Identification, characterization, and associations with agronomic traits and early vigor of mature wheat embryo size loci.

Although the mature wheat (Triticum aestivum L.) embryo constitutes only a small proportion of kernel weight, it plays a significant role in seed germination and seedling establishment. However, the genetic basis underlying wheat embryo size remains poorly understood. In this study, we measured the embryos of mature kernels from 199 recombinant inbred lines (RILs) across up to nine environments. Using linkage maps constructed with the Wheat 55 K SNP array, we identified genetic loci associated with embryo size, including embryo length (EL), embryo width (EW), embryo area (EA), and their respective ratios to kernel dimensions (EL/KL, EW/KW, and EL/EW). Nine stable quantitative trait loci (QTL) were detected within three co-located chromosomal intervals, six of which are likely novel. The major, stably expressed, and novel QTL-QEL.sicau-2CN-2D.1 and QEW.sicau-2CN-2D-were successfully validated in a natural population comprising 165 Sichuan wheat cultivars and 57 Sichuan wheat landraces across two environments. By leveraging the genomic assemblies of the two parental genotypes, we identified candidate genes for this locus on chromosome 2D. Furthermore, significant correlations were observed between embryo size and early vigor, as well as kernel traits. Collectively, these findings provide critical insights into the genetic architecture of embryo size and facilitate the fine mapping and breeding applications of this promising locus.