Development of Molecular Markers and a Preliminary Selection Index for Yield-Related QTLs in Secale cereale subsp. segetale

As a close relative of common wheat, rye is a forage crop of significant research value in China. Background: A weedy rye, Secale cereale subsp. segetale found in Xinjiang China, is characterized by superior yield-related traits such as grain length, grain width, spike length, spike width, plant height, and tiller number. The identification of genes controlling these traits provides significant assistance for rye breeding. However, its characteristics of cross-pollination and self-incompatibility complicate the genetic analysis of these traits. Despite extensive studies on stress tolerance in rye, the genetic basis of yield-related traits has been the subject of only a few studies. Methods: Our previous research preliminarily identified quantitative trait loci (QTLs) affecting yield-related traits through specific-locus amplified-fragment sequencing (SLAF-seq). In this study, we focused on the targeted development of molecular detection markers by identifying single nucleotide polymorphisms (SNPs) or simple sequence repeats (SSRs) tightly linked to these yield-related QTLs. Linked SNP/SSR markers were developed and screened across seven diverse rye populations (C2, A3–A7). Results: Through screening and validation in diverse rye populations, two SSR markers and seven KASP (Kompetitive Allele Specific PCR) markers capable of distinguishing phenotypic traits were identified. These markers effectively genotyped tiller number, stem diameter, and spikelet number. Subsequently, by annotating and screening genes adjacent to the target QTLs, we identified multiple candidate genes, including ScWN2R01G507400.1, ScWN4R01G301500.1, ScWN4R01G335200.1, and ScWN4R01G352500.1. These genes primarily encode proteins such as those containing valine-glutamine (VQ) motifs, F-Box proteins, MATH-BTB domain-containing proteins. By integrating QTL phenotypic variation explained (PVE) from SLAF-seq, molecular markers, and post-harvest agronomic traits, we constructed an exploratory marker-assisted selection index for preliminary evaluation of rye germplasm, and suggest that independent validation in larger populations and multiple environments is required. Conclusions: These findings provide valuable references for investigating the genetic basis of yield related traits in rye.