| 小麦苗期根系性状的全基因组关联分析与优异位点挖掘 |
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| 引用本文： | 王脉,董清峰,高珅奥,刘德政,卢山,乔朋放,陈亮,胡银岗.小麦苗期根系性状的全基因组关联分析与优异位点挖掘[J].中国农业科学,2023,56(5):801-820. |
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| 作者姓名： | 王脉 董清峰 高珅奥 刘德政 卢山 乔朋放 陈亮 胡银岗 |
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| 作者单位： | 1. 西北农林科技大学农学院/旱区作物逆境生物学国家重点实验室;2. 中国旱区节水农业研究院 |
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| 基金项目： | 陕西省重点研发计划(2021KWZ-23) |
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| 摘 要： | 【目的】植物根系对水分及营养的获取、作物的生长发育和产量的形成至关重要。挖掘小麦苗期根系性状显著关联的SNP位点，预测相关候选基因，为解析小麦根系建成遗传机制及选育具有优良根系构型的小麦品种奠定基础。【方法】以189份小麦品种组成的自然群体为供试材料，调查2种培养条件（霍格兰营养液和去离子水）下培育21 d的苗期根系总长度（TRL）、根系总表面积（TRA）、根系总体积（TRV）、根系平均直径（ARD）及根系干重（RDW）等5个根系性状，试验进行2次重复，同时结合小麦660K SNP芯片的分型结果进行全基因组关联分析（genome-wide association study,GWAS）。此外，通过序列比对、结构域分析和注释信息预测候选基因，并采用竞争性等位基因特异性PCR(kompetitive allele specific PCR,KASP)技术开发根系性状的分子标记。【结果】霍格兰营养液培养条件下的根系性状变异范围较大，根系整体粗短；而去离子水条件下的根系细长、侧根较多。选用贝叶斯信息与连锁不平衡迭代嵌套式模型（BLINK）、压缩式混合线性模型（CMLM）、固定随机循环概率模型（...
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| 关 键 词： | 小麦 根系性状 全基因组关联分析 共定位SNP位点 KASP标记 候选基因 |
| 收稿时间： | 2022-10-06 |
Genome-Wide Association Studies and Mining for Favorable Loci of Root Traits at Seedling Stage in Wheat |
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| WANG Mai,DONG QingFeng,GAO ShenAo,LIU DeZheng,LU Shan,QIAO PengFang,CHEN Liang,HU YinGang.Genome-Wide Association Studies and Mining for Favorable Loci of Root Traits at Seedling Stage in Wheat[J].Scientia Agricultura Sinica,2023,56(5):801-820. |
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| Authors: | WANG Mai DONG QingFeng GAO ShenAo LIU DeZheng LU Shan QIAO PengFang CHEN Liang HU YinGang |
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| Abstract: | 【Objective】Plant roots are critical for water and nutrient acquisition, crop growth and development as well as yield formation. Exploring SNP loci significantly associated with root traits in wheat at seedling stage and mining candidate genes, will lay a foundation for understanding the genetic mechanism of wheat root system architecture and breeding wheat elite varieties with better root architecture.【Method】In this study, 189 diverse wheat cultivars were assembled as an association-mapping panel, five root traits including total root length (TRL), total root area (TRA), total root volume (TRV), average root diameter (ARD) and root dry weight (RDW) were investigated by growing in two culture conditions (Hoagland nutrient solution and pure water), and the experiments were repeated twice. Then, genome-wide association studies (GWAS) were performed for the five root traits with genotypic data derived from Wheat 660K SNP Array. Candidate genes were predicted by sequence alignment, domain analysis, and annotation information. Futhermore, kompetitive allele specific PCR (KASP) markers were developed for root traits. 【Result】The root traits varied greatly among the 189 cultivars, and the roots were thick and short cultured under Hoagland nutrient solution, while slender seminal roots and more lateral roots were observed under pure water. A total of 95 QTLs significantly associated with root traits cultured in two conditions (P<10-3) were identified by genome-wide association studies with four models of BLINK (bayesian-information and linkage-disequilibrium iteratively nested keyway), CMLM (compressed mixed linear model), FarmCPU (fixed and random model circulating probability unification) and MLM (mixed linear model). Among them, 18 QTLs were detected in both culture conditions and distributed on chromosomes of 7A, 1B, 2B, 3B, 7B, 1D, 2D, and 3D, which explained 8.68%-14.07% of phenotypic variation. Of those significant loci, 4 QTLs were similar or consistent with that reported previously, and the rest were novel ones. Haplotype analysis conducted for co-localization QTLs of 10 SNPs revealed significant differences in root traits between the two haplotypes of wheat cultivars. Based on these SNPs, KASP markers XNR7143 and XNR3707 were developed for total root volume and root dry weight, respectively. In addition, 12 candidate genes possibly regulating root development were found by mining the genes within the interval of co-localization significant SNPs. Of them, TraesCS7A02G160600, encoding 3-oxoacyl-acyl-carrier-protein] synthase, is involved in the synthesis of root fatty acids; TraesCS1B02G401800, encoding syntaxin, plays an important role in plant tropism; TraesCS7B02G417900, encoding aldehyde oxidase, contributes to the synthesis of abscisic acid and regulation of crop root development. 【Conclusion】The root traits of wheat varied significantly among the wheat genotypes. Genome-wide association studies detected 18 significant QTLs linked with root traits simultaneously in two culture conditions, two KASP markers were developed for root traits, and 12 candidate genes related to root development were screened, which might provide reference for understanding the regulation mechanism of wheat root traits and molecular marker-assisted breeding for wheat improvement. |
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| Keywords: | wheat root traits genome-wide association study co-localization SNPs KASP (kompetitive allele specific PCR) markers candidate genes |
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