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Han D, Zhao X, Zhang D, Wang Z, Zhu Z, Sun H, Qu Z, Wang L, Liu Z, Zhu X, Yuan M. Genome-wide association studies reveal novel QTLs for agronomic traits in soybean. FRONTIERS IN PLANT SCIENCE 2024; 15:1375646. [PMID: 38807775 PMCID: PMC11132100 DOI: 10.3389/fpls.2024.1375646] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/24/2024] [Accepted: 04/15/2024] [Indexed: 05/30/2024]
Abstract
Introduction Soybean, as a globally significant crop, has garnered substantial attention due to its agricultural importance. The utilization of molecular approaches to enhance grain yield in soybean has gained popularity. Methods In this study, we conducted a genome-wide association study (GWAS) using 156 Chinese soybean accessions over a two-year period. We employed the general linear model (GLM) and the mixed linear model (MLM) to analyze three agronomic traits: pod number, grain number, and grain weight. Results Our findings revealed significant associations between qgPNpP-98, qgGNpP-89 and qgHGW-85 QTLs and pod number, grain number, and grain weight, respectively. These QTLs were identified on chromosome 16, a region spanning 413171bp exhibited associations with all three traits. Discussion These QTL markers identified in this study hold potential for improving yield and agronomic traits through marker-assisted selection and genomic selection in breeding programs.
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Affiliation(s)
- Dongwei Han
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
- Heilongjiang Chinese Academy of Sciences Qiuying Zhang Soybean Scientist Studio, Qiqihar, Heilongjiang, China
| | - Xi Zhao
- Biotechnology Institute, Heilongjiang Academy of Agricultural Science, Harbin, Heilongjiang, China
| | - Di Zhang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhen Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhijia Zhu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Haoyue Sun
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhongcheng Qu
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Lianxia Wang
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
| | - Zhangxiong Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xu Zhu
- Department of Research and Development, Ruibiotech Co., Ltd, Beijing, China
| | - Ming Yuan
- Qiqihar Branch of Heilongjiang Academy of Agricultural Science, Qiqihar, Heilongjiang, China
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Zatybekov A, Yermagambetova M, Genievskaya Y, Didorenko S, Abugalieva S. Genetic Diversity Analysis of Soybean Collection Using Simple Sequence Repeat Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:3445. [PMID: 37836185 PMCID: PMC10575313 DOI: 10.3390/plants12193445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/03/2023] [Revised: 09/03/2023] [Accepted: 09/15/2023] [Indexed: 10/15/2023]
Abstract
Soybean [Glycine max (L.) Merr.] is a nutrient-rich crop that offers a sustainable source of dietary protein and edible oil. Determining the level of genetic diversity and relationships between various genetic resources involved in breeding programs is very important in crop improvement strategies. This study evaluated 100 soybean accessions with diverse origins for 10 important agronomic traits, including plant height (PH), an important plant adaptation-related trait impacting yield, in conditions in southeastern Kazakhstan for 2 years. The comparison of different groups of PH (tall, middle, and short) using a t-test suggested that the group of plants with the tallest PH provided a higher yield (p < 0.001) in relatively dry field conditions. The genetic diversity of the accessions was estimated using 25 simple sequence repeat (SSR) markers previously known to be associated with plant height. The results showed a significant variation among different groups of origin for all measured agronomic traits, as well as high genetic diversity, with the PIC (polymorphism information content) varying from 0.140 to 0.732, with an average of 0.524. Nei's diversity index ranged between 0.152 and 0.747, with an average of 0.526. The principal coordinate analysis (PCoA) of the studied soybean collection showed that Kazakhstan accessions were genetically distant from European, East Asian, and North American cultivars. Twelve out of twenty-five SSR markers demonstrated significant associations with ten studied agronomic traits, including PH (p < 0.05). Six SSRs with pleiotropic effects for studied traits were selected, and their haplotypes with phenotypic effects were generated for each soybean accession. The obtained results can be used in soybean improvement programs, including molecular-assisted breeding projects.
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Affiliation(s)
- Alibek Zatybekov
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
| | - Moldir Yermagambetova
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
| | - Yuliya Genievskaya
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
| | - Svetlana Didorenko
- Department of Oilseed Crop., Kazakh Research Institute of Agriculture and Plant Growing, Almalybak 040909, Kazakhstan;
| | - Saule Abugalieva
- Laboratory of Molecular Genetics, Institute of Plant Biology and Biotechnology, Almaty 050040, Kazakhstan; (A.Z.); (M.Y.); (Y.G.)
