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

doi:10.15933/j.cnki.1004-3268.2025.10.003

Abstract

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 PHO1‐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‐onjugating 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.

Key words: Wheat, As content in grain, Genome‐wide association study, Superior and inferior haplotypes, Pyramid breeding, Candidate gene prediction

摘要： 以包含207个小麦品种（系）的自然群体为材料，利用小麦660K SNP芯片进行基因分型，并结合不同环境下表型数据和最佳线性无偏预测（BLUP）值对小麦籽粒砷（As）含量进行全基因组关联分析（GWAS），鉴定其遗传位点，预测候选基因，并利用单倍型分析、线性回归分析方法对小麦籽粒As含量稳定遗传SNP位点的优势、劣势单倍型及其聚合效应进行分析，为小麦籽粒As生物强化育种提供理论依据。结果表明，小麦自然群体籽粒As含量在多个环境下均存在明显变异，各环境下籽粒As含量均呈正态分布。采用混合线性模型（MLM）在全基因组水平上共鉴定到67个SNP与小麦籽粒As含量显著关联，其中，位于1A、2A、2D、3B、6B染色体上的6个SNP（AX-110393422、AX-110370420、AX-109339465、AX-109455432、AX-109359598、AX-111655266）在多个环境下表现稳定，为稳定遗传数量性状核苷酸位点（QTN）；同时发现在6B染色体末端存在1个SNP热点区域，峰值SNP AX-111655266在所有环境下均被检测到，且与小麦籽粒As含量关联程度最高，可解释表型变异的15.14%~21.53%，为主效QTN。基于小麦表达谱公共数据和自然群体籽粒灌浆20 d的候选基因差异表达分析结果，结合物理位置、基因功能注释等信息进行候选基因预测，发现与SNP AX-111655266 紧密连锁的候选基因TraesCS6B02G418600编码类磷酸转运蛋白PHO1，可能参与As的跨膜运输和信号转导，为控制小麦籽粒As含量的主效基因；其余5个SNP位点的候选基因分别为TraesCS1A02G346700、TraesCS2A02G106800、TraesCS2D02G171500、TraesCS3B02G131500、TraesCS3B02G252500，分别编码F-box蛋白、硫胺素焦磷酸激酶1、类GEM蛋白1、类泛素结合酶E2蛋白、蛋白磷酸酶2C家族蛋白，为控制小麦籽粒As含量的候选基因。6个稳定遗传SNP位点在所有环境下，优势单倍型群体籽粒As含量均极显著低于劣势单倍型群体。此外，随着优势单倍型数量的增加，小麦籽粒As含量逐渐降低，具有明显的加性效应。

关键词: 小麦, 籽粒As含量, 全基因组关联分析, 优势和劣势单倍型, 聚合育种, 候选基因预测

CLC Number:

S512

SHI Xia, SUN Dongling, CHANG Yang, LI Wenxu, DAI Ziju, ZHOU Zhengfu, WU Zhengqing, LEI Zhensheng. Genome‐Wide Association Study and Candidate Gene Prediction of Arsenic Content in Wheat Grains[J]. Journal of Henan Agricultural Sciences, 2025, 54(10): 21-32.

时夏, 孙东玲, 常阳, 李文旭, 代资举, 周正富, 吴政卿, 雷振生. 小麦籽粒砷含量全基因组关联分析及候选基因预测[J]. 河南农业科学, 2025, 54(10): 21-32.

Figures/Tables 10

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