Bulked QTL-Seq identified a major QTL for the awnless trait in spring wheat cultivars in Qinghai, China

The awnless trait is the favorite trait for wheat breeding in Qinghai, China, but the major gene underlying the trait is unknown. This study aimed to analyze a recombinant inbred line (RIL) population containing 112 lines by crossing common wheat varieties GY448 (awnless) and GY115 (awned) using genotyping-by-sequencing analysis. A total of 56.62 Gb of clean sequence data were generated. A major gene was identified for the awnless trait based on 101,275 single-nucleotide polymorphisms by quantitative trait locus (QTL)-seq analysis. The region from 685.50 to 709.77 Mb on chromosome 5AL contained 334 genes and 394 transcripts, including B1, the major gene controlling the awnless trait. A 25-bp indel located in the B1 promoter region has a diagnostic value for the awnless/awned genotypes in the RIL population. A total of 42 spring wheat cultivars in Qinghai, China, were analyzed. Further, 23 awnless cultivars had the alleles of the GY448 parent, while 19 awned cultivars had the alleles of the GY115 parent. B1 is crucial in the awnless trait in wheat cultivars in Qinghai, China. The findings of this study might guide the breeding of new wheat cultivars in this region.

无芒性状是中国青海小麦育种的首选目标性状，但控制该性状的主效基因尚未明确。本研究以普通小麦品种无芒GY448与有芒GY115杂交构建的包含112个株系的重组自交系（recombinant inbred line, RIL）群体为材料，采用基因型测序（genotyping-by-sequencing）技术开展分析。本研究共生成56.62 Gb的清洁序列数据。基于101,275个单核苷酸多态性（single-nucleotide polymorphisms, SNP）标记，通过数量性状位点测序（QTL-seq）分析，本研究成功定位到控制无芒性状的主效基因。该主效基因所在的5AL染色体臂685.50 Mb至709.77 Mb区间内，共包含334个基因与394个转录本，其中B1即为调控无芒性状的主效基因。位于B1基因启动子区域的25 bp插入缺失（insertion-deletion, indel）标记，可用于区分RIL群体中的无芒与有芒基因型，具备诊断应用价值。本研究进一步分析了中国青海地区的42份春小麦品种，其中23份无芒品种携带GY448亲本的等位基因，19份有芒品种则携带GY115亲本的等位基因。由此可见，B1基因在中国青海小麦品种的无芒性状调控中发挥关键作用。本研究结果可为该地区小麦新品种的选育提供理论指导。