By analyzing the genetic and breeding selection effects of the stable major QTL for spike length in wheat, its genetic effects on yield-related traits were clarified, and the future breeding application potential was evaluated. The results could provide a basis for subsequent gene mining and molecular breeding of wheat.

A major QTL for spike length, named qSl-2D, was detected in multiple environments using a recombinant inbred lines population derived from the cross of Kenong9204 and Jing411, denoted as KJ-RIL; Two molecular markers closely linked to qSl-2D were developed by using the InDel sites in target interval. The genetic effects of yield-related traits based on KJ-RIL, MY-F₂, NILs and natural mapping populations, were analyzed by combining genotype data of molecular markers or wheat 55K array, respectively. By genotyping the natural mapping population, the breeding selection effect of qSl-2D haplotype was parsed across different wheat regions and different ages.

QTL mapping results showed that qSl-2D could be detected in 7/10 sets of environmental data, and could explain 4.02%-10.10% of the phenotypic variation. The peak LOD of 5/10 sets of environmental data was positioned at 608.75 Mb. The results of genetic effect analysis showed that the enhancing allele of qSl-2D could significantly increase spike length in the four populations with different genetic backgrounds. In addition, it has positive effects on kernel number per spike and plant height, but has negative effects on thousand kernel weight, kernel weight per spike and yield per plant in most population backgrounds. Further analysis of plant height in KJ-RIL population showed that the enhancing allele had rod lowering effect on all internode lengths except the internode length below spike, which resulted in the insignificant increase in plant height. The results of qSl-2D haplotype analysis showed that the utilization rates of the long-spike haplotype Hap-AA-GG varied greatly in different wheat regions, with the highest utilization rate in the northern winter wheat region, accounting for 24%; while the short-spike haplotype Hap-CC-CC accounted for more than 30% in most wheat regions. Moreover, the utilization rate of qSl-2D long-spike haplotype showed a gradual decrease over time, while that of short-spike haplotype consistently maintained a higher selection trend.

A stable major QTL-qSl-2D for spike length was identified, the enhancing allele of qSl-2D could significantly increase spike length under different genetic backgrounds, and had certain genetic effects on yield-related traits. The closely linked molecular markers developed in the target region can be used for the genetic improvement of wheat spike length and yield-related traits in wheat.