Development of first linkage map for Silphium integrifolium (Asteraceae) enables identification of sporophytic self-incompatibility locus

Abstract

SUMMARYSilphium integrifolium (Asteraceae) has been identified as a candidate for domestication as a perennial oilseed crop and has a sporophytic self-incompatibility system—the genetic basis of which is not well understood in the Asteraceae. To address this gap, we sought to map the genomic location of the self-recognition locus (S-locus) in this species.We used a biparental population and genotyping-by-sequencing to create the first genetic linkage map for this species. Then we developed a novel crossing scheme and set of analysis methods in order to infer S-locus genotypes for a subset of these individuals, allowing us to map the trait. Finally, we identified potential gene candidates using synteny analysis with the annual sunflower (Helianthus annuus) genome.Our linkage map contains 198 SNP markers and resolved into the correct number of linkage groups. We were able to successfully map the S-locus and identify several potential gene candidates in the sunflower syntenic region.Our method is effective and efficient, allowed us to map the S. integrifolium S-locus using fewer resources than previous studies, and could be readily be applied to other species. Our best gene candidate appears to be worthy of future work in S. integrifolium and other Asteraceae species.