Simple sequence repeat marker development and mapping in cultivated sunflower, Helianthus annuus L

The cultivated sunflower (Helianthus annuus L., x = 1c7) is one of the most important annual oilseed crops in the world. There are very few publicly shared sequence-based DNA markers and genetic maps in sunflower, even though molecular DNA markers and genetic maps have become widely used in all areas of genetic research and breeding in plant species. The objectives of this study were to develop sequence-based molecular markers and utilize the markers for genetic analyses and constructing maps in the cultivated sunflower. A total of 131 functional simple sequence repeat (SSR) markers were developed for 16 elite inbred lines using a small insert genomic library enriched for short simple sequence repeats. The polymorphism information content (PIC) estimated from 74 polymorphic SSR markers ranged from 0.0 to 0.93 with mean value of 0.55. Tetranucleotide repeats were significantly more polymorphic than dinucleotide and trinucleotide repeats, and no obvious correlation was found between repeat numbers and PIC scores. Genetic distance among 16 inbred lines, estimated from 74 polymorphic SSR markers ranged 0.175 to 0.543. Principal coordinate and cluster analyses of the genetic distance matrix well explained the difference between oilseed lines and confectionery lines, and sterility maintainer lines and fertility restorer lines. A total of 1,090 SSR markers were screened for polymorphism between the parents of two mapping populations. The two genetic maps were constructed by genotyping 94 recombinant inbred lines from a cross between PHA and PHB (276 SSR loci covering 1377.4 cM with mean distance of 4.99 cM), and 94 F₂ progeny from a cross between HA370 and HA372 (122 SSR loci integrated into the existing RFLP framework map covering 1348.0 cM with mean distance of 6.77 cM). Ninety-three percent of the SSR markers were mapped to single loci and 56.5% of the loci were co-dominant. Clustering of SSR loci was observed near centromeric regions and most of the distorted loci were mapped to centromeric or distal regions. A concerted effort to develop SSR markers and generate high-resolution SSR maps will enhance future fingerprinting analyses, fine-scale genome analyses and molecular breeding in the cultivated sunflower.