Genome-Wide Association Study and Candidate Gene Prediction of Arsenic Content in Wheat Grains

SHI Xia; SUN Dongling; CHANG Yang; LI Wenxu; DAI Ziju; ZHOU Zhengfu; WU Zhengqing; LEI Zhensheng

doi:10.15933/j.cnki.1004-3268.2025.10.003

Abstract：In order to provide a theoretical basis for the arsenic(As)biofortification breeding in wheat grains,an association population comprising 207 wheat varieties(lines)was used as material,genotyping was done by wheat 660K SNP array,combining with phenotypic data under different environments and best linear unbiased prediction(BLUP)value,a genome-wide association study(GWAS)was conducted on As content in wheat grains,genetic loci were identified,and candidate genes associated with As content in wheat grains were predicted.The haplotype analysis and linear regression analysis methods were used to analyze the superior and inferior haplotypes of stable SNP loci associated with As content in wheat grains and their aggregated effect.The results showed that there were obvious variation in grain As content under multiple environments,and the grain As content exhibited a normal distribution.By using a mixed linear model(MLM),a total of 67 SNPs were identified to be significantly associated with grain As content at the genome-wide level.Among these,six SNPs located on chromosomes 1A,2A,2D,3B,and 6B(AX-110393422,AX-110370420,AX-109339465,AX-109455432,AX-109359598,AX-111655266)were consistently detected under multiple environments,and were considered as stable quantitative trait nucleotides(QTNs).Additionally,a SNP hotspot was identified at the end of chromosome 6B.The peak SNP AX-111655266 was detected under all environments,which exhibited the strongest association with grain As content,explained the phenotypic variation of 15.14％—21.53％,and was a major-effect QTN.Based on public wheat expression profile data and differential expression analysis of candidate genes at 20 days post-anthesis in the association population,combined with physical location and functional annotation information,candidate genes were predicted.The candidate gene TraesCS6B02G418600,tightly linked to SNP AX-111655266,encoding a phosphate transporter PHO 1-like protein,which may be involved in transmembrane transport and signal transduction of As,was a major-effect gene controlling grain As content in wheat.The candidate genes for the other five SNP loci were TraesCS1A02G346700,TraesCS2A02G106800,TraesCS2D02G171500,TraesCS3B02G131500,and TraesCS3B02G252500,encoding F-box protein,thiamine pyrophosphokinase 1,GEM-like protein 1,ubiquitin-conjugating enzyme E2-like protein,and protein phosphatase 2C family protein,respectively.They were candidate genes involved in regulating As accumulation in wheat grains.The grain As content in the superior haplotype group was significantly lower than that in the inferior haplotype group under all environments.Furthermore,as the number of superior haplotypes increased,the grain As content gradually decreased,demonstrating a clear additive effect.