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Haidar S, Lackey S, Charette M, Yoosefzadeh-Najafabadi M, Gahagan AC, Hotte T, Belzile F, Rajcan I, Golshani A, Morrison MJ, Cober ER, Samanfar B. Genome-wide analysis of cold imbibition stress in soybean, Glycine max. FRONTIERS IN PLANT SCIENCE 2023; 14:1221644. [PMID: 37670866 PMCID: PMC10476531 DOI: 10.3389/fpls.2023.1221644] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/17/2023] [Accepted: 07/17/2023] [Indexed: 09/07/2023]
Abstract
In Canada, the length of the frost-free season necessitates planting crops as early as possible to ensure that the plants have enough time to reach full maturity before they are harvested. Early planting carries inherent risks of cold water imbibition (specifically less than 4°C) affecting seed germination. A marker dataset developed for a previously identified Canadian soybean GWAS panel was leveraged to investigate the effect of cold water imbibition on germination. Seed from a panel of 137 soybean elite cultivars, grown in the field at Ottawa, ON, over three years, were placed on filter paper in petri dishes and allowed to imbibe water for 16 hours at either 4°C or 20°C prior to being transferred to a constant 20°C. Observations on seed germination, defined as the presence of a 1 cm radicle, were done from day two to seven. A three-parameter exponential rise to a maximum equation (3PERM) was fitted to estimate germination, time to the one-half maximum germination, and germination uniformity for each cultivar. Genotype-by-sequencing was used to identify SNPs in 137 soybean lines, and using genome-wide association studies (GWAS - rMVP R package, with GLM, MLM, and FarmCPU as methods), haplotype block analysis, and assumed linkage blocks of ±100 kbp, a threshold for significance was established using the qvalue package in R, and five significant SNPs were identified on chromosomes 1, 3, 4, 6, and 13 for maximum germination after cold water imbibition. Percent of phenotypic variance explained (PVE) and allele substitution effect (ASE) eliminated two of the five candidate SNPs, leaving three QTL regions on chromosomes 3, 6, and 13 (Chr3-3419152, Chr6-5098454, and Chr13-29649544). Based on the gene ontology (GO) enrichment analysis, 14 candidate genes whose function is predicted to include germination and cold tolerance related pathways were identified as candidate genes. The identified QTLs can be used to select future soybean cultivars tolerant to cold water imbibition and mitigate risks associated with early soybean planting.
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Affiliation(s)
- Siwar Haidar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Simon Lackey
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Martin Charette
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | | | - A. Claire Gahagan
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Thomas Hotte
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Francois Belzile
- Department of Phytology, Institut de Biologie Intégrative et des Systèmes (IBIS), Université de Laval, Quebec City, QC, Canada
| | - Istvan Rajcan
- Department of Plant Agriculture, University of Guelph, Guelph, ON, Canada
| | - Ashkan Golshani
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
| | - Malcolm J. Morrison
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Elroy R. Cober
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
| | - Bahram Samanfar
- Agriculture and Agri-Food Canada, Ottawa Research and Development Centre, Ottawa, ON, Canada
- Department of Biology, Ottawa Institute of Systems Biology, Carleton University, Ottawa, ON, Canada
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Rani R, Raza G, Ashfaq H, Rizwan M, Razzaq MK, Waheed MQ, Shimelis H, Babar AD, Arif M. Genome-wide association study of soybean ( Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits. FRONTIERS IN PLANT SCIENCE 2023; 14:1229495. [PMID: 37636105 PMCID: PMC10450938 DOI: 10.3389/fpls.2023.1229495] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 05/30/2023] [Accepted: 07/25/2023] [Indexed: 08/29/2023]
Abstract
Soybean (Glycine max [L.] Merr.) is one of the most significant crops in the world in terms of oil and protein. Owing to the rising demand for soybean products, there is an increasing need for improved varieties for more productive farming. However, complex correlation patterns among quantitative traits along with genetic interactions pose a challenge for soybean breeding. Association studies play an important role in the identification of accession with useful alleles by locating genomic sites associated with the phenotype in germplasm collections. In the present study, a genome-wide association study was carried out for seven agronomic and yield-related traits. A field experiment was conducted in 2015/2016 at two locations that include 155 diverse soybean germplasm. These germplasms were genotyped using SoySNP50K Illumina Infinium Bead-Chip. A total of 51 markers were identified for node number, plant height, pods per plant, seeds per plant, seed weight per plant, hundred-grain weight, and total yield using a multi-locus linear mixed model (MLMM) in FarmCPU. Among these significant SNPs, 18 were putative novel QTNs, while 33 co-localized with previously reported QTLs. A total of 2,356 genes were found in 250 kb upstream and downstream of significant SNPs, of which 17 genes were functional and the rest were hypothetical proteins. These 17 candidate genes were located in the region of 14 QTNs, of which ss715580365, ss715608427, ss715632502, and ss715620131 are novel QTNs for PH, PPP, SDPP, and TY respectively. Four candidate genes, Glyma.01g199200, Glyma.10g065700, Glyma.18g297900, and Glyma.14g009900, were identified in the vicinity of these novel QTNs, which encode lsd one like 1, Ergosterol biosynthesis ERG4/ERG24 family, HEAT repeat-containing protein, and RbcX2, respectively. Although further experimental validation of these candidate genes is required, several appear to be involved in growth and developmental processes related to the respective agronomic traits when compared with their homologs in Arabidopsis thaliana. This study supports the usefulness of association studies and provides valuable data for functional markers and investigating candidate genes within a diverse germplasm collection in future breeding programs.
