Identification and validation of a QTL, QSNS.caas-3D.1, for spikelet number per spike in wheat

A QTL, QSNS.caas-3D.1, was identified and found to increase spikelet number per spike and grain number per spike without compromising thousand-grain weight. This result was validated in various genetic populations. Increasing the grain number per spike (GNS) is crucial for increasing the yield potential of wheat. This goal depends on the optimization of its key components, namely, the spikelet number per spike (SNS) and kernel number per spikelet (KNS). Here, we constructed a recombinant inbred line (RIL) population comprising 1,220 lines derived from a cross between the high- spikelet-number line PB3504 and the elite cultivar Yecora Rojo (YKL), to dissect the genetic architecture of GNS-related traits. Using the Wheat 60 K SNP array, we constructed a high-density genetic map and conducted multienvironment QTL mapping. A total of 53 quantitative trait loci (QTLs) were identified, among which QSNS.caas-3D.1 was highlighted as a major and stable QTL for SNS, explaining 13.34-13.72% of the phenotypic variation. Fine mapping delimited this locus to a 5.91 Mb genomic interval on chromosome 3D. The yield-enhancing effect of QSNS.caas-3D.1 was validated in near-isogenic lines (NILs) and an independent F₂ population. Notably, under field conditions, the PB3504 allele caused a significant 14.69% increase in grain yield without compromising thousand-grain weight, suggesting its potential utility in marker-assisted selection. Within the target interval, 9 candidate genes were prioritized through comparative genomics and transcriptomic analysis. Overall, our study identifies QSNS.caas-3D.1 as a QTL for improving yield in wheat and provides a solid foundation for its map-based cloning and deployment in molecular breeding programs.