Genome-Wide Quantitative Trait Locus Mapping Identifies Multiple Major Loci for Brittle Rachis and Threshability in Tibetan Semi-Wild Wheat (Triticum aestivum ssp. tibetanum Shao)

Tibetan semi-wild wheat (Triticum aestivum ssp. tibetanum Shao) is a semi-wild hexaploid wheat resource that is only naturally distributed in the Qinghai-Tibet Plateau. Brittle rachis and hard threshing are two important characters of Tibetan semi-wild wheat. A whole-genome linkage map of T. aestivum ssp. tibetanum was constructed using a recombinant inbred line population (Q1028×ZM9023) with 186 lines, 564 diversity array technology markers, and 117 simple sequence repeat markers. Phenotypic data on brittle rachis and threshability, as two quantitative traits, were evaluated on the basis of the number of average spike rachis fragments per spike and percent threshability in 2012 and 2013, respectively. Quantitative trait locus (QTL) mapping performed using inclusive composite interval mapping analysis clearly identified four QTLs for brittle rachis and three QTLs for threshability. However, three loci on 2DS, 2DL, and 5AL showed pleiotropism for brittle rachis and threshability; they respectively explained 5.3%, 18.6%, and 18.6% of phenotypic variation for brittle rachis and 17.4%, 13.2%, and 35.2% of phenotypic variation for threshability. A locus on 3DS showed an independent effect on brittle rachis, which explained 38.7% of the phenotypic variation. The loci on 2DS and 3DS probably represented the effect of Tg and Br1, respectively. The locus on 5AL was in very close proximity to the Q gene, but was different from the predicted q in Tibetan semi-wild wheat. To our knowledge, the locus on 2DL has never been reported in common wheat but was prominent in T. aestivum ssp. tibetanum accession Q1028. It remarkably interacted with the locus on 5AL to affect brittle rachis. Several major loci for brittle rachis and threshability were identified in Tibetan semi-wild wheat, improving the understanding of these two characters and suggesting the occurrence of special evolution in Tibetan semi-wild wheat.

西藏半野生小麦（Triticum aestivum ssp. tibetanum Shao）是仅自然分布于青藏高原的半野生六倍体小麦种质资源。穗轴易碎与脱粒困难是其两个重要性状。本研究以包含186个株系的重组自交系（recombinant inbred line）群体（Q1028×ZM9023）为材料，结合564个多样性芯片技术（Diversity Array Technology, DArT）标记与117个简单序列重复（Simple Sequence Repeat, SSR）标记，构建了西藏半野生小麦的全基因组连锁图谱。将穗轴易碎性与脱粒性作为两个数量性状，分别于2012年和2013年以每穗平均穗轴断片数和脱粒率为指标开展表型数据调查。采用完备复合区间作图法进行数量性状位点（Quantitative trait locus, QTL）定位，共检测到4个控制穗轴易碎性的QTL以及3个控制脱粒性的QTL。研究发现，位于2DS、2DL与5AL染色体臂上的3个位点同时对穗轴易碎性和脱粒性具有多效性，它们分别解释了5.3%、18.6%和18.6%的穗轴易碎性表型变异，以及17.4%、13.2%和35.2%的脱粒性表型变异。位于3DS染色体臂上的1个位点仅对穗轴易碎性起作用，其解释的表型变异率达38.7%。2DS和3DS染色体臂上的位点可能分别对应Tg基因与Br1基因的作用。5AL染色体臂上的位点与Q基因紧密连锁，但不同于西藏半野生小麦中已预测的q位点。据我们所知，普通小麦中尚未报道过2DL染色体臂上的该位点，但该位点在西藏半野生小麦材料Q1028中显著存在，且与5AL染色体臂上的位点存在显著互作，共同调控穗轴易碎性。本研究在西藏半野生小麦中鉴定到多个控制穗轴易碎性与脱粒性的主效位点，加深了对这两个性状的认知，同时提示西藏半野生小麦存在特殊的进化历程。