Assessment of genetic diversity and linkage disequilibrium within sunflower heterotic groups for improved elite breeding

Abstract

Sunflower (Helianthus annuus L.) is a globally important oilseed crop with considerable economic value. The development of hybrid sunflower varieties has revolutionized production by exploiting heterosis between distinct parental pools—cytoplasmic male sterile (CMS) lines (female parents) and restorer lines (male parents). Understanding the genetic architecture and diversity within these heterotic groups is essential to optimize hybrid breeding strategies, maintain vigor, and ensure long-term genetic gain. Advances in high-throughput genotyping technologies, such as single nucleotide polymorphism (SNP) arrays, have facilitated detailed analysis of genetic variation, population structure, and linkage disequilibrium (LD) in crop germplasm collections. Deep genotyping has enabled a comprehensive genetic characterization of an elite oilseed sunflower germplasm collection, consisting of 329 restorer lines (heterotic group R, HGR) and 236 cytoplasmic male sterile (CMS) lines (heterotic group B, HGB). The analysis utilized 8,416 informative SNPs to assess population structure, genetic diversity (GD), and linkage disequilibrium (LD) across the entire set of lines (WSL), as well as within the female CMS lines (B group) and male restorer lines (R group) separately. Principal Component Analysis (PCA) and population structure analyses revealed two distinct clusters, effectively differentiating the R lines from the B lines. The results indicate that HGR exhibits significantly higher genetic diversity than HGB, as shown by LD extension analyses indicating that HGR has accumulated more recombination events than HGB. This highlights the necessity of increasing genetic diversity within the B lines. To address this, LD variation across each chromosome was examined to identify regions of low and high recombination in both HGB and HGR. These insights allowed estimation of the number of SNPs required to capture existing genetic diversity per chromosome, guiding the development of marker-assisted strategies to improve the efficiency and speed of sunflower hybrid breeding programs.