Identification, Validation and Genetic Effect Analysis of Major QTL for Spike Density in Wheat

Spike density (SD) is an important agronomic trait in wheat, and elucidating its genetic regulatory mechanisms is crucial for constructing ideal spike architecture and achieving yield breakthroughs. This study aimed to identify and genetically characterize key genetic loci controlling SD, providing a theoretical basis for molecular design breeding of wheat spike morphology.

A recombinant inbred line (RIL) population consisting of 198 F₆ lines derived from a cross between the natural mutant msf and cultivar Chuannong16 was used. Combined with a genetic linkage map based on the wheat 16K SNP array, quantitative trait loci (QTL) associated with SD were systematically identified using phenotypic data from four environments. Furthermore, two populations with different genetic backgrounds were employed to validate the major and stably expressed QTL. The genetic effects of the stable QTL on yield-related traits were analyzed, and their potential for yield improvement was evaluated.

The SD of the RIL population ranged from 0.62 to 2.35, with a heritability of 0.71. SD showed a significant positive correlation with productive tiller number and spikelet number, while exhibiting a highly significant negative correlation with grains per spike, grain weight per spike, and spike length. Nine QTLs controlling SD were identified, distributed on chromosomes 1A, 1D, 5A (2 QTLs), 5B, 7A (3 QTLs), and 7B. Among them, QSd.sicau-MC-1A was mapped between flanking markers 1A_1208254 and 1A_3911208 on chromosome 1A and detected in two environments and in the best linear unbiased prediction (BLUP) dataset, explaining 9.05%-15.84% of the phenotypic variation. This QTL, with its positive allele derived from Chuannong 16, was considered a major and stably expressed locus, and its effect was further validated in two independent genetic backgrounds. QSd.sicau-MC-7A.1 was located between markers 7A_671413788 and 7A_672390144 on chromosome 7A and also detected in two environments and BLUP. Although stably expressed, this QTL had a relatively minor effect (7.06%-10.39% phenotypic variation), with its positive allele originating from msf. The remaining seven QTLs were minor-effect loci. Genetic effect analysis revealed that the positive allele of QSd.sicau-MC-1A had negative effects on major yield-related traits, whereas QSd.sicau-MC-7A.1 exhibited positive effects. Additive effect analysis demonstrated that lines carrying both QSd.sicau-MC-1A and QSd.sicau-MC-7A.1 positive alleles had significantly higher SD (9.01% increase) compared to those carrying only one or no positive alleles. Lines with only QSd.sicau-MC-1A or QSd.sicau-MC-7A.1 showed 5.03% and 4.19% increases in SD, respectively, over lines without any positive alleles. Comparative analysis with previously reported SD QTLs suggested that QSd.sicau-MC-1A might be a novel locus.

Two stably expressed QTLs for SD, QSd.sicau-MC-1A and QSd.sicau-MC-7A.1, were identified in wheat. The latter shows greater potential for breeding applications.