (LL, 35% light-cut using white shade net). QTL analysis was performed using Inclusive Composite Interval Mapping (ICIM) with all the phenotypic data and 927 polymorphic SNPs identified by the 7 K Infinium chip. The study identified a large QTL influencing panicle numbers and yield exclusively in lowlight on chromosome 1 (qPNLL1.1, qGYLL1.1) in four consecutive seasons with LOD > 10 and PVE > 30%. The favourable alleles are from the tolerant parent, Swarnaprabha. Another grain yield improving QTL was identified on chromosome 6 (qGYLL6.1), with LOD > 3 in three consecutive seasons. In a diverse rice panel of one hundred seventeen genotypes with five different models, association analysis identified the associated marker for panicle numbers and grain yield in LL, which is also the left marker of the newly identified QTLs for the traits under LL condition. A shade-responsive gene, monoculm 2 (MOC2, LOC_Os01g64660) inside the QTL on chromosome 1, upregulated in the tolerant parent and its QTL-carrying RILs, whereas repressed in the susceptible one. Therefore, due to its significant additive effect and validation across various genotypes, the yield-improving QTL on chromosome 1 can be directly utilised in marker-assisted selection (MAS) for developing shade-tolerant rice. This can also help reduce the yield gap between wet and dry-season rice.
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Affiliation(s)
- Shamba Ganguly
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - K Nimitha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Shoumik Saha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Nilanjan Sinha Mahapatra
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Kriti Bhattacharya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Rimpa Kundu
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Sebantee Ganguly
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Poulomi Sen
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Arup Kumar Saha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Shampa Purkayastha
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Prabir Kumar Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Tirthankar Biswas
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India
| | - Somnath Bhattacharyya
- Crop Research Unit, Genetics and Plant Breeding, Bidhan Chandra Krishi Viswavidyalaya, Mohanpur, 741252, India.
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Qiao J, Xu M, Xu F, Che Z, Han P, Dai X, Miao N, Zhu M. Identification of SNPs and Candidate Genes Associated with Monocyte/Lymphocyte Ratio and Neutrophil/Lymphocyte Ratio in Duroc × Erhualian F 2 Population. Int J Mol Sci 2024; 25:9745. [PMID: 39273692 PMCID: PMC11396299 DOI: 10.3390/ijms25179745] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/22/2024] [Revised: 09/06/2024] [Accepted: 09/08/2024] [Indexed: 09/15/2024] Open
Abstract
Understanding the pig immune function is crucial for disease-resistant breeding and potentially for human health research due to shared immune system features. Immune cell ratios, like monocyte/lymphocyte ratio (MLR) and neutrophil/lymphocyte ratio (NLR), offer a more comprehensive view of immune status compared to individual cell counts. However, research on pig immune cell ratios remains limited. This study investigated MLR and NLR in a Duroc × Erhualian F2 resource population. Heritability analysis revealed high values (0.649 and 0.688 for MLR and NLR, respectively), suggesting a strong genetic component. Furthermore, we employed an ensemble-like GWAS (E-GWAS) strategy and functional annotation analysis to identify 11 MLR-associated and 6 NLR-associated candidate genes. These genes were significantly enriched in immune-related biological processes. These findings provide novel genetic markers and candidate genes associated with porcine immunity, thereby providing valuable insights for addressing biosecurity and animal welfare concerns in the pig industry.
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Affiliation(s)
- Jiakun Qiao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Minghang Xu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangjun Xu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Zhaoxuan Che
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingping Han
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Dai
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Na Miao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengjin Zhu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
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Rafi N, Dominguez M, Okello P, Mathew FM. No Common Candidate Genes for Resistance to Fusarium graminearum, F. proliferatum, F. sporotrichioides, and F. subglutinans in Soybean Accessions from Maturity Groups 0 and I: Findings from Genome-wide Association Mapping. PLANT DISEASE 2024:PDIS02240477RE. [PMID: 38640427 DOI: 10.1094/pdis-02-24-0477-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 04/21/2024]
Abstract
Seedling diseases and root rot, caused by species of Fusarium, can limit soybean (Glycine max L.) production in the United States. Currently, there are few commercially available cultivars resistant to Fusarium. This study was conducted to assess the resistance of soybean maturity group (MG) accessions from 0 and I to Fusarium proliferatum, F. sporotrichioides, and F. subglutinans, as well as to identify common quantitative trait loci (QTLs) for resistance to these pathogens, in addition to F. graminearum, using a genome-wide association study (GWAS). A total of 155, 91, and 48 accessions from the United States Department of Agriculture (USDA) soybean germplasm collection from MG 0 and I were screened with a single isolate each of F. proliferatum, F. sporotrichioides, and F. subglutinans, respectively, using the inoculum layer inoculation method in the greenhouse. The disease severity was assessed 21 days postinoculation and analyzed using nonparametric statistics to determine the relative treatment effects (RTEs). Eleven and seven accessions showed significantly lower RTEs when inoculated with F. proliferatum and F. subglutinans, respectively, compared with the susceptible cultivar 'Williams 82'. One accession was significantly less susceptible to both F. proliferatum and F. subglutinans. The GWAS conducted with 41,985 single-nucleotide markers identified one QTL associated with resistance to both F. proliferatum and F. sporotrichioides, as well as another QTL for resistance to both F. subglutinans and F. graminearum. However, no common QTLs were identified for the four pathogens. The USDA accessions and QTLs identified in this study can be utilized to selectively breed resistance to multiple species of Fusarium.[Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY 4.0 International license.
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Affiliation(s)
- Nitha Rafi
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
| | - Matias Dominguez
- EEA INTA Pergamino, Instituto Nacional de Tecnología Agropecuaria (INTA), Pergamino, Buenos Aires, Argentina
| | - Paul Okello
- Department of Agronomy, Horticulture, and Plant Science, South Dakota State University, Brookings, SD 57007, U.S.A
| | - Febina M Mathew
- Department of Plant Pathology, North Dakota State University, Fargo, ND 58102, U.S.A
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Wang F, Zhao T, Feng Y, Ji Z, Zhao Q, Meng Q, Liu B, Liu L, Chen Q, Qi J, Zhu Z, Yang C, Qin J. Identification of candidate genes and genomic prediction of soybean fatty acid components in two soybean populations. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:211. [PMID: 39210238 DOI: 10.1007/s00122-024-04716-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/04/2024] [Accepted: 08/11/2024] [Indexed: 09/04/2024]
Abstract
Soybean, a source of plant-derived lipids, contains an array of fatty acids essential for health. A comprehensive understanding of the fatty acid profiles in soybean is crucial for enhancing soybean cultivars and augmenting their qualitative attributes. Here, 180 F10 generation recombinant inbred lines (RILs), derived from the cross-breeding of the cultivated soybean variety 'Jidou 12' and the wild soybean 'Y9,' were used as primary experimental subjects. Using inclusive composite interval mapping (ICIM), this study undertook a quantitative trait locus (QTL) analysis on five distinct fatty acid components in the RIL population from 2019 to 2021. Concurrently, a genome-wide association study (GWAS) was conducted on 290 samples from a genetically diverse natural population to scrutinize the five fatty acid components during the same timeframe, thereby aiming to identify loci closely associated with fatty acid profiles. In addition, haplotype analysis and the Kyoto Encyclopedia of Genes and Genomes pathway analysis were performed to predict candidate genes. The QTL analysis elucidated 23 stable QTLs intricately associated with the five fatty acid components, exhibiting phenotypic contribution rates ranging from 2.78% to 25.37%. In addition, GWAS of the natural population unveiled 102 significant loci associated with these fatty acid components. The haplotype analysis of the colocalized loci revealed that Glyma.06G221400 on chromosome 6 exhibited a significant correlation with stearic acid content, with Hap1 showing a markedly elevated stearic acid level compared with Hap2 and Hap3. Similarly, Glyma.12G075100 on chromosome 12 was significantly associated with the contents of oleic, linoleic, and linolenic acids, suggesting its involvement in fatty acid biosynthesis. In the natural population, candidate genes associated with the contents of palmitic and linolenic acids were predominantly from the fatty acid metabolic pathway, indicating their potential role as pivotal genes in the critical steps of fatty acid metabolism. Furthermore, genomic selection (GS) for fatty acid components was conducted using ridge regression best linear unbiased prediction based on both random single nucleotide polymorphisms (SNPs) and SNPs significantly associated with fatty acid components identified by GWAS. GS accuracy was contingent upon the SNP set used. Notably, GS efficiency was enhanced when using SNPs derived from QTL mapping analysis and GWAS compared with random SNPs, and reached a plateau when the number of SNP markers exceeded 3,000. This study thus indicates that Glyma.06G221400 and Glyma.12G075100 are genes integral to the synthesis and regulatory mechanisms of fatty acids. It provides insights into the complex biosynthesis and regulation of fatty acids, with significant implications for the directed improvement of soybean oil quality and the selection of superior soybean varieties. The SNP markers delineated in this study can be instrumental in establishing an efficacious pipeline for marker-assisted selection and GS aimed at improving soybean fatty acid components.
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Affiliation(s)
- Fengmin Wang
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Tiantian Zhao
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Yan Feng
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zengfa Ji
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Qingsong Zhao
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Qingmin Meng
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Bingqiang Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Luping Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Qiang Chen
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Jin Qi
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China
| | - Zhengge Zhu
- Ministry of Education Key Laboratory of Molecular and Cellular Biology, Hebei Research Center of the Basic Discipline of Cell Biology, Hebei Collaboration Innovation Center for Cell Signaling and Environmental Adaptation, Hebei Key Laboratory of Molecular and Cellular Biology, College of Life Sciences, Hebei Normal University, Shijiazhuang, China.
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China.
| | - Jun Qin
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-Center, Huang-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, Hebei, China.
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8
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Rett-Cadman S, Weng Y, Fei Z, Thompson A, Grumet R. Genome-Wide Association Study of Cuticle and Lipid Droplet Properties of Cucumber ( Cucumis sativus L.) Fruit. Int J Mol Sci 2024; 25:9306. [PMID: 39273254 PMCID: PMC11395541 DOI: 10.3390/ijms25179306] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/30/2024] [Revised: 08/23/2024] [Accepted: 08/25/2024] [Indexed: 09/15/2024] Open
Abstract
The fruit surface is a critical first line of defense against environmental stress. Overlaying the fruit epidermis is the cuticle, comprising a matrix of cutin monomers and waxes that provides protection and mechanical support throughout development. The epidermal layer of the cucumber (Cucumis sativus L.) fruit also contains prominent lipid droplets, which have recently been recognized as dynamic organelles involved in lipid storage and metabolism, stress response, and the accumulation of specialized metabolites. Our objective was to genetically characterize natural variations for traits associated with the cuticle and lipid droplets in cucumber fruit. Phenotypic characterization and genome-wide association studies (GWAS) were performed using a resequenced cucumber core collection accounting for >96% of the allelic diversity present in the U.S. National Plant Germplasm System collection. The collection was grown in the field, and fruit were harvested at 16-20 days post-anthesis, an age when the cuticle thickness and the number and size of lipid droplets have stabilized. Fresh fruit tissue sections were prepared to measure cuticle thickness and lipid droplet size and number. The collection showed extensive variation for the measured traits. GWAS identified several QTLs corresponding with genes previously implicated in cuticle or lipid biosynthesis, including the transcription factor SHINE1/WIN1, as well as suggesting new candidate genes, including a potential lipid-transfer domain containing protein found in association with isolated lipid droplets.
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Affiliation(s)
- Stephanie Rett-Cadman
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI 48824, USA
| | - Yiqun Weng
- Department of Plant and Agroecosystem Sciences, University of Wisconsin, Madison, WI 53706, USA
- USDA-ARS Vegetable Crops Research Unit, Madison, WI 53706, USA
| | - Zhangjun Fei
- Boyce Thompson Institute, Cornell University, Ithaca, NY 14853, USA
- USDA-ARS Robert W. Holley Center for Agriculture and Health, Ithaca, NY 14853, USA
| | - Addie Thompson
- Department of Plant, Soil and Microbial Sciences, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI 48824, USA
| | - Rebecca Grumet
- Department of Horticulture, Graduate Program in Plant Breeding, Genetics and Biotechnology, Michigan State University, East Lansing, MI 48824, USA
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9
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Wang Y, Fredua-Agyeman R, Yu Z, Hwang SF, Strelkov SE. Genome-wide association study of Verticillium longisporum resistance in Brassica genotypes. FRONTIERS IN PLANT SCIENCE 2024; 15:1436982. [PMID: 39258297 PMCID: PMC11384582 DOI: 10.3389/fpls.2024.1436982] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/22/2024] [Accepted: 08/02/2024] [Indexed: 09/12/2024]
Abstract
Verticillium stripe, caused by Verticillium longisporum, presents an emerging threat to Canadian canola (Brassica napus). Initially detected in Manitoba in 2014, the presence of this pathogen has since been confirmed across western Canada. Infections by V. longisporum can result in yield losses of up to 50%, which is a cause for concern given the susceptibility of most commercial Canadian canola cultivars. The objective of this study was to screen a collection of 211 Brassica genotypes for their reactions to V. longisporum, and to use genome-wide association study (GWAS) to identify single nucleotide polymorphism (SNP) markers for resistance. The plant material consisted of 110 rutabaga (B. napus ssp. napobrassica), 35 canola, 40 Brassica rapa, and 15 Brassica oleracea accessions or cultivars, alongside 11 hosts of the European Clubroot Differential (ECD) set. These materials were screened for resistance under greenhouse conditions and were genotyped using a 19K Brassica SNP array. Three general linear models (GLM), four mixed linear models (MLM), and three GWAS methods were employed to evaluate the markers. Eleven non-commercial Brassica accessions and 9 out of 35 commercial canola cultivars displayed a low normalized area under the disease progress curve (AUDPCnorm.). The non-commercial accessions could prove valuable as potential sources of resistance against V. longisporum. Forty-five SNP markers were identified to be significantly associated with V. longisporum resistance using single-SNP based GWAS analysis. In comparison, haplotype-based GWAS analyses identified 10 to 25 haplotype blocks to be significantly associated with V. longisporum resistance. Between 20% and 56% of QTLs identified by the more conventional single-SNP based GWAS analysis were also detected by the haplotype-based GWAS analysis. The overlapping genomic regions identified by the two GWAS methods present promising hotspots for marker-assisted selection in the future development of Verticillium stripe-resistant canola.
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Affiliation(s)
- Yixiao Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Rudolph Fredua-Agyeman
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Zhiyu Yu
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Sheau-Fang Hwang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
| | - Stephen E Strelkov
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, Canada
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Concepcion JS, Noble AD, Thompson AM, Dong Y, Olson EL. Genomic regions influencing the hyperspectral phenome of deoxynivalenol infected wheat. Sci Rep 2024; 14:19340. [PMID: 39164367 PMCID: PMC11336138 DOI: 10.1038/s41598-024-69830-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/13/2024] [Accepted: 08/09/2024] [Indexed: 08/22/2024] Open
Abstract
The quantitative nature of fusarium head blight (FHB) resistance requires further exploration of the wheat genome to identify regions conferring resistance. In this study, we explored the application of hyperspectral imaging of Fusarium-infected wheat kernels and identified regions of the wheat genome contributing significantly to the accumulation of Deoxynivalenol (DON) mycotoxin. Strong correlations were identified between hyperspectral reflectance values for 204 wavebands in the 397-673 nm range and DON mycotoxin. Dimensionality reduction using principal components was performed for all 204 wavebands and 38 sliding windows across the range of wavebands. The first principal component (PC1) of all 204 wavebands explained 70% of the total variation in waveband reflectance values and was highly correlated with DON mycotoxin. PC1 was used as a phenotype in a genome wide association study and a large effect QTL on chromosome 2D was identified for PC1 of all wavebands as well as nearly all 38 sliding windows. The allele contributing variation in PC1 values also led to a substantial reduction in DON. The 2D polymorphism affecting DON levels localized to the exon of TraesCS2D02G524600 which is upregulated in wheat spike and rachis tissues during FHB infection. This work demonstrates the value of hyperspectral imaging as a correlated trait for investigating the genetic basis of resistance and developing wheat varieties with enhanced resistance to FHB.
