Allelic variation in major genes and quantitative trait loci associated with grain number in historical spring wheat cultivars

Wheat grain yield is a complex polygenic trait influenced by variation in several components, particularly number of grains per unit area and grain weight. Spikelet number per spike (SNS) plays a crucial role in determining grain numbers and overall grain yield. In this study, we analyzed the allelic variation at three functional genes and two major quantitative trait loci (QTL) associated with grain number-related characteristics in a collection of spring wheat cultivars. In addition, we developed two diagnostic markers for WAPO-A1. The frequency of favorable alleles ranged from 3.6% for TaCol-B5 to 86% for bZIPC1. The results showed that WAPO-A1b is present in the majority of cultivars (64.5%) and contributes to higher SNS and grains per spike, while WAPO-A1a is linked to lower SNS. The WAPO-A1c allele was identified in only five cultivars. Moreover, two QTL–QGNS.caas-4B and QGNS.caas-6B–were associated with yield components in historical wheat cultivars. Our study provided a detailed understanding of the genetic architecture underlying the grain number component of yield in Pakistani wheat cultivars. The diagnostic markers for WAPO-A1 developed in this study may be utilized in the future in wheat breeding.