High-density Genetic Linkage Map Construction in Sunflower (Helianthus annuus L.) Using SNP and SSR Markers

Background: Sunflower (Helianthus annuus L.) is an important oil crop only after soybean, canola and peanuts. A high-quality genetic map is the foundation of marker-assisted selection (MAS). However, for this species, the high-density maps have been reported limitedly. Objective: In this study, we proposed the construction of a high-density genetic linkage map by the F7 population of sunflowers using SNP and SSR Markers. Methods: The SLAF-seq strategy was employed to further develop SNP markers with SSR markers to construct the high-density genetic map by the HighMap software. Results: A total of 1,138 million paired-end reads (226Gb) were obtained and 518,900 SLAFs were detected. Of the polymorphic SLAFs, 2,472,245 SNPs were developed and finally, 5,700 SNPs were found to be ideal to construct a genetic map after filtering. The final high-density genetic map included 4,912 SNP and 93 SSR markers distributed in 17 linkage groups (LGs) and covered 2,425.05 cM with an average marker interval of 0.49 cM. Conclusion: The final result demonstrated that the SLAF-seq strategy is suitable for SNP markers detection. The genetic map reported in this study can be considered as one of the most high-density genetic linkage maps of sunflower and could lay a foundation for quantitative trait loci (QTLs) fine mapping or map-based gene cloning.