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Affiliation(s)
- Jonathan S Concepcion
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Amanda D Noble
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Addie M Thompson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA
| | - Yanhong Dong
- Department of Plant Pathology, University of Minnesota, St. Paul, MN, 55108, USA
| | - Eric L Olson
- Department of Plant, Soil, and Microbial Sciences, Michigan State University, East Lansing, MI, 48823, USA.
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11
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Osorio-Guarin JA, Higgins J, Toloza-Moreno DL, Di Palma F, Enriquez Valencia AL, Riveros Munévar F, De Vega JJ, Yockteng R. Genome-wide association analyses using multilocus models on bananas (Musa spp.) reveal candidate genes related to morphology, fruit quality, and yield. G3 (BETHESDA, MD.) 2024; 14:jkae108. [PMID: 38775627 PMCID: PMC11304972 DOI: 10.1093/g3journal/jkae108] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2024] [Accepted: 05/17/2024] [Indexed: 08/09/2024]
Abstract
Bananas (Musa spp.) are an essential fruit worldwide and rank as the fourth most significant food crop for addressing malnutrition due to their rich nutrients and starch content. The potential of their genetic diversity remains untapped due to limited molecular breeding tools. Our study examined a phenotypically diverse group of 124 accessions from the Colombian Musaceae Collection conserved in AGROSAVIA. We assessed 12 traits categorized into morphology, fruit quality, and yield, alongside sequence data. Our sequencing efforts provided valuable insights, with an average depth of about 7× per accession, resulting in 187,133 single-nucleotide polymorphisms (SNPs) against Musa acuminata (A genome) and 220,451 against Musa balbisiana (B genome). Population structure analysis grouped samples into four and five clusters based on the reference genome. By using different association models, we identified marker-trait associations (MTAs). The mixed linear model revealed four MTAs, while the Bayesian-information and linkage-disequilibrium iteratively nested keyway and fixed and random model for circulating probability unification models identified 82 and 70 MTAs, respectively. We identified 38 and 40 candidate genes in linkage proximity to significant MTAs for the A genome and B genome, respectively. Our findings provide insights into the genetic underpinnings of morphology, fruit quality, and yield. Once validated, the SNP markers and candidate genes can potentially drive advancements in genomic-guided breeding strategies to enhance banana crop improvement.
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Affiliation(s)
- Jaime Andrés Osorio-Guarin
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 vía Mosquera, Cundinamarca 250047, Colombia
| | - Janet Higgins
- Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, UK
| | - Deisy Lisseth Toloza-Moreno
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 vía Mosquera, Cundinamarca 250047, Colombia
| | | | - Ayda Lilia Enriquez Valencia
- Centro de Investigación Palmira, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Palmira, Valle del Cauca 763533, Colombia
| | - Fernando Riveros Munévar
- Facultad de Psicología y Ciencias del Comportamiento, Universidad de La Sabana, Chía, Cundinamarca 250001, Colombia
| | - José J De Vega
- Earlham Institute, Norwich Research Park, NR4 7UZ Norwich, UK
| | - Roxana Yockteng
- Centro de Investigación Tibaitatá, Corporación Colombiana de Investigación Agropecuaria, AGROSAVIA, Km 14 vía Mosquera, Cundinamarca 250047, Colombia
- Institut de Systématique, Evolution, Biodiversité-UMR-CNRS 7205, Muséum National d´Histoire Naturelle, Paris, Ile 75005, France
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12
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Nisa WU, Sandhu S, Nair SK, Kaur H, Kumar A, Rashid Z, Saykhedkar G, Vikal Y. Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India. BMC Genomics 2024; 25:760. [PMID: 39103778 DOI: 10.1186/s12864-024-10655-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/17/2024] [Accepted: 07/23/2024] [Indexed: 08/07/2024] Open
Abstract
BACKGROUND In the face of contemporary climatic vulnerabilities and escalating global temperatures, the prevalence of maydis leaf blight (MLB) poses a potential threat to maize production. This study endeavours to discern marker-trait associations and elucidate the candidate genes that underlie resistance to MLB in maize by employing a diverse panel comprising 336 lines. The panel was screening for MLB across four environments, employing standard artificial inoculation techniques. Genome-wide association studies (GWAS) and haplotype analysis were conducted utilizing a total of 128,490 SNPs obtained from genotyping-by-sequencing (GBS). RESULTS GWAS identified 26 highly significant SNPs associated with MLB resistance, among the markers examined. Seven of these SNPs, reported in novel chromosomal bins (9.06, 5.01, 9.01, 7.04, 4.06, 1.04, and 6.05) were associated with genes: bzip23, NAGS1, CDPK7, aspartic proteinase NEP-2, VQ4, and Wun1, which were characterized for their roles in diminishing fungal activity, fortifying defence mechanisms against necrotrophic pathogens, modulating phyto-hormone signalling, and orchestrating oxidative burst responses. Gene mining approach identified 22 potential candidate genes associated with SNPs due to their functional relevance to resistance against necrotrophic pathogens. Notably, bin 8.06, which hosts five SNPs, showed a connection to defense-regulating genes against MLB, indicating the potential formation of a functional gene cluster that triggers a cascade of reactions against MLB. In silico studies revealed gene expression levels exceeding ten fragments per kilobase million (FPKM) for most genes and demonstrated coexpression among all candidate genes in the coexpression network. Haplotype regression analysis revealed the association of 13 common significant haplotypes at Bonferroni ≤ 0.05. The phenotypic variance explained by these significant haplotypes ranged from low to moderate, suggesting a breeding strategy that combines multiple resistance alleles to enhance resistance to MLB. Additionally, one particular haplotype block (Hap_8.3) was found to consist of two SNPs (S8_152715134, S8_152460815) identified in GWAS with 9.45% variation explained (PVE). CONCLUSION The identified SNPs/ haplotypes associated with the trait of interest contribute to the enrichment of allelic diversity and hold direct applicability in Genomics Assisted Breeding for enhancing MLB resistance in maize.
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Affiliation(s)
- Wajhat- Un- Nisa
- Dept. of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Surinder Sandhu
- Dept. of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India.
| | | | - Harleen Kaur
- Dept. of Plant Breeding and Genetics, Punjab Agricultural University, Ludhiana, India
| | - Ashok Kumar
- Regional Research Station, Punjab Agricultural University, Gurdaspur, Ludhiana, India
| | - Zerka Rashid
- International Maize and Wheat Improvement Centre (CIMMYT), Hyderabad, India
| | - Gajanan Saykhedkar
- International Maize and Wheat Improvement Centre (CIMMYT), Hyderabad, India
| | - Yogesh Vikal
- School of Agricultural Biotechnology, Punjab Agricultural University, Ludhiana, India
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13
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Upadhaya A, Upadhaya SGC, Brueggeman R. Association mapping with a diverse population of Puccinia graminis f. sp. tritici identified avirulence loci interacting with the barley Rpg1 stem rust resistance gene. BMC Genomics 2024; 25:751. [PMID: 39090588 PMCID: PMC11295639 DOI: 10.1186/s12864-024-10670-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/23/2024] [Accepted: 07/26/2024] [Indexed: 08/04/2024] Open
Abstract
BACKGROUND Wheat stem rust, caused by Puccinia graminis f. sp. tritici (Pgt), is an important disease of barley and wheat. A diverse sexual Pgt population from the Pacific Northwest (PNW) region of the US contains a high proportion of individuals with virulence on the barley stem rust resistance (R) gene, Rpg1. However, the evolutionary mechanisms of this virulence on Rpg1 are mysterious considering that Rpg1 had not been deployed in the region and the gene had remained remarkably durable in the Midwestern US and prairie provinces of Canada. METHODS AND RESULTS To identify AvrRpg1 effectors, genome wide association studies (GWAS) were performed using 113 Pgt isolates collected from the PNW (n = 89 isolates) and Midwest (n = 24 isolates) regions of the US. Disease phenotype data were generated on two barley lines Morex and the Golden Promise transgenic (H228.2c) that carry the Rpg1 gene. Genotype data was generated by whole genome sequencing (WGS) of 96 isolates (PNW = 89 isolates and Midwest = 7 isolates) and RNA sequencing (RNAseq) data from 17 Midwestern isolates. Utilizing ~1.2 million SNPs generated from WGS and phenotype data (n = 96 isolates) on the transgenic line H228.2c, 53 marker trait associations (MTAs) were identified. Utilizing ~140 K common SNPs generated from combined analysis of WGS and RNAseq data, two significant MTAs were identified using the cv Morex phenotyping data. The 55 MTAs defined two distinct avirulence loci, on supercontig 2.30 and supercontig 2.11 of the Pgt reference genome of Pgt isolate CRL 75-36-700-3. The major avirulence locus designated AvrRpg1A was identified with the GWAS using both barley lines and was delimited to a 35 kb interval on supercontig 2.30 containing four candidate genes (PGTG_10878, PGTG_10884, PGTG_10885, and PGTG_10886). The minor avirulence locus designated AvrRpg1B identified with cv Morex contained a single candidate gene (PGTG_05433). AvrRpg1A haplotype analysis provided strong evidence that a dominant avirulence gene underlies the locus. CONCLUSIONS The association analysis identified strong candidate AvrRpg1 genes. Further analysis to validate the AvrRpg1 genes will fill knowledge gaps in our understanding of rust effector biology and the evolution and mechanism/s of Pgt virulence on Rpg1.
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Affiliation(s)
- Arjun Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Sudha G C Upadhaya
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA
| | - Robert Brueggeman
- Department of Crop and Soil Sciences, Washington State University, Pullman, WA, 99164-6420, USA.
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14
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Uhdre R, Coyne CJ, Bourland B, Piaskowski J, Zheng P, Ganjyal GM, Zhang Z, McGee RJ, Main D, Bandillo N, Morales M, Ma Y, Chen C, Franck W, Thrash A, Warburton ML. Association study of crude seed protein and fat concentration in a USDA pea diversity panel. THE PLANT GENOME 2024:e20485. [PMID: 39086082 DOI: 10.1002/tpg2.20485] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/16/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 08/02/2024]
Abstract
Pea (Pisum sativum L.) is a key rotational crop and is increasingly important in the food processing sector for its protein. This study focused on identifying diverse high seed protein concentration (SPC) lines in pea plant genetic resources. Objectives included identifying high-protein pea lines, exploring genetic architecture across environments, pinpointing genes and metabolic pathways associated with high protein, and documenting information for single nucleotide polymorphism (SNP)-based marker-assisted selection. From 2019 to 2021, a 487-accession pea diversity panel, More protein, More pea, More profit, was evaluated in a randomized complete block design. DNA was extracted for genomic analysis via genotype-by-sequencing. Phenotypic analysis included protein and fat measurements in seeds and flower color. Genome-wide association study (GWAS) used multiple models, and the Pathways Association Study Tool was used for metabolic pathway analysis. Significant associations were found between SNPs and pea seed protein and fat concentration. Gene Psat7g216440 on chromosome 7, which targets proteins to cellular destinations, including seed storage proteins, was identified as associated with SPC. Genes Psat4g009200, Psat1g199800, Psat1g199960, and Psat1g033960, all involved in lipid metabolism, were associated with fat concentration. GWAS also identified genes annotated for storage proteins associated with fat concentration, indicating a complex relationship between fat and protein. Metabolic pathway analysis identified 20 pathways related to fat and seven to protein concentration, involving fatty acids, amino acid and protein metabolism, and the tricarboxylic acid cycle. These findings will assist in breeding of high-protein, diverse pea cultivars, and SNPs that can be converted to breeder-friendly molecular marker assays are identified for genes associated with high protein.
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Affiliation(s)
- Renan Uhdre
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Clarice J Coyne
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
- USDA ARS, Plant Germplasm Introduction and Testing Research, Pullman, Washington, USA
- Department of Horticulture, Washington State University, Pullman, Washington, USA
| | - Britton Bourland
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | | | - Ping Zheng
- Department of Horticulture, Washington State University, Pullman, Washington, USA
| | - Girish M Ganjyal
- School of Food Science, Washington State University, Pullman, Washington, USA
| | - Zhiwu Zhang
- Department of Crop and Soil Sciences, Washington State University, Pullman, Washington, USA
| | - Rebecca J McGee
- USDA ARS, Grain Legume Genetics and Physiology Research, Pullman, Washington, USA
| | - Dorrie Main
- Department of Horticulture, Washington State University, Pullman, Washington, USA
| | - Nonoy Bandillo
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Mario Morales
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Yu Ma
- Department of Horticulture and Crop Science, The Ohio State University, Columbus, Ohio, USA
| | - Chengci Chen
- Eastern Agriculture Research Center, Montana State University, Sidney, Montana, USA
| | - William Franck
- Eastern Agriculture Research Center, Montana State University, Sidney, Montana, USA
| | - Adam Thrash
- Institute for Genomics, Biocomputing & Biotechnology, Mississippi State University, Mississippi State, Mississippi, USA
| | - Marilyn L Warburton
- USDA ARS, Plant Germplasm Introduction and Testing Research, Pullman, Washington, USA
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15
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Liu D, Li X, Wang L, Pei Q, Zhao J, Sun D, Ren Q, Tian D, Han B, Jiang H, Zhang W, Wang S, Tian F, Liu S, Zhao K. Genome-wide association studies of body size traits in Tibetan sheep. BMC Genomics 2024; 25:739. [PMID: 39080522 PMCID: PMC11290296 DOI: 10.1186/s12864-024-10633-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/02/2024] [Accepted: 07/17/2024] [Indexed: 08/02/2024] Open
Abstract
BACKGROUND Elucidating the genetic variation underlying phenotypic diversity will facilitate improving production performance in livestock species. The Tibetan sheep breed in China holds significant historical importance, serving as a fundamental pillar of Qinghai's animal husbandry sector. The Plateau-type Tibetan sheep, comprising 90% of the province's population, are characterized by their tall stature and serve as the primary breed among Tibetan sheep. In contrast, Zhashijia sheep exhibit larger size and superior meat quality. These two species provide an excellent model for elucidating the genetic basis of body size variation. Therefore, this study aims to conduct a comprehensive genome-wide association study on these two Tibetan sheep breeds to identify single nucleotide polymorphism loci and regulatory genes that influence body size traits in Tibetan sheep. RESULT In this study, the phenotypic traits of body weight, body length, body height, chest circumference, chest depth, chest width, waist angle width, and pipe circumference were evaluated in two Tibetan sheep breeds: Plateau-type sheep and Zhashijia Tibetan sheep. Whole genome sequencing generated 48,215,130 high-quality SNPs for genome-wide association study. Four methods were applied and identified 623 SNPs significantly associated with body size traits. The significantly associated single nucleotide polymorphisms identified in this study are located near or within 111 candidate genes. These genes exhibit enrichment in the cAMP and Rap1 signaling pathways, significantly affecting animal growth, and body size. Specifically, the following genes were associated: ASAP1, CDK6, FRYL, NAV2, PTPRM, GPC6, PTPRG, KANK1, NTRK2 and ADCY8. CONCLUSION By genome-wide association study, we identified 16 SNPs and 10 candidate genes associated with body size traits in Tibetan sheep, which hold potential for application in genomic selection breeding programs in sheep. Identifying these candidate genes will establish a solid foundation for applying molecular marker-assisted selection in sheep breeding and improve our understanding of body size control in farmed animals.
