Genome-wide association mapping of grain yield in a diverse collection of spring wheat (Triticum aestivum L.) evaluated in southern Australia

Wheat landraces, wild relatives and other ‘exotic’ accessions are important sources of new favorable alleles. The use of those exotic alleles is facilitated by having access to information on the association of specific genomic regions with desirable traits. Here, we conducted a genome-wide association study (GWAS) using a wheat panel that includes landraces, synthetic hexaploids and other exotic wheat accessions to identify loci that contribute to increases in grain yield in southern Australia. The 568 accessions were grown in the field during the 2014 and 2015 seasons and measured for plant height, maturity, spike length, spike number, grain yield, plant biomass, HI and TGW. We used the 90K SNP array and two GWAS approaches (GAPIT and QTCAT) to identify loci associated with the different traits. We identified 17 loci with GAPIT and 25 with QTCAT. Ten of these loci were associated with known genes that are routinely employed in marker assisted selection such as Ppd-D1 for maturity and Rht-D1 for plant height and seven of those were detected with both methods. We identified one locus for yield per se in 2014 on chromosome 6B with QTCAT and three in 2015, on chromosomes 4B and 5A with GAPIT and 6B with QTCAT. The 6B loci corresponded to the same region in both years. The favorable haplotypes for yield at the 5A and 6B loci are widespread in Australian accessions with 112 out of 153 carrying the favorable haplotype at the 5A locus and 136 out of 146 carrying the favorable haplotype at the 6A locus, while the favorable haplotype at 4B is only present in 65 out of 149 Australian accessions. The low number of yield QTL in our study corroborate with other GWAS for yield in wheat, where most of the identified loci have very small effects.

小麦地方品种、野生近缘种及其他‘外来’种质资源是新型优良等位基因的重要供体来源。获取特定基因组区域与优良性状间的关联信息，可极大推动这类外来等位基因的研究与利用。本研究以涵盖地方品种、人工合成六倍体小麦及其他外来小麦种质的小麦关联群体为材料，开展全基因组关联分析（Genome-Wide Association Study, GWAS），旨在鉴定澳大利亚南部地区小麦籽粒产量提升相关的遗传位点。
本研究于2014与2015年在田间种植568份小麦种质，并对株高、成熟期、穗长、穗数、籽粒产量、植株生物量、收获指数（Harvest Index, HI）及千粒重（Thousand Grain Weight, TGW）开展表型鉴定。本研究采用90K SNP芯片进行基因分型，并结合两种GWAS分析工具（GAPIT与QTCAT）开展性状关联位点的挖掘。最终通过GAPIT鉴定到17个关联位点，QTCAT则鉴定到25个；其中10个位点与常规标记辅助选择所使用的已知功能基因共定位，例如调控抽穗成熟期的Ppd-D1基因与调控株高的Rht-D1基因，且有7个位点可被两种分析工具同时检测到。
针对籽粒产量本身的性状，本研究通过QTCAT在2014年的6B染色体上鉴定到1个关联位点；2015年则分别通过GAPIT在4B、5A染色体以及通过QTCAT在6B染色体上鉴定到3个产量关联位点。两年间鉴定到的6B染色体位点处于同一基因组区域。5A与6B位点的产量优良单倍型在澳大利亚本土种质中分布广泛：153份供试澳大利亚种质中有112份携带5A位点的优良单倍型，146份种质中有136份携带6A位点的优良单倍型；而4B位点的优良单倍型仅在149份澳大利亚种质中的65份中存在。
本研究中鉴定到的产量相关数量性状位点（Quantitative Trait Locus, QTL）数量较少，这与其他小麦产量性状GWAS研究结果一致：多数已鉴定的位点遗传效应极小。