Spike length (SL) plays an important role in the yield improvement of wheat and is significantly associated with other traits. Here, we used a recombinant inbred line (RIL) population derived from a cross between Yangmai 12 (YM12) and Yanzhan 1 (YZ1) to construct a genetic linkage map and identify quantitative trait loci (QTL) for SL. A total of 5 QTL were identified for SL, among which QSl.yaas-3A and QSl.yaas-5B are two novel QTL for SL. The YZ1 alleles at QSl.yaas-2D and QSl.yaas-5A, and the YM12 alleles at QSl.yaas-2A, QSl.yaas-3A, and QSl.yaas-5B conferred increasing SL effects. Two major QTL QSl.yaas-5A and QSl.yaas-5B explained 9.11–15.85% and 9.01–12.85% of the phenotypic variations, respectively. Moreover, the positive alleles of QSl.yaas-5A and QSl.yaas-5B could significantly increase Fusarium head blight (FHB) resistance (soil surface inoculation and spray inoculation were used) and thousand-grain weight (TGW) in the RIL population. Kompetitive allele-specific PCR (KASP) markers for QSl.yaas-5A and QSl.yaas-5B were developed and validated in an additional panel of 180 wheat cultivars/lines. The cultivars/lines harboring both the positive alleles of QSl.yaas-5A and QSl.yaas-5B accounted for only 28.33% of the validation populations and had the longest SL, best FHB resistance (using spray inoculation), and highest TGW. A total of 358 and 200 high-confidence annotated genes in QSl.yaas-5A and QSl.yaas-5B were identified, respectively. Some of the genes in these two regions were involved in cell development, disease resistance, and so on. The results of this study will provide a basis for directional breeding of longer SL, higher TGW, and better FHB resistance varieties and a solid foundation for fine-mapping QSl.yaas-5A and QSl.yaas-5B in future.

穗长（SL）在小麦产量提高中发挥着重要作用，并与其他性状显着相关。在这里，我们使用源自扬麦12号（YM12）和燕展1号（YZ1）杂交的重组自交系（RIL）群体构建遗传连锁图谱并鉴定SL的数量性状位点（QTL）。共鉴定出5个SL QTL，其中QSl.yaas-3A和QSl.yaas-5B是两个新的SL QTL。QSl.yaas-2D和QSl.yaas-5A处的 YZ1 等位基因以及QSl.yaas-2A、QSl.yaas-3A和QSl.yaas-5B处的 YM12 等位基因赋予 SL 效应增加。两个主要QTL QSl.yaas-5A和QSl.yaas-5B分别解释了9.11-15.85%和9.01-12.85%的表型变异。此外， QSl.yaas-5A和QSl.yaas-5B的阳性等位基因可以显着提高RIL群体的赤霉病（FHB）抗性（采用土表接种和喷雾接种）和千粒重（TGW）。QSl.yaas-5A和QSl.yaas-5B的竞争性等位基因特异性 PCR (KASP) 标记在另外 180 个小麦品种/品系中进行了开发和验证。同时携带QSl.yaas-5A和QSl.yaas-5B阳性等位基因的品种/系仅占验证群体的28.33%，并且具有最长的SL、最好的FHB抗性（使用喷雾接种）和最高的TGW。在QSl.yaas-5A和QSl.yaas-5B中分别鉴定出总共358个和200个高置信度注释基因。这两个区域的一些基因与细胞发育、抗病性等有关。本研究结果将为定向育种更长SL、更高TGW和更好FHB抗性品种提供依据，并为今后QSl.yaas-5A和QSl.yaas-5B的精细定位打下坚实的基础。