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Affiliation(s)
- Dehui Liu
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
- Branch of Animal Husbandry and Veterinary of Heilongjiang Academy of Agricultural Sciences, Qiqihar, 161005, China
| | - Xue Li
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China
| | - Lei Wang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Quanbang Pei
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Jincai Zhao
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - De Sun
- Animal Husbandry and Veterinary Station of Huzhu County of Qinghai Province, Huzhu, Qinghai, 810500, China
| | - Qianben Ren
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Dehong Tian
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China
| | - Buying Han
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hanjing Jiang
- Qinghai Livestock and Poultry Genetic Resources Protection and Utilization Center, Xining, 810000, China
| | - Wenkui Zhang
- Qinghai Sheep Breeding and Promotion Service Center, Gangcha, Qinghai, 812300, China
| | - Song Wang
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Fei Tian
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China
| | - Sijia Liu
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China
| | - Kai Zhao
- Qinghai Provincial Key Laboratory of Animal Ecological Genomics, Key Laboratory of Adaptation and Evolution of Plateau Biota, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, No. 23 Xinning Road, Xining, Qinghai, 810001, China.
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Lhamo D, Sun Q, Friesen TL, Karmacharya A, Li X, Fiedler JD, Faris JD, Xia G, Luo M, Gu YQ, Liu Z, Xu SS. Association mapping of tan spot and septoria nodorum blotch resistance in cultivated emmer wheat. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:193. [PMID: 39073628 DOI: 10.1007/s00122-024-04700-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/10/2024] [Accepted: 07/21/2024] [Indexed: 07/30/2024]
Abstract
KEY MESSAGE A total of 65 SNPs associated with resistance to tan spot and septoria nodorum blotch were identified in a panel of 180 cultivated emmer accessions through association mapping Tan spot and septoria nodorum blotch (SNB) are foliar diseases caused by the respective fungal pathogens Pyrenophora tritici-repentis and Parastagonospora nodorum that affect global wheat production. To find new sources of resistance, we evaluated a panel of 180 cultivated emmer wheat (Triticum turgidum ssp. dicoccum) accessions for reactions to four P. tritici-repentis isolates Pti2, 86-124, 331-9 and DW5, two P. nodorum isolate, Sn4 and Sn2000, and four necrotrophic effectors (NEs) produced by the pathogens. About 8-36% of the accessions exhibited resistance to the four P. tritici-repentis isolates, with five accessions demonstrating resistance to all isolates. For SNB, 64% accessions showed resistance to Sn4, 43% to Sn2000 and 36% to both isolates, with Spain (11% accessions) as the most common origin of resistance. To understand the genetic basis of resistance, association mapping was performed using SNP (single nucleotide polymorphism) markers generated by genotype-by-sequencing and the 9 K SNP Infinium array. A total of 46 SNPs were significantly associated with tan spot and 19 SNPs with SNB resistance or susceptibility. Six trait loci on chromosome arms 1BL, 3BL, 4AL (2), 6BL and 7AL conferred resistance to two or more isolates. Known NE sensitivity genes for disease development were undetected except Snn5 for Sn2000, suggesting novel genetic factors are controlling host-pathogen interaction in cultivated emmer. The emmer accessions with the highest levels of resistance to the six pathogen isolates (e.g., CItr 14133-1, PI 94634-1 and PI 377672) could serve as donors for tan spot and SNB resistance in wheat breeding programs.
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Affiliation(s)
- Dhondup Lhamo
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA
| | - Qun Sun
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Timothy L Friesen
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Anil Karmacharya
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108, USA
| | - Jason D Fiedler
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Justin D Faris
- USDA-ARS, Cereal Crops Research Unit, Edward T. Schafer Agricultural Research Center, Fargo, ND, 58102, USA
| | - Guangmin Xia
- Key Laboratory of Plant Development and Environmental Adaptation Biology, School of Life Science, Shandong University, Qingdao, 266237, China
| | - Mingcheng Luo
- Department of Plant Sciences, University of California, Davis, CA, 95616, USA
| | - Yong-Qiang Gu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA
| | - Zhaohui Liu
- Department of Plant Pathology, North Dakota State University, Fargo, ND, 58108, USA.
| | - Steven S Xu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, CA, 94710, USA.
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17
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Rychel-Bielska S, Bielski W, Surma A, Annicchiarico P, Belter J, Kozak B, Galek R, Harzic N, Książkiewicz M. A GWAS study highlights significant associations between a series of indels in a FLOWERING LOCUS T gene promoter and flowering time in white lupin (Lupinus albus L.). BMC PLANT BIOLOGY 2024; 24:722. [PMID: 39075363 PMCID: PMC11285409 DOI: 10.1186/s12870-024-05438-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2023] [Accepted: 07/19/2024] [Indexed: 07/31/2024]
Abstract
BACKGROUND White lupin (Lupinus albus L.) is a high-protein Old World grain legume with remarkable food and feed production interest. It is sown in autumn or early spring, depending on the local agroclimatic conditions. This study aimed to identify allelic variants associated with vernalization responsiveness, in order to improve our knowledge of legume flowering regulatory pathways and develop molecular selection tools for the desired phenology as required for current breeding and adaptation to the changing climate. RESULTS Some 120 white lupin accessions originating from a wide range of environments of Europe, Africa, and Asia were phenotyped under field conditions in three environments with different intensities of vernalization, namely, a Mediterranean and a subcontinental climate sites of Italy under autumn sowing, and a suboceanic climate site of France under spring sowing. Two hundred sixty-two individual genotypes extracted from them were phenotyped in a greenhouse under long-day photoperiod without vernalization. Phenology data, and marker data generated by Diversity Arrays Technology sequencing (DArT-seq) and by PCR-based screening targeting published quantitative trait loci (QTLs) from linkage map and newly identified insertion/deletion polymorphisms in the promoter region of the FLOWERING LOCUS T homolog, LalbFTc1 gene (Lalb_Chr14g0364281), were subjected to a genome-wide association study (GWAS). Population structure followed differences in phenology and isolation by distance pattern. The GWAS highlighted numerous loci significantly associated with flowering time, including four LalbFTc1 gene promoter deletions: 2388 bp and 2126 bp deletions at the 5' end, a 264 bp deletion in the middle and a 28 bp deletion at the 3' end of the promoter. Besides LalbFTc1 deletions, this set contained DArT-seq markers that matched previously published major QTLs in chromosomes Lalb_Chr02, Lalb_Chr13 and Lalb_Chr16, and newly discovered QTLs in other chromosomes. CONCLUSIONS This study highlighted novel QTLs for flowering time and validated those already published, thereby providing novel evidence on the convergence of FTc1 gene functional evolution into the vernalization pathway in Old World lupin species. Moreover, this research provided the set of loci specific for extreme phenotypes (the earliest or the latest) awaiting further implementation in marker-assisted selection for spring- or winter sowing.
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Affiliation(s)
- Sandra Rychel-Bielska
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, Wrocław, 50-363, Poland
| | - Wojciech Bielski
- Department of Genetics and Plant Breeding, Poznań University of Life Sciences, Dojazd 11, Poznan, 60-632, Poland
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland
| | - Anna Surma
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland
| | - Paolo Annicchiarico
- Council for Agricultural Research and Economics, Research Centre for Animal Production and Aquaculture, Viale Piacenza 29, Lodi, 26900, Italy
| | - Jolanta Belter
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland
| | - Bartosz Kozak
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, Wrocław, 50-363, Poland
| | - Renata Galek
- Department of Genetics, Plant Breeding and Seed Production, Wroclaw University of Environmental and Life Sciences, Plac Grunwaldzki 24A, Wrocław, 50-363, Poland
| | - Nathalie Harzic
- Cérience, 1 Allée de la Sapinière, Saint Sauvant, 86600, France
| | - Michał Książkiewicz
- Department of Gene Structure and Function, Institute of Plant Genetics, Polish Academy of Sciences, Strzeszynska 34, Poznań, 60-479, Poland.
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18
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Lhamo D, Li G, Song G, Li X, Sen TZ, Gu YQ, Xu X, Xu SS. Genome-wide association studies on resistance to powdery mildew in cultivated emmer wheat. THE PLANT GENOME 2024:e20493. [PMID: 39073025 DOI: 10.1002/tpg2.20493] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/09/2024] [Revised: 05/01/2024] [Accepted: 06/30/2024] [Indexed: 07/30/2024]
Abstract
Powdery mildew, caused by the fungal pathogen Blumeria graminis (DC.) E. O. Speer f. sp. tritici Em. Marchal (Bgt), is a constant threat to global wheat (Triticum aestivum L.) production. Although ∼100 powdery mildew (Pm) resistance genes and alleles have been identified in wheat and its relatives, more is needed to minimize Bgt's fast evolving virulence. In tetraploid wheat (Triticum turgidum L.), wild emmer wheat [T. turgidum ssp. dicoccoides (Körn. ex Asch. & Graebn.) Thell.] accessions from Israel have contributed many Pm resistance genes. However, the diverse genetic reservoirs of cultivated emmer wheat [T. turgidum ssp. dicoccum (Schrank ex Schübl.) Thell.] have not been fully exploited. In the present study, we evaluated a diverse panel of 174 cultivated emmer accessions for their reaction to Bgt isolate OKS(14)-B-3-1 and found that 66% of accessions, particularly those of Ethiopian (30.5%) and Indian (6.3%) origins, exhibited high resistance. To determine the genetic basis of Bgt resistance in the panel, genome-wide association studies were performed using 46,383 single nucleotide polymorphisms (SNPs) from genotype-by-sequencing and 4331 SNPs from the 9K SNP Infinium array. Twenty-five significant SNP markers were identified to be associated with Bgt resistance, of which 21 SNPs are likely novel loci, whereas four possibly represent emmer derived Pm4a, Pm5a, PmG16, and Pm64. Most novel loci exhibited minor effects, whereas three novel loci on chromosome arms 2AS, 3BS, and 5AL had major effect on the phenotypic variance. This study demonstrates cultivated emmer as a rich source of powdery mildew resistance, and the resistant accessions and novel loci found herein can be utilized in wheat breeding programs to enhance Bgt resistance in wheat.
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Affiliation(s)
- Dhondup Lhamo
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Genqiao Li
- USDA-ARS Peanut and Small Grains Research Unit, Stillwater, Oklahoma, USA
| | - George Song
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Xuehui Li
- Department of Plant Sciences, North Dakota State University, Fargo, North Dakota, USA
| | - Taner Z Sen
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Yong-Qiang Gu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
| | - Xiangyang Xu
- USDA-ARS Peanut and Small Grains Research Unit, Stillwater, Oklahoma, USA
| | - Steven S Xu
- USDA-ARS, Crop Improvement and Genetics Research Unit, Western Regional Research Center, Albany, California, USA
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19
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Sullivan KA, Miller JI, Townsend A, Morgan M, Lane M, Pavicic M, Shah M, Cashman M, Jacobson DA. MENTOR: Multiplex Embedding of Networks for Team-Based Omics Research. BIORXIV : THE PREPRINT SERVER FOR BIOLOGY 2024:2024.07.17.603821. [PMID: 39091782 PMCID: PMC11291001 DOI: 10.1101/2024.07.17.603821] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 08/04/2024]
Abstract
While the proliferation of data-driven omics technologies has continued to accelerate, methods of identifying relationships among large-scale changes from omics experiments have stagnated. It is therefore imperative to develop methods that can identify key mechanisms among one or more omics experiments in order to advance biological discovery. To solve this problem, here we describe the network-based algorithm MENTOR - Multiplex Embedding of Networks for Team-Based Omics Research. We demonstrate MENTOR's utility as a supervised learning approach to successfully partition a gene set containing multiple ontological functions into their respective functions. Subsequently, we used MENTOR as an unsupervised learning approach to identify important biological functions pertaining to the host genetic architectures in Populus trichocarpa associated with microbial abundance of multiple taxa. Moreover, as open source software designed with scientific teams in mind, we demonstrate the ability to use the output of MENTOR to facilitate distributed interpretation of omics experiments.
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20
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Osuna-Caballero S, Cobos MJ, Ruiz CM, Wohor OZ, Rispail N, Rubiales D. Genome-Wide Association Studies on Resistance to Pea Weevil: Identification of Novel Sources of Resistance and Associated Markers. Int J Mol Sci 2024; 25:7920. [PMID: 39063162 PMCID: PMC11276686 DOI: 10.3390/ijms25147920] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/24/2024] [Revised: 07/16/2024] [Accepted: 07/17/2024] [Indexed: 07/28/2024] Open
Abstract
Little resistance to the pea weevil insect pest (Bruchus pisorum) is available in pea (Pisum sativum) cultivars, highlighting the need to search for sources of resistance in Pisum germplasm and to decipher the genetic basis of resistance. To address this need, we screened the response to pea weevil in a Pisum germplasm collection (324 accession, previously genotyped) under field conditions over four environments. Significant variation for weevil seed infestation (SI) was identified, with resistance being frequent in P. fulvum, followed by P. sativum ssp. elatius, P. abyssinicum, and P. sativum ssp. humile. SI tended to be higher in accessions with lighter seed color. SI was also affected by environmental factors, being favored by high humidity during flowering and hampered by warm winter temperatures and high evapotranspiration during and after flowering. Merging the phenotypic and genotypic data allowed genome-wide association studies (GWAS) yielding 73 markers significantly associated with SI. Through the GWAS models, 23 candidate genes were found associated with weevil resistance, highlighting the interest of five genes located on chromosome 6. These included gene 127136761 encoding squalene epoxidase; gene 127091639 encoding a transcription factor MYB SRM1; gene 127097033 encoding a 60S ribosomal protein L14; gene 127092211, encoding a BolA-like family protein, which, interestingly, was located within QTL BpLD.I, earlier described as conferring resistance to weevil in pea; and gene 127096593 encoding a methyltransferase. These associated genes offer valuable potential for developing pea varieties resistant to Bruchus spp. and efficient utilization of genomic resources through marker-assisted selection (MAS).
