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Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits

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 tr...

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Autores principales: Rani, Reena, Raza, Ghulam, Ashfaq, Hamza, Rizwan, Muhammad, Razzaq, Muhammad Khuram, Waheed, Muhammad Qandeel, Shimelis, Hussein, Babar, Allah Ditta, Arif, Muhammad
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Frontiers Media S.A. 2023
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10450938/
https://www.ncbi.nlm.nih.gov/pubmed/37636105
http://dx.doi.org/10.3389/fpls.2023.1229495
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author Rani, Reena
Raza, Ghulam
Ashfaq, Hamza
Rizwan, Muhammad
Razzaq, Muhammad Khuram
Waheed, Muhammad Qandeel
Shimelis, Hussein
Babar, Allah Ditta
Arif, Muhammad
author_facet Rani, Reena
Raza, Ghulam
Ashfaq, Hamza
Rizwan, Muhammad
Razzaq, Muhammad Khuram
Waheed, Muhammad Qandeel
Shimelis, Hussein
Babar, Allah Ditta
Arif, Muhammad
author_sort Rani, Reena
collection PubMed
description 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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spelling pubmed-104509382023-08-26 Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits Rani, Reena Raza, Ghulam Ashfaq, Hamza Rizwan, Muhammad Razzaq, Muhammad Khuram Waheed, Muhammad Qandeel Shimelis, Hussein Babar, Allah Ditta Arif, Muhammad Front Plant Sci Plant Science 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. Frontiers Media S.A. 2023-08-11 /pmc/articles/PMC10450938/ /pubmed/37636105 http://dx.doi.org/10.3389/fpls.2023.1229495 Text en Copyright © 2023 Rani, Raza, Ashfaq, Rizwan, Razzaq, Waheed, Shimelis, Babar and Arif https://creativecommons.org/licenses/by/4.0/This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
spellingShingle Plant Science
Rani, Reena
Raza, Ghulam
Ashfaq, Hamza
Rizwan, Muhammad
Razzaq, Muhammad Khuram
Waheed, Muhammad Qandeel
Shimelis, Hussein
Babar, Allah Ditta
Arif, Muhammad
Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits
title Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits
title_full Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits
title_fullStr Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits
title_full_unstemmed Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits
title_short Genome-wide association study of soybean (Glycine max [L.] Merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits
title_sort genome-wide association study of soybean (glycine max [l.] merr.) germplasm for dissecting the quantitative trait nucleotides and candidate genes underlying yield-related traits
topic Plant Science
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC10450938/
https://www.ncbi.nlm.nih.gov/pubmed/37636105
http://dx.doi.org/10.3389/fpls.2023.1229495
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