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Affiliation(s)
- Reena Rani
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Ghulam Raza
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hamza Ashfaq
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Rizwan
- Plant Breeding and Genetics Division, Nuclear Institute of Agriculture (NIA), Tando Jam, Pakistan
| | - Muhammad Khuram Razzaq
- Soybean Research Institute, National Center for Soybean Improvement, Nanjing Agricultural University, Nanjing, China
| | - Muhammad Qandeel Waheed
- Plant Breeding and Genetics Division, Nuclear Institute for Agriculture and Biology (NIAB), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Hussein Shimelis
- School of Agricultural, Earth and Environmental Sciences, African Centre for Crop Improvement, University of KwaZulu-Natal, Pietermaritzburg, South Africa
| | - Allah Ditta Babar
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
| | - Muhammad Arif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College Pakistan Institute of Engineering and Applied Sciences (PIEAS), Faisalabad, Pakistan
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Ahn E, Botkin J, Curtin SJ, Zsögön A. Ideotype breeding and genome engineering for legume crop improvement. Curr Opin Biotechnol 2023; 82:102961. [PMID: 37331239 DOI: 10.1016/j.copbio.2023.102961] [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: 10/10/2022] [Revised: 12/20/2022] [Accepted: 05/22/2023] [Indexed: 06/20/2023]
Abstract
Ideotype breeding is a strategy whereby traits are modeled a priori and then introduced into a model or crop species to assess their impact on yield. Thus, knowledge about the connection between genotype and phenotype is required for ideotype breeding to be deployed successfully. The growing understanding of the genetic basis of yield-related traits, combined with increasingly efficient genome engineering tools, improved transformation efficiency, and high-throughput genotyping of regenerants paves the way for the widespread adoption of ideotype breeding as a complement to conventional breeding. We briefly discuss how ideotype breeding, coupled with such state-of-the-art biotechnological tools, could contribute to knowledge-based legume breeding and accelerate yield gains to ensure food security in the coming decades.
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Affiliation(s)
- Ezekiel Ahn
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA
| | - Jacob Botkin
- Department of Plant Pathology, University of Minnesota, St. Paul, MN 55108, USA
| | - Shaun J Curtin
- United States Department of Agriculture, Plant Science Research Unit, St Paul, MN 55108, USA; Department of Agronomy and Plant Genetics, University of Minnesota, St. Paul, MN 55108, USA; Center for Plant Precision Genomics, University of Minnesota, St. Paul, MN 55108, USA; Center for Genome Engineering, University of Minnesota, St. Paul, MN 55108, USA
| | - Agustin Zsögön
- Departamento de Biologia Vegetal, Universidade Federal de Viçosa, Viçosa 36570-900, MG, Brazil.
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Lukanda MM, Dramadri IO, Adjei EA, Badji A, Arusei P, Gitonga HW, Wasswa P, Edema R, Ochwo-Ssemakula M, Tukamuhabwa P, Muthuri HM, Tusiime G. Genome-Wide Association Analysis for Resistance to Coniothyrium glycines Causing Red Leaf Blotch Disease in Soybean. Genes (Basel) 2023; 14:1271. [PMID: 37372451 DOI: 10.3390/genes14061271] [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: 03/12/2023] [Revised: 06/06/2023] [Accepted: 06/08/2023] [Indexed: 06/29/2023] Open
Abstract
Soybean is a high oil and protein-rich legume with several production constraints. Globally, several fungi, viruses, nematodes, and bacteria cause significant yield losses in soybean. Coniothyrium glycines (CG), the causal pathogen for red leaf blotch disease, is the least researched and causes severe damage to soybean. The identification of resistant soybean genotypes and mapping of genomic regions associated with resistance to CG is critical for developing improved cultivars for sustainable soybean production. This study used single nucleotide polymorphism (SNP) markers generated from a Diversity Arrays Technology (DArT) platform to conduct a genome-wide association (GWAS) analysis of resistance to CG using 279 soybean genotypes grown in three environments. A total of 6395 SNPs was used to perform the GWAS applying a multilocus model Fixed and random model Circulating Probability Unification (FarmCPU) with correction of the population structure and a statistical test p-value threshold of 5%. A total of 19 significant marker-trait associations for resistance to CG were identified on chromosomes 1, 5, 6, 9, 10, 12, 13, 15, 16, 17, 19, and 20. Approximately 113 putative genes associated with significant markers for resistance to red leaf blotch disease were identified across soybean genome. Positional candidate genes associated with significant SNP loci-encoding proteins involved in plant defense responses and that could be associated with soybean defenses against CG infection were identified. The results of this study provide valuable insight for further dissection of the genetic architecture of resistance to CG in soybean. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving resistance traits in soybean.