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Affiliation(s)
- Salvador Osuna-Caballero
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
| | | | | | | | | | - Diego Rubiales
- Institute for Sustainable Agriculture, Spanish National Research Council (CSIC), Av. Menéndez Pidal s/n, 14004 Córdoba, Spain
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21
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Mazumder AK, Yadav R, Kumar M, Babu P, Kumar N, Singh SK, Solanke AU, Wani SH, Alalawy AI, Alasmari A, Gaikwad KB. Discovering novel genomic regions explaining adaptation of bread wheat to conservation agriculture through GWAS. Sci Rep 2024; 14:16351. [PMID: 39013994 PMCID: PMC11252282 DOI: 10.1038/s41598-024-66903-3] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 07/05/2024] [Indexed: 07/18/2024] Open
Abstract
To sustainably increase wheat yield to meet the growing world population's food demand in the face of climate change, Conservation Agriculture (CA) is a promising approach. Still, there is a lack of genomic studies investigating the genetic basis of crop adaptation to CA. To dissect the genetic architecture of 19 morpho-physiological traits that could be involved in the enhanced adaptation and performance of genotypes under CA, we performed GWAS to identify MTAs under four contrasting production regimes viz., conventional tillage timely sown (CTTS), conservation agriculture timely sown (CATS), conventional tillage late sown (CTLS) and conservation agriculture late sown (CALS) using an association panel of 183 advanced wheat breeding lines along with 5 checks. Traits like Phi2 (Quantum yield of photosystem II; CATS:0.37, CALS: 0.31), RC (Relative chlorophyll content; CATS:55.51, CALS: 54.47) and PS1 (Active photosystem I centers; CATS:2.45, CALS: 2.23) have higher mean values in CA compared to CT under both sowing times. GWAS identified 80 MTAs for the studied traits across four production environments. The phenotypic variation explained (PVE) by these QTNs ranged from 2.15 to 40.22%. Gene annotation provided highly informative SNPs associated with Phi2, NPQ (Quantum yield of non-photochemical quenching), PS1, and RC which were linked with genes that play crucial roles in the physiological adaptation under both CA and CT. A highly significant SNP AX94651261 (9.43% PVE) was identified to be associated with Phi2, while two SNP markers AX94730536 (30.90% PVE) and AX94683305 (16.99% PVE) were associated with NPQ. Identified QTNs upon validation can be used in marker-assisted breeding programs to develop CA adaptive genotypes.
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Affiliation(s)
- Amit Kumar Mazumder
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Rajbir Yadav
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Manjeet Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Prashanth Babu
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Naresh Kumar
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | - Sanjay Kumar Singh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India
| | | | - Shabir H Wani
- Mountain Research Centre for Field Crops, Khudwani, 192101, India
- Sher-E-Kashmir University of Agricultural Sciences and Technology-Kashmir (SKUAST-K), Srinagar, Jammu-Kashmir, India
| | - Adel I Alalawy
- Department of Biochemistry, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Abdulrahman Alasmari
- Department of Biology, Faculty of Science, University of Tabuk, Tabuk, Saudi Arabia
| | - Kiran B Gaikwad
- Division of Genetics, ICAR-Indian Agricultural Research Institute, New Delhi, 110012, India.
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22
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Wu C, Acuña A, Florez-Palacios L, Harrison D, Rogers D, Mozzoni L, Mian R, Canella Vieira C. Across-environment seed protein stability and genetic architecture of seed components in soybean. Sci Rep 2024; 14:16452. [PMID: 39013958 PMCID: PMC11252131 DOI: 10.1038/s41598-024-67035-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2023] [Accepted: 07/08/2024] [Indexed: 07/18/2024] Open
Abstract
The recent surge in the plant-based protein market has resulted in high demands for soybean genotypes with improved grain yield, seed protein and oil content, and essential amino acids (EAAs). Given the quantitative nature of these traits, complex interactions among seed components, as well as between seed components and environmental factors and management practices, add complexity to the development of desired genotypes. In this study, the across-environment seed protein stability of 449 genetically diverse plant introductions was assessed, revealing that genotypes may display varying sensitivities to such environmental stimuli. The EAAs valine, phenylalanine, and threonine showed the highest variable importance toward the variation in stability, while both seed protein and oil contents were among the explanatory variables with the lowest importance. In addition, 56 single nucleotide polymorphism (SNP) markers were significantly associated with various seed components. Despite the strong phenotypic Pearson's correlation observed among most seed components, many independent genomic regions associated with one or few seed components were identified. These findings provide insights for improving the seed concentration of specific EAAs and reducing the negative correlation between seed protein and oil contents.
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Affiliation(s)
- Chengjun Wu
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Andrea Acuña
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Liliana Florez-Palacios
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Derrick Harrison
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Daniel Rogers
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Leandro Mozzoni
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Rouf Mian
- Soybean and Nitrogen Fixation Research Unit, USDA-Agricultural Research Service, Raleigh, NC, 27607, USA
| | - Caio Canella Vieira
- Department of Crop, Soil, and Environmental Sciences, University of Arkansas, Fayetteville, AR, 72701, USA.
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23
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Li Y, Lin P, You Q, Huang J, Yao W, Wang J, Zhang M. Identification of candidate single-nucleotide polymorphisms (SNPs) and genes associated with sugarcane leaf scald disease. Sci Rep 2024; 14:16214. [PMID: 39003420 PMCID: PMC11246479 DOI: 10.1038/s41598-024-67059-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/17/2024] [Accepted: 07/08/2024] [Indexed: 07/15/2024] Open
Abstract
Leaf scald, caused by Xanthomonas albilineans, is a severe disease affecting sugarcane worldwide. One of the most practical ways to control it is by developing resistant sugarcane cultivars. It is essential to identify genes associated with the response to leaf scald. A panel of 170 sugarcane genotypes was evaluated for resistance to leaf scald in field conditions for 2 years, followed by a 1-year greenhouse experiment. The phenotypic evaluation data showed a wide continuous distribution, with heritability values ranging from 0.58 to 0.84. Thirteen single nucleotide polymorphisms (SNPs) were identified, significantly associated with leaf scald resistance. Among these, eight were stable across multiple environments and association models. The candidate genes identified and validated based on RNA-seq and qRT-PCR included two genes that encode NB-ARC leucine-rich repeat (LRR)-containing domain disease-resistance protein. These findings provide a basis for developing marker-assisted selection strategies in sugarcane breeding programs.
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Affiliation(s)
- Yisha Li
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Pingping Lin
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Qian You
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Jiangfeng Huang
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Wei Yao
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China
| | - Jianping Wang
- Agronomy Department, IFAS, University of Florida, Gainesville, FL, 32611, USA
| | - Muqing Zhang
- Guangxi Key Laboratory for Sugarcane Biology, College of Agriculture, Guangxi University, Nanning, 530005, China.
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24
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Chen Y, Liu Z, Han D, Yang Q, Li C, Shi X, Zhang M, Yang C, Qiu L, Jia H, Wang S, Lu W, Ma Q, Yan L. Cold tolerance SNPs and candidate gene mining in the soybean germination stage based on genome-wide association analysis. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:178. [PMID: 38976061 DOI: 10.1007/s00122-024-04685-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/05/2024] [Accepted: 06/25/2024] [Indexed: 07/09/2024]
Abstract
KEY MESSAGE Three QTLs associated with low-temperature tolerance were identified by genome-wide association analysis, and 15 candidate genes were identified by haplotype analysis and gene expression analyses. Low temperature is a critical factor affecting the geographical distribution, growth, development, and yield of soybeans, with cold stress during seed germination leading to substantial productivity loss. In this study, an association panel comprising 260 soybean accessions was evaluated for four germination traits and four cold tolerance index traits, revealing extensive variation in cold tolerance. Genome-wide association study (GWAS) identified 10 quantitative trait nucleotides (QTNs) associated with cold tolerance, utilizing 30,799 single nucleotide polymorphisms (SNPs) and four GWAS models. Linkage disequilibrium (LD) analysis positioned these QTNs within three cold-tolerance quantitative trait loci (QTL) and, with QTL19-1, was positioned by three multi-locus models, underscoring its importance as a key QTL. Integrative haplotype analysis, supplemented by transcriptome analysis, uncovered 15 candidate genes. The haplotypes within the genes Glyma.18G044200, Glyma.18G044300, Glyma.18G044900, Glyma.18G045100, Glyma.19G222500, and Glyma.19G222600 exhibited significant phenotypic variations, with differential expression in materials with varying cold tolerance. The QTNs and candidate genes identified in this study offer substantial potential for marker-assisted selection and gene editing in breeding cold-tolerant soybeans, providing valuable insights into the genetic mechanisms underlying cold tolerance during soybean germination.
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Affiliation(s)
- Yuehan Chen
- College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Zhi Liu
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Dezhi Han
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Qing Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Chenhui Li
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Xiaolei Shi
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Mengchen Zhang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Chunyan Yang
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Lijuan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Germplasm and Biotechnology (MARA), Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100081, China
| | - Hongchang Jia
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Shu Wang
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China
| | - Wencheng Lu
- Heihe Branch of Heilongjiang Academy of Agricultural Sciences, Heihe, 164300, China.
| | - Qian Ma
- College of Life Science, Qingdao Agricultural University, Qingdao, 266109, China.
| | - Long Yan
- Hebei Laboratory of Crop Genetics and Breeding, National Soybean Improvement Center Shijiazhuang Sub-center, Hebei-Huai-Hai Key Laboratory of Biology and Genetic Improvement of Soybean, Ministry of Agriculture and Rural Affairs, Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China.
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25
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Yalcin HA, Jacott CN, Ramirez-Gonzalez RH, Steuernagel B, Sidhu GS, Kirby R, Verbeek E, Schoonbeek HJ, Ridout CJ, Wells R. A complex receptor locus confers responsiveness to necrosis and ethylene-inducing like peptides in Brassica napus. THE PLANT JOURNAL : FOR CELL AND MOLECULAR BIOLOGY 2024; 119:266-282. [PMID: 38605581 DOI: 10.1111/tpj.16760] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/17/2023] [Revised: 03/02/2024] [Accepted: 03/27/2024] [Indexed: 04/13/2024]
Abstract
Brassica crops are susceptible to diseases which can be mitigated by breeding for resistance. MAMPs (microbe-associated molecular patterns) are conserved molecules of pathogens that elicit host defences known as pattern-triggered immunity (PTI). Necrosis and Ethylene-inducing peptide 1-like proteins (NLPs) are MAMPs found in a wide range of phytopathogens. We studied the response to BcNEP2, a representative NLP from Botrytis cinerea, and showed that it contributes to disease resistance in Brassica napus. To map regions conferring NLP response, we used the production of reactive oxygen species (ROS) induced during PTI across a population of diverse B. napus accessions for associative transcriptomics (AT), and bulk segregant analysis (BSA) on DNA pools created from a cross of NLP-responsive and non-responsive lines. In silico mapping with AT identified two peaks for NLP responsiveness on chromosomes A04 and C05 whereas the BSA identified one peak on A04. BSA delimited the region for NLP-responsiveness to 3 Mbp, containing ~245 genes on the Darmor-bzh reference genome and four co-segregating KASP markers were identified. The same pipeline with the ZS11 genome confirmed the highest-associated region on chromosome A04. Comparative BLAST analysis revealed unannotated clusters of receptor-like protein (RLP) homologues on ZS11 chromosome A04. However, no specific RLP homologue conferring NLP response could be identified. Our results also suggest that BR-SIGNALLING KINASE1 may be involved with modulating the NLP response. Overall, we demonstrate that responsiveness to NLP contributes to disease resistance in B. napus and define the associated genomic location. These results can have practical application in crop improvement.
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Affiliation(s)
- Hicret Asli Yalcin
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- TUBITAK Marmara Research Centre, Life Sciences, TUBITAK, Gebze, Kocaeli, 41470, Türkiye
| | - Catherine N Jacott
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- Department of Microbiology, Faculty of Biology, University of Seville, Seville, Spain
| | | | | | | | - Rachel Kirby
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Emma Verbeek
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
| | - Henk-Jan Schoonbeek
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
- University of East Anglia, Norwich Research Park, Norwich, NR4 7TJ, UK
| | | | - Rachel Wells
- John Innes Centre, Norwich Research Park, Colney Lane, Norwich, NR4 7UH, UK
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26
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Prohaska A, Rey-Serra P, Petit J, Petit A, Perrotte J, Rothan C, Denoyes B. Exploration of a European-centered strawberry diversity panel provides markers and candidate genes for the control of fruit quality traits. HORTICULTURE RESEARCH 2024; 11:uhae137. [PMID: 38988619 PMCID: PMC11233882 DOI: 10.1093/hr/uhae137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/04/2024] [Accepted: 05/05/2024] [Indexed: 07/12/2024]
Abstract
Fruit quality traits are major breeding targets in cultivated strawberry (Fragaria × ananassa). Taking into account the requirements of both growers and consumers when selecting high-quality cultivars is a real challenge. Here, we used a diversity panel enriched with unique European accessions and the 50 K FanaSNP array to highlight the evolution of strawberry diversity over the past 160 years, investigate the molecular basis of 12 major fruit quality traits by genome-wide association studies (GWAS), and provide genetic markers for breeding. Results show that considerable improvements of key breeding targets including fruit weight, firmness, composition, and appearance occurred simultaneously in European and American cultivars. Despite the high genetic diversity of our panel, we observed a drop in nucleotide diversity in certain chromosomal regions, revealing the impact of selection. GWAS identified 71 associations with 11 quality traits and, while validating known associations (firmness, sugar), highlighted the predominance of new quantitative trait locus (QTL), demonstrating the value of using untapped genetic resources. Three of the six selective sweeps detected are related to glossiness or skin resistance, two little-studied traits important for fruit attractiveness and, potentially, postharvest shelf life. Moreover, major QTL for firmness, glossiness, skin resistance, and susceptibility to bruising are found within a low diversity region of chromosome 3D. Stringent search for candidate genes underlying QTL uncovered strong candidates for fruit color, firmness, sugar and acid composition, glossiness, and skin resistance. Overall, our study provides a potential avenue for extending shelf life without compromising flavor and color as well as the genetic markers needed to achieve this goal.
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Affiliation(s)
- Alexandre Prohaska
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | - Pol Rey-Serra
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
| | - Johann Petit
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
| | - Aurélie Petit
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | - Justine Perrotte
- Invenio, MIN de Brienne, 110 Quai de Paludate, 33000 Bordeaux, France
| | | | - Béatrice Denoyes
- Univ. Bordeaux, INRAE, UMR BFP, F-33140 Villenave d'Ornon, France
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27
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Arrones A, Antar O, Pereira-Dias L, Solana A, Ferrante P, Aprea G, Plazas M, Prohens J, Díez MJ, Giuliano G, Gramazio P, Vilanova S. A novel tomato interspecific ( Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm. HORTICULTURE RESEARCH 2024; 11:uhae154. [PMID: 39005998 PMCID: PMC11246243 DOI: 10.1093/hr/uhae154] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/29/2024] [Accepted: 05/23/2024] [Indexed: 07/16/2024]
Abstract
We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of Solanum lycopersicum var. cerasiforme and Solanum pimpinellifolium, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.
