Genome wide association mapping of soybean elite germplasm for spring-season adaptation by using high-density SNP array.
7 affiliations
- 1Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan.
- 2National Seed Research and Training Center, University of Agriculture, Faisalabad, Pakistan.
- 3College of Resources and Environment, Shandong Agricultural University, 61 Daizong Street, Tai'an, Shandong Province, 271000, China.
- 4Department of Plant Breeding and Genetics, University of Agriculture, Faisalabad, Pakistan.
- 5Institute of Horticultural Sciences, University of Agriculture, Faisalabad, Pakistan.
- 6Department of Biotechnology, University of Narowal, Narowal, Pakistan.
- 7Center of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan. [email protected].
Abstract
Soybean (Glycine max L.) is a globally important crop and a major source of edible oil and plant-based protein; however, spring-season cultivation exposes soybean to elevated temperatures during critical reproductive stages, adversely affecting yield and seed quality. A panel of 100 advanced soybean accessions was screened across two variable planting dates of the spring season for two consecutive growing years, 2020 and 2021. Phenotypic data of six yield-related traits, i.e., plant height (PH), number of pods per plant (Pods), number of seeds per plant (Seeds), 100-seed weight (HSW), yield per plant (YPP), and days to maturity (DM) were collected. A genome-wide association study (GWAS) was conducted using the Fixed and Random Model Circulating Probability Unification (Farm-CPU) method by using 42,449 high-quality single-nucleotide polymorphisms (SNPs) from the SoySNP50K array. A total of 77 significant marker trait associations (MTAs) were identified. The highest number of MTAs is linked with plant height, and the lowest number of MTAs is linked with yield per plant. Genome-wide means of major allele frequency (MAF), genetic diversity (GD), and polymorphic information content (PIC) were 0.78, 0.28, and 0.28, respectively. Population structure and phylogenetic tree analysis were used to divide the whole population into two distinct groups. Furthermore, seven SNPs, i.e., ss715582919, ss715588087, ss715588504, ss715592876, ss715599604, ss715599732, and ss715599766, were associated with multiple traits across planting dates. Various clusters of significant SNPs were marked on chromosomes Gm08, Gm10, Gm17, Gm02, Gm12, Gm15, and Gm16 associated with various yield traits. Candidate gene analysis identified genes related to thermotolerance (HSP90, HSFA2), flowering time (FT2a), pod number (NAC29), and carbohydrate transport (SWEET15) within flanking regions of key SNPs. A comprehensive insight into the genetic architecture of soybean yield under spring-season conditions is a prerequisite for the development of climate-resilient soybean genotypes. These findings will contribute to devising future breeding strategies in soybean.
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BibTeX
@article{ghuman2026genome,
title = {{Genome wide association mapping of soybean elite germplasm for spring-season adaptation by using high-density SNP array.}},
author = {Hasham Feroz Ghuman and Madiha Habib and Shabbir Hussain and Zaheer Ahmed and Muhammad Murad and Kiran Hameed and Bilal Ahmed Awan and Muhammad Salman Mubarik and Faisal Saeed Awan},
journal = {BMC plant biology},
year = {2026},
month = aug,
doi = {10.1186/s12870-026-09434-5},
url = {https://europepmc.org/article/MED/42958485},
note = {CC BY-NC-ND},
}
RIS
TY - JOUR
TI - Genome wide association mapping of soybean elite germplasm for spring-season adaptation by using high-density SNP array.
AU - Hasham Feroz Ghuman
AU - Madiha Habib
AU - Shabbir Hussain
AU - Zaheer Ahmed
AU - Muhammad Murad
AU - Kiran Hameed
AU - Bilal Ahmed Awan
AU - Muhammad Salman Mubarik
AU - Faisal Saeed Awan
PY - 2026
DA - 2026/08/01
JO - BMC plant biology
DO - 10.1186/s12870-026-09434-5
UR - https://europepmc.org/article/MED/42958485
AB - Soybean (Glycine max L.) is a globally important crop and a major source of edible oil and plant-based protein; however, spring-season cultivation exposes soybean to elevated temperatures during critical reproductive stages, adversely affecting yield and seed quality. A panel of 100 advanced soybean accessions was screened across two variable planting dates of the spring season for two consecutive growing years, 2020 and 2021. Phenotypic data of six yield-related traits, i.e., plant height (PH), number of pods per plant (Pods), number of seeds per plant (Seeds), 100-seed weight (HSW), yield per plant (YPP), and days to maturity (DM) were collected. A genome-wide association study (GWAS) was conducted using the Fixed and Random Model Circulating Probability Unification (Farm-CPU) method by using 42,449 high-quality single-nucleotide polymorphisms (SNPs) from the SoySNP50K array. A total of 77 significant marker trait associations (MTAs) were identified. The highest number of MTAs is linked with plant height, and the lowest number of MTAs is linked with yield per plant. Genome-wide means of major allele frequency (MAF), genetic diversity (GD), and polymorphic information content (PIC) were 0.78, 0.28, and 0.28, respectively. Population structure and phylogenetic tree analysis were used to divide the whole population into two distinct groups. Furthermore, seven SNPs, i.e., ss715582919, ss715588087, ss715588504, ss715592876, ss715599604, ss715599732, and ss715599766, were associated with multiple traits across planting dates. Various clusters of significant SNPs were marked on chromosomes Gm08, Gm10, Gm17, Gm02, Gm12, Gm15, and Gm16 associated with various yield traits. Candidate gene analysis identified genes related to thermotolerance (HSP90, HSFA2), flowering time (FT2a), pod number (NAC29), and carbohydrate transport (SWEET15) within flanking regions of key SNPs. A comprehensive insight into the genetic architecture of soybean yield under spring-season conditions is a prerequisite for the development of climate-resilient soybean genotypes. These findings will contribute to devising future breeding strategies in soybean.
SN - 1471-2229
ER -