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Affiliation(s)
- Musondolya Mathe Lukanda
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Faculté des Sciences Agronomiques, Université Catholique du Graben, Butembo P.O. Box 29, Democratic Republic of the Congo
| | - Isaac Onziga Dramadri
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Emmanuel Amponsah Adjei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Council for Scientific and Industrial Research-Savanna Agricultural Research Institute, Tamale P.O. Box TL 52, Ghana
| | - Arfang Badji
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Perpetua Arusei
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
- Department of Biological Sciences, Moi University, Eldoret P.O. Box 3900-30100, Kenya
| | - Hellen Wairimu Gitonga
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Peter Wasswa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Richard Edema
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
- Makerere Regional Center for Crop Improvement (MaRCCI), Makerere University, Kampala P.O. Box 7062, Uganda
| | - Mildred Ochwo-Ssemakula
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Phinehas Tukamuhabwa
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
| | - Harun Murithi Muthuri
- Agricultural Research Service Research Participation Program, Oak Ridge Institute for Science and Education, Oak Ridge, TN 37831, USA
- International Institute of Tropical Agriculture (IITA), ILRI, Nairobi P.O. Box 30709-00100, Kenya
| | - Geoffrey Tusiime
- Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere University, Kampala P.O. Box 7062, Uganda
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Yadav AK, Singh CK, Kalia RK, Mittal S, Wankhede DP, Kakani RK, Ujjainwal S, Saroha A, Nathawat NS, Rani R, Panchariya P, Choudhary M, Solanki K, Chaturvedi KK, Archak S, Singh K, Singh GP, Singh AK. Genetic diversity, population structure, and genome-wide association study for the flowering trait in a diverse panel of 428 moth bean (Vigna aconitifolia) accessions using genotyping by sequencing. BMC PLANT BIOLOGY 2023; 23:228. [PMID: 37120525 PMCID: PMC10148550 DOI: 10.1186/s12870-023-04215-w] [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: 02/01/2023] [Accepted: 04/05/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Moth bean (Vigna aconitifolia) is an underutilized, protein-rich legume that is grown in arid and semi-arid areas of south Asia and is highly resistant to abiotic stresses such as heat and drought. Despite its economic importance, the crop remains unexplored at the genomic level for genetic diversity and trait mapping studies. To date, there is no report of SNP marker discovery and association mapping of any trait in this crop. Therefore, this study aimed to dissect the genetic diversity, population structure and marker-trait association for the flowering trait in a diversity panel of 428 moth bean accessions using genotyping by sequencing (GBS) approach. RESULTS A total of 9078 high-quality single nucleotide polymorphisms (SNPs) were discovered by genotyping of 428 moth bean accessions. Model-based structure analysis and PCA grouped the moth bean accessions into two subpopulations. Cluster analysis revealed accessions belonging to the Northwestern region of India had higher variability than accessions from the other regions suggesting that this region represents its center of diversity. AMOVA revealed more variations within individuals (74%) and among the individuals (24%) than among the populations (2%). Marker-trait association analysis using seven multi-locus models including mrMLM, FASTmrEMMA FASTmrEMMA, ISIS EM-BLASSO, MLMM, BLINK and FarmCPU revealed 29 potential genomic regions for the trait days to 50% flowering, which were consistently detected in three or more models. Analysis of the allelic effect of the major genomic regions explaining phenotypic variance of more than 10% and those detected in at least 2 environments showed 4 genomic regions with significant phenotypic effect on this trait. Further, we also analyzed genetic relationships among the Vigna species using SNP markers. The genomic localization of moth bean SNPs on genomes of closely related Vigna species demonstrated that maximum numbers of SNPs were getting localized on Vigna mungo. This suggested that the moth bean is most closely related to V. mungo. CONCLUSION Our study shows that the north-western regions of India represent the center of diversity of the moth bean. Further, the study revealed flowering-related genomic regions/candidate genes which can be potentially exploited in breeding programs to develop early-maturity moth bean varieties.