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Affiliation(s)
- Andrea Arrones
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Oussama Antar
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Leandro Pereira-Dias
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Andrea Solana
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Paola Ferrante
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Giuseppe Aprea
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Mariola Plazas
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Jaime Prohens
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - María José Díez
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Giovanni Giuliano
- Agenzia Nazionale Per Le Nuove Tecnologie, L’energia e Lo Sviluppo Economico Sostenibile (ENEA), Casaccia Research Centre, Via Anguillarese 301, 00123 Rome, Italy
| | - Pietro Gramazio
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
| | - Santiago Vilanova
- Instituto de Conservación y Mejora de la Agrodiversidad Valenciana, Universitat Politècnica de València, Camino de Vera 14, 46022 Valencia, Spain
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28
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Rehman AU, Iso-Touru T, Junkers J, Rantanen M, Karhu S, Fischer D, Alsheikh M, Hjeltnes SH, Mezzetti B, Davik J, Schulman AH, Hytönen T, Haikonen T. Multi-model GWAS reveals key loci for horticultural traits in reconstructed garden strawberry. PHYSIOLOGIA PLANTARUM 2024; 176:e14440. [PMID: 39030778 DOI: 10.1111/ppl.14440] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 06/08/2024] [Accepted: 06/10/2024] [Indexed: 07/22/2024]
Abstract
The cultivated garden strawberry (Fragaria × ananassa) has a rich history, originating from the hybridization of two wild octoploid strawberry species in the 18th century. Two-step reconstruction of Fragaria × ananassa through controlled crossings between pre-improved selections of its parental species is a promising approach for enriching the breeding germplasm of strawberry for wider adaptability. We created a population of reconstructed strawberry by hybridizing elite selections of F. virginiana and F. chiloensis. A replicated field experiment was conducted to evaluate the population's performance for eleven horticulturally important traits, over multiple years. Population structure analyses based on Fana-50 k SNP array data confirmed pedigree-based grouping of the progenies into four distinct groups. As complex traits are often influenced by environmental variables, and population structure can lead to spurious associations, we tested multiple genome-wide association study (GWAS) models. GWAS uncovered 39 quantitative trait loci (QTL) regions for eight traits distributed across twenty chromosomes, including 11 consistent and 28 putative QTLs. Candidate genes for traits including winter survival, flowering time, runnering vigor, and hermaphrodism were identified within the QTL regions. To our knowledge, this study marks the first comprehensive investigation of adaptive and horticultural traits in a large, multi-familial reconstructed strawberry population using SNP markers.
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Affiliation(s)
- Attiq Ur Rehman
- Natural Resources Institute Finland (Luke), Finland
- Doctoral Program in Plant Sciences, University of Helsinki, Finland
| | | | - Jakob Junkers
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | | | - Saila Karhu
- Natural Resources Institute Finland (Luke), Finland
| | | | - Muath Alsheikh
- Graminor AS, Norway
- Faculty of Life Sciences, Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | | | - Bruno Mezzetti
- Department of Agriculture, Food and Environmental Sciences, Università Politecnica delle Marche, Ancona, Italy
| | - Jahn Davik
- Norwegian Institute of Bioeconomy Research, Ås, Norway
| | - Alan H Schulman
- Natural Resources Institute Finland (Luke), Finland
- Viikki Plant Science Centre, Finland
- Institute of Biotechnology, University of Helsinki, Finland
| | - Timo Hytönen
- Viikki Plant Science Centre, Finland
- Department of Agricultural Sciences, University of Helsinki, Finland
| | - Tuuli Haikonen
- Natural Resources Institute Finland (Luke), Finland
- Viikki Plant Science Centre, Finland
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29
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Qiao J, Li K, Miao N, Xu F, Han P, Dai X, Abdelkarim OF, Zhu M, Zhao Y. Additive and Dominance Genome-Wide Association Studies Reveal the Genetic Basis of Heterosis Related to Growth Traits of Duhua Hybrid Pigs. Animals (Basel) 2024; 14:1944. [PMID: 38998055 PMCID: PMC11240614 DOI: 10.3390/ani14131944] [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: 06/03/2024] [Revised: 06/26/2024] [Accepted: 06/28/2024] [Indexed: 07/14/2024] Open
Abstract
Heterosis has been extensively used for pig genetic breeding and production, but the genetic basis of heterosis remains largely elusive. Crossbreeding between commercial and native breeds provides a good model to parse the genetic basis of heterosis. This study uses Duhua hybrid pigs, a crossbreed of Duroc and Liangguang small spotted pigs, as materials to explore the genetic basis underlying heterosis related to growth traits at the genomic level. The mid-parent heterosis (MPH) analysis showed heterosis of this Duhua offspring on growth traits. In this study, we examined the impact of additive and dominance effects on 100 AGE (age adjusted to 100 kg) and 100 BF (backfat thickness adjusted to 100 kg) of Duhua hybrid pigs. Meanwhile, we successfully identified SNPs associated with growth traits through both additive and dominance GWASs (genome-wide association studies). These findings will facilitate the subsequent in-depth studies of heterosis in the growth traits of Duhua pigs.
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Affiliation(s)
- Jiakun Qiao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Kebiao Li
- School of Life Science and Engineering, Foshan University, Foshan 528000, China
| | - Na Miao
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangjun Xu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingping Han
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangyu Dai
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Omnia Fathy Abdelkarim
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
| | - Mengjin Zhu
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education, Huazhong Agricultural University, Wuhan 430070, China
- The Cooperative Innovation Center for Sustainable Pig Production, Huazhong Agricultural University, Wuhan 430070, China
| | - Yunxiang Zhao
- College of Animal Science and Technology, Guangxi University, Nanning 530004, China
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30
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Li D, Wang Q, Tian Y, Lyv X, Zhang H, Hong H, Gao H, Li YF, Zhao C, Wang J, Wang R, Yang J, Liu B, Schnable PS, Schnable JC, Li YH, Qiu LJ. TWAS facilitates gene-scale trait genetic dissection through gene expression, structural variations, and alternative splicing in soybean. PLANT COMMUNICATIONS 2024:101010. [PMID: 38918950 DOI: 10.1016/j.xplc.2024.101010] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/13/2023] [Revised: 05/15/2024] [Accepted: 06/23/2024] [Indexed: 06/27/2024]
Abstract
A genome-wide association study (GWAS) identifies trait-associated loci, but identifying the causal genes can be a bottleneck, due in part to slow decay of linkage disequilibrium (LD). A transcriptome-wide association study (TWAS) addresses this issue by identifying gene expression-phenotype associations or integrating gene expression quantitative trait loci with GWAS results. Here, we used self-pollinated soybean (Glycine max [L.] Merr.) as a model to evaluate the application of TWAS to the genetic dissection of traits in plant species with slow LD decay. We generated RNA sequencing data for a soybean diversity panel and identified the genetic expression regulation of 29 286 soybean genes. Different TWAS solutions were less affected by LD and were robust to the source of expression, identifing known genes related to traits from different tissues and developmental stages. The novel pod-color gene L2 was identified via TWAS and functionally validated by genome editing. By introducing a new exon proportion feature, we significantly improved the detection of expression variations that resulted from structural variations and alternative splicing. As a result, the genes identified through our TWAS approach exhibited a diverse range of causal variations, including SNPs, insertions or deletions, gene fusion, copy number variations, and alternative splicing. Using this approach, we identified genes associated with flowering time, including both previously known genes and novel genes that had not previously been linked to this trait, providing insights complementary to those from GWAS. In summary, this study supports the application of TWAS for candidate gene identification in species with low rates of LD decay.
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Affiliation(s)
- Delin Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Qi Wang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; College of Agriculture, Northeast Agricultural University, Harbin 150030, China
| | - Yu Tian
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Xiangguang Lyv
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Hao Zhang
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huilong Hong
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Huawei Gao
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China; National Nanfan Research Institute (Sanya), Chinese Academy of Agricultural Sciences, Sanya 572024, China
| | - Yan-Fei Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | - Chaosen Zhao
- Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jiajun Wang
- Soybean Research Institute, Heilongjiang Academy of Agricultural Sciences, Harbin 150086, China
| | - Ruizhen Wang
- Crops Research Institute of Jiangxi Academy of Agricultural Sciences, Nanchang 330200, China
| | - Jinliang Yang
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Bin Liu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China
| | | | - James C Schnable
- Department of Agronomy and Horticulture, University of Nebraska-Lincoln, Lincoln, NE 68583, USA.
| | - Ying-Hui Li
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
| | - Li-Juan Qiu
- The National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI)/Key Laboratory of Crop Gene Resource and Germplasm Enhancement (MOA)/State Key Laboratory of Crop Gene Resources and Breeding, Institute of Crop Science, Chinese Academy of Agricultural Sciences, Beijing 100081, China.
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31
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Aleliūnas A, Gorash A, Armonienė R, Tamm I, Ingver A, Bleidere M, Fetere V, Kollist H, Mroz T, Lillemo M, Brazauskas G. Genome-wide association study reveals 18 QTL for major agronomic traits in a Nordic-Baltic spring wheat germplasm. FRONTIERS IN PLANT SCIENCE 2024; 15:1393170. [PMID: 38974985 PMCID: PMC11224466 DOI: 10.3389/fpls.2024.1393170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 02/28/2024] [Accepted: 05/20/2024] [Indexed: 07/09/2024]
Abstract
Spring wheat (Triticum aestivum L.) remains an important alternative to winter wheat cultivation at Northern latitudes due to high risk of overwintering or delayed sowing of winter wheat. We studied nine major agronomic traits in a set of 299 spring wheat genotypes in trials across 12-year-site combinations in Lithuania, Latvia, Estonia, and Norway for three consecutive years. The dataset analyzed here consisted of previously published phenotypic data collected in 2021 and 2022, supplemented with additional phenotypic data from the 2023 field season collected in this study. We combined these phenotypic datasets with previously published genotypic data generated using a 25K single nucleotide polymorphism (SNP) array that yielded 18,467 markers with a minor allele frequency above 0.05. Analysis of these datasets via genome-wide association study revealed 18 consistent quantitative trait loci (QTL) replicated in two or more trials that explained more than 5% of phenotypic variance for plant height, grain protein content, thousand kernel weight, or heading date. The most consistent markers across the tested environments were detected for plant height, thousand kernel weight, and days to heading in eight, five, and six trials, respectively. No beneficial effect of the semi-dwarfing alleles Rht-B1b and Rht-D1b on grain yield performance was observed across the 12 tested trials. Moreover, the cultivars carrying these alleles were low yielding in general. Based on principal component analysis, wheat genotypes developed in the Northern European region clustered separately from those developed at the southern latitudes, and markers associated with the clustering were identified. Important phenotypic traits, such as grain yield, days to heading, grain protein content, and thousand kernel weight were associated with this clustering of the genotype sets. Interestingly, despite being adapted to the Nordic environment, genotypes in the Northern set demonstrated lower grain yield performance across all tested environments. The results indicate that spring wheat germplasm harbors valuable QTL/alleles, and the identified trait-marker associations might be useful in improving Nordic-Baltic spring wheat germplasm under global warming conditions.
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Affiliation(s)
- Andrius Aleliūnas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Andrii Gorash
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Rita Armonienė
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
| | - Ilmar Tamm
- Centre of Estonian Rural Research and Knowledge, Jõgeva Alevik, Estonia
| | - Anne Ingver
- Centre of Estonian Rural Research and Knowledge, Jõgeva Alevik, Estonia
| | - Māra Bleidere
- Crop Research Department, Institute of Agricultural Resources and Economics, Stende Research Centre, Dižstende, Latvia
| | - Valentīna Fetere
- Crop Research Department, Institute of Agricultural Resources and Economics, Stende Research Centre, Dižstende, Latvia
| | - Hannes Kollist
- Institute of Bioengineering, University of Tartu, Tartu, Estonia
| | - Tomasz Mroz
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Morten Lillemo
- Department of Plant Sciences, Norwegian University of Life Sciences, Ås, Norway
| | - Gintaras Brazauskas
- Institute of Agriculture, Lithuanian Research Centre for Agriculture and Forestry, Akademija, Lithuania
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32
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Schwertfirm G, Schneider M, Haase F, Riedel C, Lazzaro M, Ruge-Wehling B, Schweizer G. Genome-wide association study revealed significant SNPs for anthracnose resistance, seed alkaloids and protein content in white lupin. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:155. [PMID: 38858311 PMCID: PMC11164739 DOI: 10.1007/s00122-024-04665-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/10/2024] [Accepted: 05/28/2024] [Indexed: 06/12/2024]
Abstract
White lupin (Lupinus albus L.) is a high-protein grain legume alternative to soybean in Central Europe, but its cultivation is risky due to the fungal disease anthracnose that can cause severe yield damage. In addition, management of seed alkaloids is critical for human nutrition and animal feed. We report on a white lupin collection of genebank accessions, advanced breeding lines and cultivars that was genotyped and phenotypically characterized for anthracnose resistance and seed alkaloids and protein levels. Using genotyping by sequencing (GBS), SeqSNP-targeted GBS, BiomarkX genotyping and Sanger sequencing, a genetic resource of genome-wide SNPs for white lupin was established. We determined anthracnose resistance in two years field trials at four locations with infection rows and measured seed alkaloids and protein levels by near-infrared spectroscopy (NIRS). Few white lupin breeding lines showed anthracnose resistance comparable or better than Celina and Frieda, currently the best commercial cultivars in Germany. NIRS estimates for seed alkaloids and protein levels revealed variation in the white lupin collection. Using genome-wide association studies (GWAS), we identified SNPs significantly associated with anthracnose resistance in the field representing known and new genomic regions. We confirmed the pauper locus and detected new SNP markers significantly associated with seed alkaloids. For the first time, we present loci associated with total grain protein content. Finally, we tested the potential of genomic prediction (GP) in predicting the phenotype of these three quantitative traits. Application of results and resources are discussed in the context of fostering breeding programs for white lupin.
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Affiliation(s)
- Grit Schwertfirm
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany.
| | - Michael Schneider
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, Box 219, 5070, Frick, Switzerland
| | - Florian Haase
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research On Agricultural Crops, Julius Kuehn-Institute (JKI), Rudolf Schick Platz 3a, 18190, Groß Lüsewitz, Germany
| | - Christine Riedel
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Kleeberg 14, 94099, Ruhstorf a. d. Rott, Germany
| | - Mariateresa Lazzaro
- Department of Crop Sciences, Research Institute of Organic Agriculture (FiBL), Ackerstrasse 113, Box 219, 5070, Frick, Switzerland
| | - Brigitte Ruge-Wehling
- Federal Research Centre for Cultivated Plants, Institute for Breeding Research On Agricultural Crops, Julius Kuehn-Institute (JKI), Rudolf Schick Platz 3a, 18190, Groß Lüsewitz, Germany
| | - Guenther Schweizer
- Bavarian State Research Center for Agriculture (LfL), Institute for Crop Science and Plant Breeding, Am Gereuth 2, 85354, Freising, Germany
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Katuuramu DN, Levi A, Wechter WP. Mapping the genetic architecture of low-temperature stress tolerance in citron watermelon. THE PLANT GENOME 2024; 17:e20443. [PMID: 38462711 DOI: 10.1002/tpg2.20443] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/10/2023] [Revised: 12/02/2023] [Accepted: 02/07/2024] [Indexed: 03/12/2024]
Abstract
Sweet-fleshed watermelon (Citrullus lanatus) is an important vegetable crop of the tropical origin. It is widely grown and consumed around the world for its hydration and nutritional quality values. Low-temperature stress can affect early planting, seedling establishment, and expansion of crop production to new areas. A collection of 122 citron watermelon (Citrullus amarus) accessions were obtained from the USDA's National Plant Germplasm Repository System gene bank in Griffin, GA. The accessions were genotyped using whole genome resequencing to generate single nucleotide polymorphisms (SNPs) molecular markers and screened under cold-stressed and non-stressed control conditions. Four low-temperature stress tolerance related traits including shoot biomass, vine length, maximum quantum efficiency of photosystem II, and chlorophyll content were measured under cold-stressed and non-stressed control treatment conditions. Correlation analysis revealed the presence of positive relationships among traits. Broad-sense heritability for all traits ranged from 0.35 to 0.73, implying the presence of genetic contributions to the observed phenotypic variation. Genomic regions underlying these traits across several citron watermelon chromosomes were identified. Four low-temperature stress tolerance related putative candidate genes co-located with the peak SNPs from genome-wide association study. These genomic regions and marker information could potentially be used in molecular breeding to accelerate genetic improvements for low-temperature stress tolerance in watermelon.
