Mapping and characterization of stable major QTL for heading date and spikelet number in wheat

Optimization of heading date (HD) and spike formation, two sequential development phases, is essential for improving wheat acclimation and yield. Identification of quantitative trait loci (QTL) for HD and spikelet number will contribute to breeding early maturing and high-yielding cultivars. Zhongmai 578 (ZM578) and Jimai 22 (JM22) are elite cultivars with significant differences in HD and spikelet number. Here, 14 environmentally stable QTL for HD, spikelet number per spike (SNS), and fertile spikelet number per spike (FSN) were identified in a population of 262 recombinant inbred lines from the cross ZM578/JM22. Among them, QHd.caas-3A.1, QHd.caas-4A, QHd.caas-5B, QHd.caas-7A, QHd.caas-7D, QFsn.caas-7A, QSns.caas-7A, and QSns.caas-7D explained up to 13.4%, 14.5%, 49.7%, 14.6%, 11.3%, 35.6%, 34.1%, and 16.2% of the phenotypic variances, respectively. Genome resequencing, transcriptome, and genetic linkage analyses identified TaFT-A1 and TaSEP3-D1 as candidate genes for QHd.caas-7A and QTL pair QHd.caas-7D and QSns.caas-7D, respectively. WAPO-A1 was identified as a candidate gene for the QTL cluster that included QSns.caas-7A and QFsn.caas-7A. We also predicted candidate genes for the remaining stable QTL based on genome and transcriptome analyses. Considering that the genetic effect of WAPO-A1 was confirmed previously, we developed breeder-friendly markers for the other major QTL to validate genetic effects in a diverse wheat cultivar panel. Marker-trait association analyses revealed that the favorable alleles of these QTL, except QHd.caas-5B, conferred early HD without yield penalty, which was also confirmed by pyramiding effects. These results provide useful genetic resources and molecular tools for improving adaptation and yield potential in wheat.