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Journal of Integrative Agriculture  2024, Vol. 23 Issue (5): 1468-1480    DOI: 10.1016/j.jia.2023.06.030
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Genome-wide association study of grain micronutrient concentrations in bread wheat

Yongchao Hao1, Fanmei Kong2, Lili Wang3, Yu Zhao1, Mengyao Li1, Naixiu Che1, Shuang Li2, Min Wang2, Ming Hao4, Xiaocun Zhang2#, Yan Zhao1# 

1 State Key Laboratory of Crop Biology/College of Agronomy, Shandong Agricultural University, Tai’an 271018, China

2 College of Resources and Environment, Shandong Agricultural University, Tai’an 271018, China

3 Jining Liangshan Ecological Environment Affairs Center, Jining 272100, China

4 College of Forestry, Shandong Agricultural University, Tai’an 271018, China

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摘要  

小麦(Triticum aestivum)是全球主要的粮食作物。对重要营养特征的遗传解剖对于小麦的生物强化以满足世界人口不断增长的营养需求至关重要。本研究利用55K芯片阵列的45298个单核苷酸多态性(SNP)标记对768个小麦品种进行了全基因组关联分析(GWAS),在3个环境下检测到8个性状的154个数量性状位点(QTL)。在不同环境或性状下重复检测到3QTLqMn-3B.1qFe-3B.4qSe-3B.1 / qFe-3B.6),并基于连锁不平衡衰减和显著SNPp值进行了后续分析。在三个QTL区域中的显著性SNP形成了qMn-3B.1的六个单倍型,qFe-3B.4的三个单倍型和qSe-3B.1 / qFe-3B.6的三个单倍型。表型分析揭示了单倍型之间的显著差异。这些结果表明,在landrace小麦驯化为现代栽培小麦的过程中,几种营养元素的浓度发生了变化。根据QTL区间,我们确定了15个高置信基因,其中8个在不同组织和/或发育阶段中稳定表达。根据GO分析,推测qMn-3B.1中的TraesCS3B02G046100qSe-3B.1 / qFe-3B.6中的TraesCS3B02G199500与金属离子相互作用。属于qSe-3B.1 / qFe-3B.6TraesCS3B02G199000被确定为WRKY基因家族的成员。总的来说,本研究提供了几个可靠的QTL,可能会显著影响小麦谷物中营养元素的浓度,并且这些信息将有助于育种出具有改善谷物性质的小麦品种。



Abstract  

Bread wheat (Triticum aestivum) is a staple food crop worldwide.  The genetic dissection of important nutrient traits is essential for the biofortification of wheat to meet the nutritional needs of the world’s growing population.  Here, 45,298 single-nucleotide polymorphisms (SNPs) from 55K chip arrays were used to genotype a panel of 768 wheat cultivars, and a total of 154 quantitative trait loci (QTLs) were detected for eight traits under three environments by genome-wide association study (GWAS).  Three QTLs (qMn-3B.1, qFe-3B.4, and qSe-3B.1/qFe-3B.6) detected repeatedly under different environments or traits were subjected to subsequent analyses based on linkage disequilibrium decay and the P-values of significant SNPs.  Significant SNPs in the three QTL regions formed six haplotypes for qMn-3B.1, three haplotypes for qFe-3B.4, and three haplotypes for qSe-3B.1/qFe-3B.6.  Phenotypic analysis revealed significant differences among haplotypes.  These results indicated that the concentrations of several nutrient elements have been modified during the domestication of landraces to modern wheat.  Based on the QTL regions, we identified 15 high-confidence genes, eight of which were stably expressed in different tissues and/or developmental stages.  TraesCS3B02G046100 in qMn-3B.1 and TraesCS3B02G199500 in qSe-3B.1/qFe-3B.6 were both inferred to interact with metal ions according to the Gene Ontology (GO) analysis.  TraesCS3B02G199000, which belongs to qSe-3B.1/qFe-3B.6, was determined to be a member of the WRKY gene family.  Overall, this study provides several reliable QTLs that may significantly affect the concentrations of nutrient elements in wheat grain, and this information will facilitate the breeding of wheat cultivars with improved grain properties.

Keywords:  bread wheat        nutritional element        GWAS        domestication        haplotype   
Online: 27 February 2023   Accepted: 07 June 2023
Fund: This work was supported by grants from the Natural Science Foundation of Shandong Province, China (ZR2020MC096, ZR2021ZD31, and ZR2020MC151) and the Agricultural Variety Improvement Project of Shandong Province, China (2021LZGC013 and 2022LZGC002).

About author:  Yongchao Hao, E-mail: 2021010018@sdau.edu.cn; #Correspondence Yan Zhao, E-mail: yzhao1216@sdau.edu.cn; Xiaocun Zhang, E-mail: xczhang@sdau.edu.cn

Cite this article: 

Yongchao Hao, Fanmei Kong, Lili Wang, Yu Zhao, Mengyao Li, Naixiu Che, Shuang Li, Min Wang, Ming Hao, Xiaocun Zhang, Yan Zhao. 2024.

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