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Affiliation(s)
| | - Amnon Levi
- USDS-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
| | - William P Wechter
- USDS-ARS, U.S. Vegetable Laboratory, Charleston, South Carolina, USA
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Aghogho CI, Kayondo SI, Eleblu SJY, Ige A, Asante I, Offei SK, Parkes E, Egesi C, Mbanjo EGN, Shah T, Kulakow P, Rabbi IY. Genome-wide association study for yield and quality of granulated cassava processed product. THE PLANT GENOME 2024; 17:e20469. [PMID: 38880944 DOI: 10.1002/tpg2.20469] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/09/2023] [Revised: 04/27/2024] [Accepted: 05/03/2024] [Indexed: 06/18/2024]
Abstract
The starchy storage roots of cassava are commonly processed into a variety of products, including cassava granulated processed products (gari). The commercial value of cassava roots depends on the yield and quality of processed products, directly influencing the acceptance of new varieties by farmers, processors, and consumers. This study aims to estimate genetic advance through phenotypic selection and identify genomic regions associated and candidate genes linked with gari yield and quality. Higher single nucleotide polymorphism (SNP)-based heritability estimates compared to broad-sense heritability estimates were observed for most traits highlighting the influence of genetic factors on observed variation. Using genome-wide association analysis of 188 clones, genotyped using 53,150 genome-wide SNPs, nine SNPs located on seven chromosomes were significantly associated with peel loss, gari yield, color parameters for gari and eba, bulk density, swelling index, and textural properties of eba. Future research will focus on validating and understanding the functions of identified genes and their influence on gari yield and quality traits.
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Affiliation(s)
- Cynthia Idhigu Aghogho
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Siraj Ismail Kayondo
- International Institute of Tropical Agriculture (IITA), Eastern Africa Hub, Dar es Salaam, Tanzania
| | - Saviour J Y Eleblu
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Adenike Ige
- Department of Agronomy and Plant Genetics, University of Minnesota, Minneapolis, Minnesota, USA
| | - Isaac Asante
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Samuel K Offei
- West Africa Centre for Crop Improvement (WACCI), College of Basic and Applied Sciences, University of Ghana, Legon, Ghana
| | - Elizabeth Parkes
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Chiedozie Egesi
- National Root Crops Research Institute, Umuahia, Nigeria
- Plant Breeding and Genetics Section, School of Integrative Plant Science, College of Agriculture and Life Sciences, Cornell University, Ithaca, New York, USA
| | | | - Trushar Shah
- International Institute of Tropical Agriculture (IITA), c/o ILRI, Nairobi, Kenya
| | - Peter Kulakow
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
| | - Ismail Y Rabbi
- International Institute of Tropical Agriculture (IITA), Ibadan, Nigeria
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Kumar K, Kumari A, Durgesh K, Sevanthi AM, Sharma S, Singh NK, Gaikwad K. Identification of superior haplotypes for flowering time in pigeonpea through candidate gene-based association study of a diverse minicore collection. PLANT CELL REPORTS 2024; 43:156. [PMID: 38819495 DOI: 10.1007/s00299-024-03230-x] [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: 02/23/2024] [Accepted: 05/05/2024] [Indexed: 06/01/2024]
Abstract
KEY MESSAGE In current study candidate gene (261 genes) based association mapping on 144 pigeonpea accessions for flowering time and related traits and 29 MTAs producing eight superior haplotypes were identified. In the current study, we have conducted an association analysis for flowering-associated traits in a diverse pigeonpea mini-core collection comprising 144 accessions using the SNP data of 261 flowering-related genes. In total, 13,449 SNPs were detected in the current study, which ranged from 743 (ICP10228) to 1469 (ICP6668) among the individuals. The nucleotide diversity (0.28) and Watterson estimates (0.34) reflected substantial diversity, while Tajima's D (-0.70) indicated the abundance of rare alleles in the collection. A total of 29 marker trait associations (MTAs) were identified, among which 19 were unique to days to first flowering (DOF) and/or days to fifty percent flowering (DFF), 9 to plant height (PH), and 1 to determinate (Det) growth habit using 3 years of phenotypic data. Among these MTAs, six were common to DOF and/or DFF, and four were common to DOF/DFF along with the PH, reflecting their pleiotropic action. These 29 MTAs spanned 25 genes, among which 10 genes clustered in the protein-protein network analysis, indicating their concerted involvement in floral induction. Furthermore, we identified eight haplotypes, four of which regulate late flowering, while the remaining four regulate early flowering using the MTAs. Interestingly, haplotypes conferring late flowering (H001, H002, and H008) were found to be taller, while those involved in early flowering (H003) were shorter in height. The expression pattern of these genes, as inferred from the transcriptome data, also underpinned their involvement in floral induction. The haplotypes identified will be highly useful to the pigeonpea breeding community for haplotype-based breeding.
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Affiliation(s)
- Kuldeep Kumar
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
- ICAR-Indian Institute of Pulses Research, Kanpur, Uttar Pradesh, India
- The Graduate School, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | - Anita Kumari
- Department of Botany, North Campus, University of Delhi, Delhi, New Delhi, India
| | - Kumar Durgesh
- Division of Genetics, ICAR-Indian Agricultural Research Institute, Pusa, New Delhi, India
| | | | - Sandhya Sharma
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India
| | | | - Kishor Gaikwad
- ICAR-National Institute for Plant Biotechnology, Pusa, New Delhi, India.
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Smitchger JA, Taylor JB, Mousel MR, Schaub D, Thorne JW, Becker GM, Murdoch BM. Genome-wide associations with longevity and reproductive traits in U.S. rangeland ewes. Front Genet 2024; 15:1398123. [PMID: 38859938 PMCID: PMC11163081 DOI: 10.3389/fgene.2024.1398123] [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: 03/08/2024] [Accepted: 04/18/2024] [Indexed: 06/12/2024] Open
Abstract
Introduction: Improving ewe longevity is an important breeding and management goal, as death loss and early culling of mature ewes are economic burdens in the sheep industry. Ewe longevity can be improved by selecting for positive reproductive outcomes. However, the breeding approaches for accomplishing this come with the challenge of recording a lifetime trait. Characterizing genetic factors underpinning ewe longevity and related traits could result in the development of genomic selection strategies to improve the stayability of sheep through early, informed selection of replacement ewes. Methods: Towards this aim, a genome-wide association study (GWAS) was performed to identify genetic markers associated with ewe longevity, reproductive, and production traits. Traits evaluated included longevity (i.e., length of time in the flock), parity and the lifetime number of lambs born, lambs born alive, lambs weaned, and weight of lambs weaned. Ewe records from previous studies were used. Specifically, Rambouillet (n = 480), Polypay (n = 404), Suffolk (n = 182), and Columbia (n = 64) breed ewes (N = 1,130) were analyzed against 503,617 SNPs in across-breed and within-breed GWAS conducted with the Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model in R. Results: The across-breed GWAS identified 25 significant SNPs and the within-breed GWAS for Rambouillet, Polypay, and Suffolk ewes identified an additional 19 significant SNPs. The most significant markers were rs411309094 (13:22,467,143) associated with longevity in across-breed GWAS (p-value = 8.3E-13) and rs429525276 (2:148,398,336) associated with both longevity (p-value = 6.4E-15) and parity (p-value = 4.8E-15) in Rambouillet GWAS. Significant SNPs were identified within or in proximity (±50 kb) of genes with known or proposed roles in reproduction, dentition, and the immune system. These genes include ALPL, ANOS1, ARHGEF26, ASIC2, ASTN2, ATP8A2, CAMK2D, CEP89, DISC1, ITGB6, KCNH8, MBNL3, MINDY4, MTSS1, PLEKHA7, PRIM2, RNF43, ROBO2, SLCO1A2, TMEM266, TNFRSF21, and ZNF804B. Discussion: This study proposes multiple SNPs as candidates for use in selection indices and suggests genes for further research towards improving understanding of the genetic factors contributing to longevity, reproductive, and production traits of ewes.
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Affiliation(s)
- Jamin A. Smitchger
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - J. Bret Taylor
- USDA, Agriculture Research Service, Range Sheep Production Efficiency Research Unit, U.S. Sheep Experiment Station, Dubois, ID, United States
| | - Michelle R. Mousel
- Animal Diseases Research Unit, Agricultural Research Service, US Department of Agriculture, Pullman, WA, United States
| | - Daniel Schaub
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Jacob W. Thorne
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
- Texas A&M AgriLife Research and Extension, San Angelo, TX, United States
| | - Gabrielle M. Becker
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
| | - Brenda M. Murdoch
- Department of Animal, Veterinary and Food Sciences, University of Idaho, Moscow, ID, United States
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Wang JT, Chang XY, Zhao Q, Zhang YM. FastBiCmrMLM: a fast and powerful compressed variance component mixed logistic model for big genomic case-control genome-wide association study. Brief Bioinform 2024; 25:bbae290. [PMID: 38888457 PMCID: PMC11184901 DOI: 10.1093/bib/bbae290] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2024] [Revised: 05/19/2024] [Accepted: 06/09/2024] [Indexed: 06/20/2024] Open
Abstract
Large sample datasets have been regarded as the primary basis for innovative discoveries and the solution to missing heritability in genome-wide association studies. However, their computational complexity cannot consider all comprehensive effects and all polygenic backgrounds, which reduces the effectiveness of large datasets. To address these challenges, we included all effects and polygenic backgrounds in a mixed logistic model for binary traits and compressed four variance components into two. The compressed model combined three computational algorithms to develop an innovative method, called FastBiCmrMLM, for large data analysis. These algorithms were tailored to sample size, computational speed, and reduced memory requirements. To mine additional genes, linkage disequilibrium markers were replaced by bin-based haplotypes, which are analyzed by FastBiCmrMLM, named FastBiCmrMLM-Hap. Simulation studies highlighted the superiority of FastBiCmrMLM over GMMAT, SAIGE and fastGWA-GLMM in identifying dominant, small α (allele substitution effect), and rare variants. In the UK Biobank-scale dataset, we demonstrated that FastBiCmrMLM could detect variants as small as 0.03% and with α ≈ 0. In re-analyses of seven diseases in the WTCCC datasets, 29 candidate genes, with both functional and TWAS evidence, around 36 variants identified only by the new methods, strongly validated the new methods. These methods offer a new way to decipher the genetic architecture of binary traits and address the challenges outlined above.
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Affiliation(s)
| | | | | | - Yuan-Ming Zhang
- Corresponding author. College of Plant Science and Technology, Huazhong Agricultural University, Wuhan 430070, China. Tel.: +086-13505161564; E-mail:
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Gao H, Wu G, Wu F, Zhou X, Zhou Y, Xu K, Li Y, Zhang W, Zhao K, Jing Y, Feng C, Wang N, Li H. Genome-Wide Association Analysis of Yield-Related Traits and Candidate Genes in Vegetable Soybean. PLANTS (BASEL, SWITZERLAND) 2024; 13:1442. [PMID: 38891251 PMCID: PMC11174663 DOI: 10.3390/plants13111442] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2024] [Revised: 05/12/2024] [Accepted: 05/21/2024] [Indexed: 06/21/2024]
Abstract
Owing to the rising demand for vegetable soybean products, there is an increasing need for high-yield soybean varieties. However, the complex correlation patterns among quantitative traits with genetic architecture pose a challenge for improving vegetable soybean through breeding. Herein, a genome-wide association study (GWAS) was applied to 6 yield-related traits in 188 vegetable soybean accessions. Using a BLINK model, a total of 116 single nucleotide polymorphisms (SNPs) were identified for plant height, pod length, pod number, pod thickness, pod width, and fresh pod weight. Furthermore, a total of 220 genes were found in the 200 kb upstream and downstream regions of significant SNPs, including 11 genes encoding functional proteins. Among them, four candidate genes, Glyma.13G109100, Glyma.03G183200, Glyma.09G102200, and Glyma.09G102300 were analyzed for significant haplotype variations and to be in LD block, which encode MYB-related transcription factor, auxin-responsive protein, F-box protein, and CYP450, respectively. The relative expression of candidate genes in V030 and V071 vegetable soybean (for the plant height, pod number, and fresh pod weight of V030 were lower than those of the V071 strains) was significantly different, and these genes could be involved in plant growth and development via various pathways. Altogether, we identified four candidate genes for pod yield and plant height from vegetable soybean germplasm. This study provides insights into the genomic basis for improving soybean and crucial genomic resources that can facilitate genome-assisted high-yielding vegetable soybean breeding.
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Affiliation(s)
- Hongtao Gao
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Guanji Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Feifei Wu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Xunjun Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Yonggang Zhou
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Keheng Xu
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Yaxin Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Wenping Zhang
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Kuan Zhao
- Changchun Academy of Agricultural Science, Changchun 130118, China
| | - Yan Jing
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Chen Feng
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
| | - Nan Wang
- Changchun Academy of Agricultural Science, Changchun 130118, China
| | - Haiyan Li
- School of Breeding and Multiplication (Sanya Institute of Breeding and Multiplication), Hainan University, Haikou 572025, China; (H.G.); (G.W.); (F.W.); (X.Z.); (Y.Z.); (K.X.); (Y.L.)
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Zhou X, Qiang C, Chen L, Qing D, Huang J, Li J, Pan Y. The Landscape of Presence/Absence Variations during the Improvement of Rice. Genes (Basel) 2024; 15:645. [PMID: 38790274 PMCID: PMC11120952 DOI: 10.3390/genes15050645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/26/2024] [Revised: 05/15/2024] [Accepted: 05/17/2024] [Indexed: 05/26/2024] Open
Abstract
Rice is one of the most important staple crops in the world; therefore, the improvement of rice holds great significance for enhancing agricultural production and addressing food security challenges. Although there have been numerous studies on the role of single-nucleotide polymorphisms (SNPs) in rice improvement with the development of next-generation sequencing technologies, research on the role of presence/absence variations (PAVs) in the improvement of rice is limited. In particular, there is a scarcity of studies exploring the traits and genes that may be affected by PAVs in rice. Here, we extracted PAVs utilizing resequencing data from 148 improved rice varieties distributed in Asia. We detected a total of 33,220 PAVs and found that the number of variations decreased gradually as the length of the PAVs increased. The number of PAVs was the highest on chromosome 1. Furthermore, we identified a 6 Mb hotspot region on chromosome 11 containing 1091 PAVs in which there were 29 genes related to defense responses. By conducting a genome-wide association study (GWAS) using PAV variation data and phenotypic data for five traits (flowering time, plant height, flag leaf length, flag leaf width, and panicle number) across all materials, we identified 186 significantly associated PAVs involving 20 cloned genes. A haplotype analysis and expression analysis of candidate genes revealed that important genes might be affected by PAVs, such as the flowering time gene OsSFL1 and the flag leaf width gene NAL1. Our work investigated the pattern in PAVs and explored important PAV key functional genes associated with agronomic traits. Consequently, these results provide potential and exploitable genetic resources for rice breeding.
