Linkage Mapping and Genome-Wide Association Studies of the Rf Gene Cluster in Sunflower ( Helianthus annuus L.) and Their Distribution in World Sunflower Collections

Commercial hybrid seed production in sunflower currently relies on a single cytoplasmic male sterility (CMS) source, PET1 and the major fertility restoration gene, , leaving the crop highly vulnerable to issues with genetic bottlenecks. Therefore, having multiple CMS/ systems is important for sustainable sunflower production. Here, we report the identification of a new fertility restoration gene, , which is tightly linked to a new downy mildew (DM) resistance gene, , in the USDA sunflower inbred line, RHA 428. The gene was genetically mapped to an interval of 0.6 cM on the lower end of linkage group (LG) 13, while was mapped 2.1 cM proximal to the . Both the genes are located in a cluster of and genes. To gain further insights into the distribution of genes in the sunflower breeding lines, we used a genome-wide association study (GWAS) approach to identify markers associated with the fertility restoration trait in a panel of 333 sunflower lines genotyped with 8,723 single nucleotide polymorphism (SNP) markers. Twenty-four SNP markers on the lower end of LG13 spanning a genomic region of 2.47 cM were significantly associated with the trait. The significant markers were surveyed in a world collection panel of 548 sunflower lines and validated to be associated with the gene. The SNP haplotypes for the gene are different from and the gene located in the gene cluster on LG13. The SNP and SSR markers tightly flanking the gene and the gene would benefit the sunflower breeders in facilitating marker assisted selection (MAS) of and genes.