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

Abstract

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, Pl34, 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 Pl34 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 Rf7gene located in the Rf gene cluster on LG13. The SNP and SSR markers tightly flanking the Rf7 gene and the Pl34 gene would benefit the sunflower breeders in facilitating marker assisted selection (MAS) of Rf and Pl genes.

Registration of Oilseed Sunflower Germplasms RHA 485, RHA 486, and HA 487, Selected for Resistance to Phomopsis Stalk Canker and Sclerotinia, in a High‐Yielding and High‐Oil Background

“…‘RHA 426’ (PI 617099) and ‘RHA 428’ are restorer inbred germplasms developed by the USDA‐ARS and the North Dakota Agricultural Experiment Station (NDAES) possessing imidazolinone herbicide tolerance and DM resistance conditioned by the Pl 34 gene, respectively (Miller and Al‐Khatib, 2002; Miller et al, 2002; Talukder et al, 2019). ‘RHA 463’ (PI 655014) is a restorer oilseed germplasm developed by the USDA‐ARS and the NDAES in 2006 (Hulke et al, 2018).…”

“…This disease can cause leaf discoloration, stunting of growth, and death in the seedling stage (Gascuel et al, 2015). There is a suite of genes that contribute to resistance to DM (Pecrix et al, 2018), and a new one, named Pl 34 , was just mapped in the USDA inbred line RHA 428 (PI 619206; Miller et al, 2002; Talukder et al, 2019).…”

Validated markers for sunflower (Helianthus annuusL.) breeding

“…The mapped position of resistance genes were reported by Dimitrijevic and Horn (2018) and Talukder et al (2019) and are presented in Table 2. MAS and backcrossing were used to develop two resistant confection sunflower lines.…”

Mapping of the New Fertility Restorer Gene Rf-PET2 Close to Rf1 on Linkage Group 13 in Sunflower (Helianthus annuus L.)

“…All three genes are based in the 3.9-Mb region between 169,655,088 (ORS1030) and 173,581,392 (OP-H13) [36]. Genome-wide association studies using whole sunflower genome sequences [37][38][39] and data from SNP arrays [40] had also identified the distal region of LG13 for Rf1 but could not tag a specific gene due to the insufficient resolution of the whole genome analyses.…”