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利用通用小麦(Triticum aestivum L.)90K SNP 阵列进行全基因组关联研究,以了解收获前发芽耐性。

Genome-wide association study of pre-harvest sprouting tolerance using a 90K SNP array in common wheat (Triticum aestivum L.).

机构信息

College of Agronomy, Anhui Agricultural University, Key Laboratory of Wheat Biology and Genetic Improvement On Southern Yellow and Huai River Valley, Ministry of Agriculture, Hefei, 230036, Anhui, China.

Institute of Crop Sciences, National Wheat Improvement Center, Chinese Academy of Agricultural Sciences (CAAS), 12 Zhongguancun South Street, Beijing, 100081, China.

出版信息

Theor Appl Genet. 2019 Nov;132(11):2947-2963. doi: 10.1007/s00122-019-03398-x. Epub 2019 Jul 19.

Abstract

Three major loci for pre-harvest sprouting tolerance (PHST) were mapped on chromosomes 1AL, 3BS, and 6BL, and two CAPS and one dCAPS markers were validated. Sixteen lines with favorable alleles and increased PHST were identified. Pre-harvest sprouting (PHS) significantly affects wheat grain yield and quality. In the present study, the PHS tolerance (PHST) of 192 wheat varieties (lines) was evaluated by assessment of field sprouting, seed germination index, and period of dormancy in different environments. A high-density Illumina iSelect 90K SNP array was used to genotype the panel. A genome-wide association study (GWAS) based on single- and multi-locus mixed linear models was used to detect loci for PHST. The single-locus model identified 23 loci for PHST (P < 0.0001) and explained 6.0-18.9% of the phenotypic variance. Twenty loci were consistent with known quantitative trait loci (QTLs). Three single-nucleotide polymorphism markers closely linked with three major loci (Qphs.ahau-1A, Qphs.ahau-3B, and Qphs.ahau-6B) on chromosomes 1AL, 3BS, and 6BL, respectively, were converted to two cleaved amplified polymorphic sequences (CAPS) and one derived-CAPS markers, and validated in 374 wheat varieties (lines). The CAPS marker EX06323 for Qphs.ahau-6B co-segregated with a novel major QTL underlying PHST in a recombinant inbred line population raised from the cross Jing 411 × Wanxianbaimaizi. Linear regression showed a clear dependence of PHST on the number of favorable alleles. Sixteen varieties showing an elevated degree of PHST were identified and harbored more than 16 favorable alleles. The multi-locus model detected 39 marker-trait associations for PHST (P < 0.0001), of which five may be novel. Six loci common to the two models were identified. The combination of the two GWAS methods contributes to efficient dissection of the complex genetic mechanism of PHST.

摘要

三个主要的耐穗发芽位点(PHST)被定位在染色体 1AL、3BS 和 6BL 上,并验证了两个 CAPS 和一个 dCAPS 标记。鉴定出 16 个具有有利等位基因和增加 PHST 的品系。穗发芽(PHS)显著影响小麦籽粒产量和品质。在本研究中,通过评估田间发芽、种子发芽指数和不同环境下的休眠期,对 192 个小麦品种(系)的 PHS 耐性(PHST)进行了评价。使用高密度 Illumina iSelect 90K SNP 芯片对该群体进行了基因型分析。基于单基因座和多基因座混合线性模型的全基因组关联研究(GWAS)用于检测 PHST 的基因座。单基因座模型鉴定出 23 个 PHST 基因座(P < 0.0001),解释了 6.0-18.9%的表型方差。20 个基因座与已知的数量性状基因座(QTL)一致。三个单核苷酸多态性标记与染色体 1AL、3BS 和 6BL 上的三个主要基因座(Qphs.ahau-1A、Qphs.ahau-3B 和 Qphs.ahau-6B)紧密连锁,分别转化为两个切割扩增多态性序列(CAPS)和一个衍生的 CAPS 标记,并在 374 个小麦品种(系)中进行了验证。CAPS 标记 EX06323 与 Jing 411×Wanxianbaimaizi 杂交重组自交系群体中一个新的主要 PHST 基因座 Qphs.ahau-6B 共分离。线性回归表明,PHST 与有利等位基因的数量有明显的依赖关系。鉴定出 16 个具有升高程度 PHST 的品种,并且含有 16 个以上的有利等位基因。多基因座模型检测到 39 个与 PHST 相关的标记-性状关联(P < 0.0001),其中 5 个可能是新的。两个模型共有的 6 个基因座。两种 GWAS 方法的结合有助于有效解析 PHST 的复杂遗传机制。

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