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Commercial hybrid seed production in sunflower currently relies on a single cytoplasmic male sterility (CMS) source, PET1 and the major fertility restoration gene,  Rf1 , leaving the crop highly vulnerable to issues with genetic bottlenecks. Therefore, having multiple CMS/ Rf  systems is important for sustainable sunflower production. Here, we report the identification of a new fertility restoration gene,  Rf7 , which is tightly linked to a new downy mildew (DM) resistance gene,  Pl 34  , in the USDA sunflower inbred line, RHA 428. The  Rf7  gene was genetically mapped to an interval of 0.6 cM on the lower end of linkage group (LG) 13, while  Pl 34   was mapped 2.1 cM proximal to the  Rf7 . Both the genes are located in a cluster of  Rf  and  Pl  genes. To gain further insights into the distribution of  Rf  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  Rf1  gene. The SNP haplotypes for the  Rf1  gene are different from  Rf5  and the  Rf7 gene located in the  Rf  gene cluster on LG13. The SNP and SSR markers tightly flanking the  Rf7  gene and the  Pl 34   gene would benefit the sunflower breeders in facilitating marker assisted selection (MAS) of  Rf  and  Pl  genes.

frontiers in genetics

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