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Affiliation(s)
- Xia Zhou
- Urban Construction School, Beijing City University, Beijing 101300, China;
| | - Chenggen Qiang
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Lei Chen
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
| | - Dongjin Qing
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
| | - Juan Huang
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
| | - Jilong Li
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China;
| | - Yinghua Pan
- Guangxi Key Laboratory of Rice Genetics and Breeding, Rice Research Institute, Guangxi Academy of Agricultural Sciences, Nanning 530007, China; (L.C.); (D.Q.); (J.H.)
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Khan H, Krishnappa G, Kumar S, Devate NB, Rathan ND, Kumar S, Mishra CN, Ram S, Tiwari R, Parkash O, Ahlawat OP, Mamrutha HM, Singh GP, Singh G. Genome-wide association study identifies novel loci and candidate genes for rust resistance in wheat (Triticum aestivum L.). BMC PLANT BIOLOGY 2024; 24:411. [PMID: 38760694 PMCID: PMC11100168 DOI: 10.1186/s12870-024-05124-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 01/27/2024] [Accepted: 05/09/2024] [Indexed: 05/19/2024]
Abstract
BACKGROUND Wheat rusts are important biotic stresses, development of rust resistant cultivars through molecular approaches is both economical and sustainable. Extensive phenotyping of large mapping populations under diverse production conditions and high-density genotyping would be the ideal strategy to identify major genomic regions for rust resistance in wheat. The genome-wide association study (GWAS) population of 280 genotypes was genotyped using a 35 K Axiom single nucleotide polymorphism (SNP) array and phenotyped at eight, 10, and, 10 environments, respectively for stem/black rust (SR), stripe/yellow rust (YR), and leaf/brown rust (LR). RESULTS Forty-one Bonferroni corrected marker-trait associations (MTAs) were identified, including 17 for SR and 24 for YR. Ten stable MTAs and their best combinations were also identified. For YR, AX-94990952 on 1A + AX-95203560 on 4A + AX-94723806 on 3D + AX-95172478 on 1A showed the best combination with an average co-efficient of infection (ACI) score of 1.36. Similarly, for SR, AX-94883961 on 7B + AX-94843704 on 1B and AX-94883961 on 7B + AX-94580041 on 3D + AX-94843704 on 1B showed the best combination with an ACI score of around 9.0. The genotype PBW827 have the best MTA combinations for both YR and SR resistance. In silico study identifies key prospective candidate genes that are located within MTA regions. Further, the expression analysis revealed that 18 transcripts were upregulated to the tune of more than 1.5 folds including 19.36 folds (TraesCS3D02G519600) and 7.23 folds (TraesCS2D02G038900) under stress conditions compared to the control conditions. Furthermore, highly expressed genes in silico under stress conditions were analyzed to find out the potential links to the rust phenotype, and all four genes were found to be associated with the rust phenotype. CONCLUSION The identified novel MTAs, particularly stable and highly expressed MTAs are valuable for further validation and subsequent application in wheat rust resistance breeding. The genotypes with favorable MTA combinations can be used as prospective donors to develop elite cultivars with YR and SR resistance.
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Affiliation(s)
- Hanif Khan
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Gopalareddy Krishnappa
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India.
- ICAR-Sugarcane Breeding Institute, Coimbatore, 641007, India.
| | - Sudheer Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Narayana Bhat Devate
- International Centre for Agriculture Research in the Dry Area - Food Legume Research Platform, Amlaha, MP, 466113, India
| | | | - Satish Kumar
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | | | - Sewa Ram
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Ratan Tiwari
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Om Parkash
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | - Om Parkash Ahlawat
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
| | | | - Gyanendra Pratap Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
- ICAR-National Bureau of Plant Genetic Resources, New Delhi, 110012, India
| | - Gyanendra Singh
- ICAR-Indian Institute of Wheat and Barley Research, Karnal, 132001, India
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Sahu TK, Verma SK, Gayacharan, Singh NP, Joshi DC, Wankhede DP, Singh M, Bhardwaj R, Singh B, Parida SK, Chattopadhyay D, Singh GP, Singh AK. Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata). BMC PLANT BIOLOGY 2024; 24:379. [PMID: 38720284 PMCID: PMC11077894 DOI: 10.1186/s12870-024-04976-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/19/2023] [Accepted: 04/02/2024] [Indexed: 05/12/2024]
Abstract
BACKGROUND Rice bean (Vigna umbellata), an underrated legume, adapts to diverse climatic conditions with the potential to support food and nutritional security worldwide. It is used as a vegetable, minor food crop and a fodder crop, being a rich source of proteins, minerals, and essential fatty acids. However, little effort has been made to decipher the genetic and molecular basis of various useful traits in this crop. Therefore, we considered three economically important traits i.e., flowering, maturity and seed weight of rice bean and identified the associated candidate genes employing an associative transcriptomics approach on 100 diverse genotypes out of 1800 evaluated rice bean accessions from the Indian National Genebank. RESULTS The transcriptomics-based genotyping of one-hundred diverse rice bean cultivars followed by pre-processing of genotypic data resulted in 49,271 filtered markers. The STRUCTURE, PCA and Neighbor-Joining clustering of 100 genotypes revealed three putative sub-populations. The marker-trait association analysis involving various genome-wide association study (GWAS) models revealed significant association of 82 markers on 48 transcripts for flowering, 26 markers on 22 transcripts for maturity and 22 markers on 21 transcripts for seed weight. The transcript annotation provided information on the putative candidate genes for the considered traits. The candidate genes identified for flowering include HSC80, P-II PsbX, phospholipid-transporting-ATPase-9, pectin-acetylesterase-8 and E3-ubiquitin-protein-ligase-RHG1A. Further, the WRKY1 and DEAD-box-RH27 were found to be associated with seed weight. Furthermore, the associations of PIF3 and pentatricopeptide-repeat-containing-gene with maturity and seed weight, and aldo-keto-reductase with flowering and maturity were revealed. CONCLUSION This study offers insights into the genetic basis of key agronomic traits in rice bean, including flowering, maturity, and seed weight. The identified markers and associated candidate genes provide valuable resources for future exploration and targeted breeding, aiming to enhance the agronomic performance of rice bean cultivars. Notably, this research represents the first transcriptome-wide association study in pulse crop, uncovering the candidate genes for agronomically useful traits.
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Affiliation(s)
- Tanmaya Kumar Sahu
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
- ICAR-Indian Grassland and Fodder Research Institute, Jhansi, Uttar Pradesh, India
| | - Sachin Kumar Verma
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Gayacharan
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | | | - Dinesh Chandra Joshi
- ICAR-Vivekananda Parvatiya Krishi Anusandhan Sansthan, Almora, Uttarakhand, India
| | - D P Wankhede
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Mohar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Rakesh Bhardwaj
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Badal Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India
| | - Swarup Kumar Parida
- National Institute of Plant Genome Research, Aruna Asaf Ali Marg, New Delhi, India
| | | | | | - Amit Kumar Singh
- ICAR-National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, 110012, India.
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Keller B, Jung M, Bühlmann-Schütz S, Hodel M, Studer B, Broggini GAL, Patocchi A. The genetic basis of apple shape and size unraveled by digital phenotyping. G3 (BETHESDA, MD.) 2024; 14:jkae045. [PMID: 38441135 PMCID: PMC11075547 DOI: 10.1093/g3journal/jkae045] [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: 01/23/2024] [Accepted: 02/22/2024] [Indexed: 05/08/2024]
Abstract
Great diversity of shape, size, and skin color is observed among the fruits of different apple genotypes. These traits are critical for consumers and therefore interesting targets for breeding new apple varieties. However, they are difficult to phenotype and their genetic basis, especially for fruit shape and ground color, is largely unknown. We used the FruitPhenoBox to digitally phenotype 525 genotypes of the apple reference population (apple REFPOP) genotyped for 303,148 single nucleotide polymorphism (SNP) markers. From the apple images, 573 highly heritable features describing fruit shape and size as well as 17 highly heritable features for fruit skin color were extracted to explore genotype-phenotype relationships. Out of these features, seven principal components (PCs) and 16 features with the Pearson's correlation r < 0.75 (selected features) were chosen to carry out genome-wide association studies (GWAS) for fruit shape and size. Four PCs and eight selected features were used in GWAS for fruit skin color. In total, 69 SNPs scattered over all 17 apple chromosomes were significantly associated with round, conical, cylindrical, or symmetric fruit shapes and fruit size. Novel associations with major effect on round or conical fruit shapes and fruit size were identified on chromosomes 1 and 2. Additionally, 16 SNPs associated with PCs and selected features related to red overcolor as well as green and yellow ground color were found on eight chromosomes. The identified associations can be used to advance marker-assisted selection in apple fruit breeding to systematically select for desired fruit appearance.
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Affiliation(s)
- Beat Keller
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Michaela Jung
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Simone Bühlmann-Schütz
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Marius Hodel
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
| | - Bruno Studer
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Giovanni A L Broggini
- Molecular Plant Breeding, Institute of Agricultural Sciences, ETH Zurich, Universitaetstrasse 2, Zurich 8092, Switzerland
| | - Andrea Patocchi
- Division of Plant Breeding, Agroscope, Mueller-Thurgau-Strasse 29, Waedenswil 8820, Switzerland
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Xiong H, Chen Y, Ravelombola W, Mou B, Sun X, Zhang Q, Xiao Y, Tian Y, Luo Q, Alatawi I, Chiwina KE, Alkabkabi HM, Shi A. Genetic Dissection of Diverse Seed Coat Patterns in Cowpea through a Comprehensive GWAS Approach. PLANTS (BASEL, SWITZERLAND) 2024; 13:1275. [PMID: 38732490 PMCID: PMC11085092 DOI: 10.3390/plants13091275] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/08/2024] [Revised: 04/27/2024] [Accepted: 05/02/2024] [Indexed: 05/13/2024]
Abstract
This study investigates the genetic determinants of seed coat color and pattern variations in cowpea (Vigna unguiculata), employing a genome-wide association approach. Analyzing a mapping panel of 296 cowpea varieties with 110,000 single nucleotide polymorphisms (SNPs), we focused on eight unique coat patterns: (1) Red and (2) Cream seed; (3) White and (4) Brown/Tan seed coat; (5) Pink, (6) Black, (7) Browneye and (8) Red/Brown Holstein. Across six GWAS models (GLM, SRM, MLM, MLMM, FarmCPU from GAPIT3, and TASSEL5), 13 significant SNP markers were identified and led to the discovery of 23 candidate genes. Among these, four specific genes may play a direct role in determining seed coat pigment. These findings lay a foundational basis for future breeding programs aimed at creating cowpea varieties aligned with consumer preferences and market requirements.
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Affiliation(s)
- Haizheng Xiong
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | - Yilin Chen
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | | | - Beiquan Mou
- Sam Farr U.S. Crop Improvement and Protection Research Center, U.S. Department of Agriculture, Agricultural Research Service (USDA-ARS), Salinas, CA 93905, USA
| | - Xiaolun Sun
- Department of Poultry Science & The Center of Excellence for Poultry Science, University of Arkansas, Fayetteville, AR 72701, USA
| | - Qingyang Zhang
- Mathematical Sciences, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yiting Xiao
- Biological Engineering, University of Arkansas, Fayetteville, AR 72701, USA
| | - Yang Tian
- Program of Material Science and Engineering, Fayetteville, AR 72701, USA
| | - Qun Luo
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | - Ibtisam Alatawi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | - Kenani Edward Chiwina
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
| | | | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR 72701, USA; (Y.C.)
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Rajput P, Urfan M, Sharma S, Hakla HR, Nandan B, Das R, Roychowdhury R, Chowdhary SP. Natural variation in root traits identifies significant SNPs and candidate genes for phosphate deficiency tolerance in Zea mays L. PHYSIOLOGIA PLANTARUM 2024; 176:e14396. [PMID: 38887929 DOI: 10.1111/ppl.14396] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/31/2024] [Revised: 05/08/2024] [Accepted: 05/30/2024] [Indexed: 06/20/2024]
Abstract
Phosphorus (P) is a crucial macronutrient required for normal plant growth. Its effective uptake from the soil is a trait of agronomic importance. Natural variation in maize (339 accessions) root traits, namely root length and number of primary, seminal, and crown roots, root and shoot phosphate (Pi) contents, and root-to-shoot Pi translocation (root: shoot Pi) under normal (control, 40 ppm) and low phosphate (LP, 1 ppm) conditions, were used for genome-wide association studies (GWAS). The Bayesian-information and Linkage-disequilibrium Iteratively Nested Keyway (BLINK) model of GWAS provided 23 single nucleotide polymorphisms (SNPs) and 12 relevant candidate genes putatively linked with root Pi, root: shoot Pi, and crown root number (CRN) under LP. The DNA-protein interaction analysis of Zm00001d002842, Zm00001d002837, Zm00001d002843 for root Pi, and Zm00001d044312, Zm00001d045550, Zm00001d025915, Zm00001d044313, Zm00001d051842 for root: shoot Pi, and Zm00001d031561, Zm00001d001803, and Zm00001d001804 for CRN showed the presence of potential binding sites of key transcription factors like MYB62, bZIP11, ARF4, ARF7, ARF10 and ARF16 known for induction/suppression of phosphate starvation response (PHR). The in-silico RNA-seq analysis revealed up or down-regulation of candidate genes along with key transcription factors of PHR, while Uniprot analysis provided genetic relatedness. Candidate genes that may play a role in P uptake and root-to-shoot Pi translocation under LP are proposed using common PHR signaling components like MYB62, ARF4, ARF7, ARF10, ARF16, and bZIP11 to induce changes in root growth in maize. Candidate genes may be used to improve low P tolerance in maize using the CRISPR strategy.
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Affiliation(s)
- Prakriti Rajput
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, India
| | - Mohammad Urfan
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, India
| | - Shubham Sharma
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, India
| | - Haroon Rashid Hakla
- Plant Physiology Laboratory, Department of Botany, University of Jammu, Jammu, India
| | - Brij Nandan
- Agronomy Division, SKUAST-JAMMU, Union Territory of Jammu & Kashmir, India
| | - Ranjan Das
- Department of Crop Physiology, Assam Agricultural University, Jorhat, Assam, India
| | - Rajib Roychowdhury
- Department of Plant Pathology and Weed Research, Institute of Plant Protection, Agricultural Research Organization (ARO) - Volcani Institute, Rishon Lezion, Israel
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Gai W, Yuan L, Yang F, Ahiakpa JK, Li F, Ge P, Zhang X, Tao J, Wang F, Yang Y, Zhang Y. Genome-wide variants and optimal allelic combinations for citric acid in tomato. HORTICULTURE RESEARCH 2024; 11:uhae070. [PMID: 38725459 PMCID: PMC11079488 DOI: 10.1093/hr/uhae070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/15/2023] [Accepted: 02/25/2024] [Indexed: 05/12/2024]
Abstract
Citric acid (CA) plays a crucial role as a fruit flavor enhancer and serves as a mediator in multiple metabolic pathways in tomato fruit development. Understanding factors influencing CA metabolism is essential for enhancing fruit flavor and CA-mediated biological processes. The accumulation of CA, however, is influenced by a complex interplay of genetic and environmental factors, leading to challenges in accurately predicting and regulating its levels. In this study, we conducted a genome-wide association study (GWAS) on CA, employing six landmark models based on genome-wide variations including structural variants, insertions and deletions, and single nucleotide polymorphisms. The identification of 11 high-confidence candidate genes was further facilitated by leveraging linkage disequilibrium and causal variants associated with CA. The transcriptome data from candidate genes were examined, revealing higher correlations between the expression of certain candidate genes and changes in CA metabolism. Three CA-associated genes exerted a positive regulatory effect on CA accumulation, while the remaining genes exhibited negative impacts based on gene cluster and correlation analyses. The CA content of tomatoes is primarily influenced by improvement sweeps with minimal influence from domestication sweeps in the long-term breeding history, as evidenced by population differentiation and variants distribution. The presence of various causal variants within candidate genes is implicated in the heterogeneity of CA content observed among the tomato accessions. This observation suggests a potential correlation between the number of alternative alleles and CA content. This study offers significant function-based markers that can be utilized in marker-assisted breeding, thereby enhancing their value and applicability.
