Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.)

Javaid Akhter Bhat; Kehinde Adewole Adeboye; Showkat Ahmad Ganie; Rutwik Barmukh; Dezhou Hu; Rajeev K. Varshney; Deyue Yu

doi:10.3389/fgene.2022.953833

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Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.)

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Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.)

Javaid Akhter Bhat, Kehinde Adewole Adeboye, Showkat Ahmad Ganie, Rutwik Barmukh, Dezhou Hu, Rajeev K. Varshney and Deyue Yu

Frontiers in genetics, Vol.13, 953833

2022

DOI: https://doi.org/10.3389/fgene.2022.953833

PMID: 36419833

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Abstract

candidate genes

crop improvement

Genetics

GWAS

haplotype-based breeding

legumes

seed yield

Identifying the genetic components underlying yield-related traits in soybean is crucial for improving its production and productivity. Here, 211 soybean genotypes were evaluated across six environments for four yield-related traits, including seed yield per plant (SYP), number of pods per plant number of seeds per plant and 100-seed weight (HSW). Genome-wide association study (GWAS) and genomic prediction (GP) analyses were performed using 12,617 single nucleotide polymorphism markers from NJAU 355K SoySNP Array. A total of 57 SNPs were significantly associated with four traits across six environments and a combined environment using five Genome-wide association study models. Out of these, six significant SNPs were consistently identified in more than three environments using multiple GWAS models. The genomic regions (±670 kb) flanking these six consistent SNPs were considered stable QTL regions. Gene annotation and in silico expression analysis revealed 15 putative genes underlying the stable QTLs that might regulate soybean yield. Haplotype analysis using six significant SNPs revealed various allelic combinations regulating diverse phenotypes for the studied traits. Furthermore, the GP analysis revealed that accurate breeding values for the studied soybean traits is attainable at an earlier generation. Our study paved the way for increasing soybean yield performance within a short breeding cycle.

Details

Title: Genome-wide association study, haplotype analysis, and genomic prediction reveal the genetic basis of yield-related traits in soybean (Glycine max L.)
Authors/Creators: Javaid Akhter Bhat - Nanjing Agricultural University
Kehinde Adewole Adeboye - , , , , , , , , , , , , , , , , , , , , , , ,
Showkat Ahmad Ganie - Royal Holloway University of London
Rutwik Barmukh - International Crops Research Institute for the Semi-Arid Tropics
Dezhou Hu - Nanjing Agricultural University
Rajeev K. Varshney - Murdoch University, Food Futures Institute
Deyue Yu - Nanjing Agricultural University
Publication Details: Frontiers in genetics, Vol.13, 953833
Publisher: Frontiers Media S.A
Grant note: 32090065 / 2017YFE0111000 / 727312 /
Identifiers: 991005585967907891
Murdoch Affiliation: Centre for Crop and Food Innovation; State Agricultural Biotechnology Centre
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Genetics & Heredity
ESI research areas: Molecular Biology & Genetics