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Affiliation(s)
- Arvind Kumar Yadav
- ICAR- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, Delhi, India
| | - Chandan Kumar Singh
- ICAR- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, Delhi, India
| | - Rajwant K Kalia
- ICAR- Central Arid Zone Research Institute, Jodhpur, Rajasthan, India
| | - Shikha Mittal
- Department of Biotechnology and Bioinformatics, Jaypee University of Information Technology, Solan, Himachal Pradesh, India
| | | | - Rajesh K Kakani
- ICAR- Central Arid Zone Research Institute, Jodhpur, Rajasthan, India
| | - Shraddha Ujjainwal
- ICAR- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, Delhi, India
| | - Ankit Saroha
- ICAR- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, Delhi, India
| | - N S Nathawat
- ICAR- Central Arid Zone Research Institute, Regional Research Station, Bikaner, Rajasthan, India
| | - Reena Rani
- ICAR- Central Arid Zone Research Institute, Jodhpur, Rajasthan, India
| | - Pooja Panchariya
- ICAR- Central Arid Zone Research Institute, Jodhpur, Rajasthan, India
| | - Manoj Choudhary
- ICAR- Central Arid Zone Research Institute, Jodhpur, Rajasthan, India
| | - Kantilal Solanki
- ICAR- Central Arid Zone Research Institute, Jodhpur, Rajasthan, India
| | - K K Chaturvedi
- ICAR- Indian Agricultural Statistics Research Institute, New Delhi, Delhi, India
| | - Sunil Archak
- ICAR- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, Delhi, India
| | - Kuldeep Singh
- ICAR- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, Delhi, India
- International Crops Research Institute for the Semi-Arid Tropics, Hyderabad, Telangana, India
| | | | - Amit Kumar Singh
- ICAR- National Bureau of Plant Genetic Resources, Pusa Campus, New Delhi, Delhi, India.
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Liyanage DK, Torkamaneh D, Belzile F, Balasubramanian P, Hill B, Thilakarathna MS. The Genotypic Variability among Short-Season Soybean Cultivars for Nitrogen Fixation under Drought Stress. PLANTS (BASEL, SWITZERLAND) 2023; 12:1004. [PMID: 36903865 PMCID: PMC10005650 DOI: 10.3390/plants12051004] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/26/2023] [Revised: 02/16/2023] [Accepted: 02/20/2023] [Indexed: 06/18/2023]
Abstract
Soybean fixes atmospheric nitrogen through the symbiotic rhizobia bacteria that inhabit root nodules. Drought stress negatively affect symbiotic nitrogen fixation (SNF) in soybean. The main objective of this study was to identify allelic variations associated with SNF in short-season Canadian soybean varieties under drought stress. A diversity panel of 103 early-maturity Canadian soybean varieties was evaluated under greenhouse conditions to determine SNF-related traits under drought stress. Drought was imposed after three weeks of plant growth, where plants were maintained at 30% field capacity (FC) (drought) and 80% FC (well-watered) until seed maturity. Under drought stress, soybean plants had lower seed yield, yield components, seed nitrogen content, % nitrogen derived from the atmosphere (%Ndfa), and total seed nitrogen fixed compared to those under well-watered conditions. Significant genotypic variability among soybean varieties was found for yield, yield parameters, and nitrogen fixation traits. A genome-wide association study (GWAS) was conducted using 2.16 M single nucleotide single nucleotide polymorphisms (SNPs) for different yield and nitrogen fixation related parameters for 30% FC and their relative performance (30% FC/80% FC). In total, five quantitative trait locus (QTL) regions, including candidate genes, were detected as significantly associated with %Ndfa under drought stress and relative performance. These genes can potentially aid in future breeding efforts to develop drought-resistant soybean varieties.
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Affiliation(s)
- Dilrukshi Kombala Liyanage
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
| | - Davoud Torkamaneh
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - François Belzile
- Département de Phytologie, Université Laval, Québec City, QC G1V 0A6, Canada
- Institut de Biologie Intégrative et des Systèmes (IBIS), Université Laval, Québec City, QC G1V 0A6, Canada
| | - Parthiba Balasubramanian
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Brett Hill
- Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre, Lethbridge, AB T1J 4B1, Canada
| | - Malinda S. Thilakarathna
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB T6G 2P5, Canada
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