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Affiliation(s)
- Wenxian Gai
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Liangdan Yuan
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fan Yang
- College of Horticulture, Northwest A&F University, Yangling 712100, China
| | - John Kojo Ahiakpa
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fangman Li
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Pingfei Ge
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Xingyu Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Jinbao Tao
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Fei Wang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Yang Yang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
| | - Yuyang Zhang
- National Key Laboratory for Germplasm Innovation & Utilization of Horticultural Crops, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Hongshan Laboratory, Wuhan 430070, China
- Shenzhen Institute of Nutrition and Health, Huazhong Agricultural University, Wuhan 430070, China
- Shenzhen Branch, Guangdong Laboratory for Lingnan Modern Agriculture, Genome Analysis Laboratory of the Ministry of Agriculture, Agricultural Genomics Institute at Shenzhen, Chinese Academy of Agricultural Sciences, Shenzhen 518000, China
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Song J, Liu Y, Guo R, Pacheco A, Muñoz-Zavala C, Song W, Wang H, Cao S, Hu G, Zheng H, Dhliwayo T, San Vicente F, Prasanna BM, Wang C, Zhang X. Exploiting genomic tools for genetic dissection and improving the resistance to Fusarium stalk rot in tropical maize. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:109. [PMID: 38649662 DOI: 10.1007/s00122-024-04597-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/18/2023] [Accepted: 03/07/2024] [Indexed: 04/25/2024]
Abstract
KEY MESSAGE A stable genomic region conferring FSR resistance at ~250 Mb on chromosome 1 was identified by GWAS. Genomic prediction has the potential to improve FSR resistance. Fusarium stalk rot (FSR) is a global destructive disease in maize; the efficiency of phenotypic selection for improving FSR resistance was low. Novel genomic tools of genome-wide association study (GWAS) and genomic prediction (GP) provide an opportunity for genetic dissection and improving FSR resistance. In this study, GWAS and GP analyses were performed on 562 tropical maize inbred lines consisting of two populations. In total, 15 SNPs significantly associated with FSR resistance were identified across two populations and the combinedPOP consisting of all 562 inbred lines, with the P-values ranging from 1.99 × 10-7 to 8.27 × 10-13, and the phenotypic variance explained (PVE) values ranging from 0.94 to 8.30%. The genetic effects of the 15 favorable alleles ranged from -4.29 to -14.21% of the FSR severity. One stable genomic region at ~ 250 Mb on chromosome 1 was detected across all populations, and the PVE values of the SNPs detected in this region ranged from 2.16 to 5.18%. Prediction accuracies of FSR severity estimated with the genome-wide SNPs were moderate and ranged from 0.29 to 0.51. By incorporating genotype-by-environment interaction, prediction accuracies were improved between 0.36 and 0.55 in different breeding scenarios. Considering both the genome coverage and the threshold of the P-value of SNPs to select a subset of molecular markers further improved the prediction accuracies. These findings extend the knowledge of exploiting genomic tools for genetic dissection and improving FSR resistance in tropical maize.
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Affiliation(s)
- Junqiao Song
- Henan University of Science and Technology, Luoyang, 471000, Henan, China
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Anyang Academy of Agricultural Sciences, Anyang, 455000, Henan, China
| | - Yubo Liu
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Rui Guo
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Angela Pacheco
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Carlos Muñoz-Zavala
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Wei Song
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Cereal and Oil Crops, Hebei Academy of Agricultural and Forestry Sciences, Shijiazhuang, 050035, Hebei, China
| | - Hui Wang
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Shiliang Cao
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150070, Heilongjiang, China
| | - Guanghui Hu
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
- Institute of Maize Research, Heilongjiang Academy of Agricultural Sciences, Harbin, 150070, Heilongjiang, China
| | - Hongjian Zheng
- CIMMYT-China Specialty Maize Research Center, Crop Breeding and Cultivation Research Institute, Shanghai Academy of Agricultural Sciences, Shanghai, 200063, China
| | - Thanda Dhliwayo
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Felix San Vicente
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico
| | - Boddupalli M Prasanna
- International Maize and Wheat Improvement Center (CIMMYT), Village Market, P. O. Box 1041, Nairobi, 00621, Kenya
| | - Chunping Wang
- Henan University of Science and Technology, Luoyang, 471000, Henan, China.
| | - Xuecai Zhang
- International Maize and Wheat Improvement Center (CIMMYT), 56237, Texcoco, Mexico.
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences (CAAS), CIMMYT-China Office, 12 Zhongguancun South Street, Beijing, 100081, China.
- Nanfan Research Institute, CAAS, Sanya, 572024, Hainan, China.
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de Ronne M, Lapierre É, Torkamaneh D. Genetic insights into agronomic and morphological traits of drug-type cannabis revealed by genome-wide association studies. Sci Rep 2024; 14:9162. [PMID: 38644388 PMCID: PMC11033274 DOI: 10.1038/s41598-024-58931-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/09/2023] [Accepted: 04/04/2024] [Indexed: 04/23/2024] Open
Abstract
Cannabis sativa L., previously concealed by prohibition, is now a versatile and promising plant, thanks to recent legalization, opening doors for medical research and industry growth. However, years of prohibition have left the Cannabis research community lagging behind in understanding Cannabis genetics and trait inheritance compared to other major crops. To address this gap, we conducted a comprehensive genome-wide association study (GWAS) of nine key agronomic and morphological traits, using a panel of 176 drug-type Cannabis accessions from the Canadian legal market. Utilizing high-density genotyping-by-sequencing (HD-GBS), we successfully generated dense genotyping data in Cannabis, resulting in a catalog of 800 K genetic variants, of which 282 K common variants were retained for GWAS analysis. Through GWAS analysis, we identified 18 markers significantly associated with agronomic and morphological traits. Several identified markers exert a substantial phenotypic impact, guided us to putative candidate genes that reside in high linkage-disequilibrium (LD) with the markers. These findings lay a solid foundation for an innovative cannabis research, leveraging genetic markers to inform breeding programs aimed at meeting diverse needs in the industry.
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Affiliation(s)
- Maxime de Ronne
- Département de Phytologie, Université Laval, Quebec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
- Centre de Recherche et d'innovation sur les Végétaux (CRIV), Université Laval, Quebec City, Québec, Canada
- Institut Intelligence et Données (IID), Université Laval, Quebec City, Québec, Canada
| | - Éliana Lapierre
- Département de Phytologie, Université Laval, Quebec City, Québec, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Québec, Canada
- Centre de Recherche et d'innovation sur les Végétaux (CRIV), Université Laval, Quebec City, Québec, Canada
- Institut Intelligence et Données (IID), Université Laval, Quebec City, Québec, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Quebec City, Québec, Canada.
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Quebec City, Québec, Canada.
- Centre de Recherche et d'innovation sur les Végétaux (CRIV), Université Laval, Quebec City, Québec, Canada.
- Institut Intelligence et Données (IID), Université Laval, Quebec City, Québec, Canada.
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Chang-Brahim I, Koppensteiner LJ, Beltrame L, Bodner G, Saranti A, Salzinger J, Fanta-Jende P, Sulzbachner C, Bruckmüller F, Trognitz F, Samad-Zamini M, Zechner E, Holzinger A, Molin EM. Reviewing the essential roles of remote phenotyping, GWAS and explainable AI in practical marker-assisted selection for drought-tolerant winter wheat breeding. FRONTIERS IN PLANT SCIENCE 2024; 15:1319938. [PMID: 38699541 PMCID: PMC11064034 DOI: 10.3389/fpls.2024.1319938] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 10/11/2023] [Accepted: 03/13/2024] [Indexed: 05/05/2024]
Abstract
Marker-assisted selection (MAS) plays a crucial role in crop breeding improving the speed and precision of conventional breeding programmes by quickly and reliably identifying and selecting plants with desired traits. However, the efficacy of MAS depends on several prerequisites, with precise phenotyping being a key aspect of any plant breeding programme. Recent advancements in high-throughput remote phenotyping, facilitated by unmanned aerial vehicles coupled to machine learning, offer a non-destructive and efficient alternative to traditional, time-consuming, and labour-intensive methods. Furthermore, MAS relies on knowledge of marker-trait associations, commonly obtained through genome-wide association studies (GWAS), to understand complex traits such as drought tolerance, including yield components and phenology. However, GWAS has limitations that artificial intelligence (AI) has been shown to partially overcome. Additionally, AI and its explainable variants, which ensure transparency and interpretability, are increasingly being used as recognised problem-solving tools throughout the breeding process. Given these rapid technological advancements, this review provides an overview of state-of-the-art methods and processes underlying each MAS, from phenotyping, genotyping and association analyses to the integration of explainable AI along the entire workflow. In this context, we specifically address the challenges and importance of breeding winter wheat for greater drought tolerance with stable yields, as regional droughts during critical developmental stages pose a threat to winter wheat production. Finally, we explore the transition from scientific progress to practical implementation and discuss ways to bridge the gap between cutting-edge developments and breeders, expediting MAS-based winter wheat breeding for drought tolerance.
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Affiliation(s)
- Ignacio Chang-Brahim
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Lorenzo Beltrame
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Gernot Bodner
- Department of Crop Sciences, Institute of Agronomy, University of Natural Resources and Life Sciences Vienna, Tulln, Austria
| | - Anna Saranti
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Jules Salzinger
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Phillipp Fanta-Jende
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Christoph Sulzbachner
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Felix Bruckmüller
- Unit Assistive and Autonomous Systems, Center for Vision, Automation & Control, AIT Austrian Institute of Technology, Vienna, Austria
| | - Friederike Trognitz
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
| | | | - Elisabeth Zechner
- Verein zur Förderung einer nachhaltigen und regionalen Pflanzenzüchtung, Zwettl, Austria
| | - Andreas Holzinger
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
| | - Eva M. Molin
- Unit Bioresources, Center for Health & Bioresources, AIT Austrian Institute of Technology, Tulln, Austria
- Human-Centered AI Lab, Department of Forest- and Soil Sciences, Institute of Forest Engineering, University of Natural Resources and Life Sciences Vienna, Vienna, Austria
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49
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Gong W, Proud C, Vinarao R, Fukai S, Mitchell J. Genome-Wide Association Study of Early Vigour-Related Traits for a Rice ( Oryza sativa L.) japonica Diversity Set Grown in Aerobic Conditions. BIOLOGY 2024; 13:261. [PMID: 38666873 PMCID: PMC11048181 DOI: 10.3390/biology13040261] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/13/2024] [Revised: 04/02/2024] [Accepted: 04/12/2024] [Indexed: 04/28/2024]
Abstract
Aerobic rice production is a relatively new system in which rice is direct-seeded and grown in non-flooded but well-watered conditions to improve water productivity. Early vigour-related traits are likely to be important in aerobic conditions. This study aimed to identify quantitative trait loci (QTL) and candidate genes associated with early vigour-related traits in aerobic conditions using a japonica rice diversity set. Field experiments and glasshouse experiments conducted under aerobic conditions revealed significant genotypic variation in early vigour-related traits. Genome-wide association analysis identified 32 QTL associated with early vigour-related traits. Notably, two QTL, qAEV1.5 and qAEV8, associated with both early vigour score and mesocotyl length, explained up to 22.1% of the phenotypic variance. In total, 23 candidate genes related to plant growth development and abiotic stress response were identified in the two regions. This study provides novel insights into the genetic basis of early vigour under aerobic conditions. Validation of identified QTL and candidate genes in different genetic backgrounds is crucial for future studies. Moreover, testing the effect of QTL on yield under different environments would be valuable. After validation, these QTL and genes can be considered for developing markers in marker-assisted selection for aerobic rice production.
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Affiliation(s)
- Wenliu Gong
- School of Agriculture and Food Sustainability, The University of Queensland, Brisbane, QLD 4072, Australia (J.M.)
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50
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Yu H, Bhat JA, Li C, Zhao B, Bu M, Zhang Z, Guo T, Feng X. Identification of superior and rare haplotypes to optimize branch number in soybean. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2024; 137:93. [PMID: 38570354 PMCID: PMC10991007 DOI: 10.1007/s00122-024-04596-y] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/30/2023] [Accepted: 03/07/2024] [Indexed: 04/05/2024]
Abstract
KEY MESSAGE Using the integrated approach in the present study, we identified eleven significant SNPs, seven stable QTLs and 20 candidate genes associated with branch number in soybean. Branch number is a key yield-related quantitative trait that directly affects the number of pods and seeds per soybean plant. In this study, an integrated approach with a genome-wide association study (GWAS) and haplotype and candidate gene analyses was used to determine the detailed genetic basis of branch number across a diverse set of soybean accessions. The GWAS revealed a total of eleven SNPs significantly associated with branch number across three environments using the five GWAS models. Based on the consistency of the SNP detection in multiple GWAS models and environments, seven genomic regions within the physical distance of ± 202.4 kb were delineated as stable QTLs. Of these QTLs, six QTLs were novel, viz., qBN7, qBN13, qBN16, qBN18, qBN19 and qBN20, whereas the remaining one, viz., qBN12, has been previously reported. Moreover, 11 haplotype blocks, viz., Hap4, Hap7, Hap12, Hap13A, Hap13B, Hap16, Hap17, Hap18, Hap19A, Hap19B and Hap20, were identified on nine different chromosomes. Haplotype allele number across the identified haplotype blocks varies from two to five, and different branch number phenotype is regulated by these alleles ranging from the lowest to highest through intermediate branching. Furthermore, 20 genes were identified underlying the genomic region of ± 202.4 kb of the identified SNPs as putative candidates; and six of them showed significant differential expression patterns among the soybean cultivars possessing contrasting branch number, which might be the potential candidates regulating branch number in soybean. The findings of this study can assist the soybean breeding programs for developing cultivars with desirable branch numbers.
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Affiliation(s)
- Hui Yu
- 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
- Zhejiang Lab, Hangzhou, 310012, China
| | | | - Candong Li
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Beifang Zhao
- 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
| | - Moran Bu
- 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
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China
| | - Zhirui 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
| | - Tai Guo
- Jiamusi Branch Academy of Heilongjiang Academy of Agricultural Sciences, Jiamusi, 154007, China
| | - Xianzhong Feng
- 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.
- Zhejiang Lab, Hangzhou, 310012, China.
- College of Advanced Agricultural Sciences, University of Chinese Academy of Sciences, Beijing, 101408, China.
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