Diversity analysis and genomic prediction of Sclerotinia resistance in sunflower using a new 25 K SNP genotyping array.

KEY MESSAGE: We have developed a SNP array for sunflower containing more than 25 K markers, representing single loci mostly in or near transcribed regions of the genome. The array was successfully applied to genotype a diversity panel of lines, hybrids, and mapping populations and represented well the genetic diversity of cultivated sunflower. Results of PCoA and population substructure analysis underlined the complexity of the genetic composition of current elite breeding material. The performance of this genotyping platform for genome-based prediction of phenotypes and detection of QTL with improved resolution could be demonstrated based on the re-evaluation of a population segregating for resistance to Sclerotinia midstalk rot. Given our results, the newly developed 25 K SNP array is expected to be of great utility for the most important applications in genome-based sunflower breeding and research. ABSTRACT: Genotyping with a large number of molecular markers is a prerequisite to conduct genome-based genetic analyses with high precision. Here, we report the design and performance of a 25 K SNP genotyping array for sunflower (Helianthus annuus L.). SNPs were discovered based on variant calling in de novo assembled, UniGene-based contigs of sunflower derived from whole genome sequencing and amplicon sequences originating from four and 48 inbred lines, respectively. After inclusion of publically available transcriptome-derived SNPs, in silico design of the Illumina(®) Infinium iSelect HD BeadChip yielded successful assays for 22,299 predominantly haplotype-specific SNPs. The array was validated in a sunflower diversity panel including inbred lines, open-pollinated varieties, introgression lines, landraces, recombinant inbred lines, and F2 populations. Validation provided 20,502 high-quality bi-allelic SNPs with stable cluster performance whereby each SNP marker represents a single locus mostly in or near transcribed regions of the sunflower genome. Analyses of population structure and quantitative resistance to Sclerotinia midstalk rot demonstrate that this array represents a significant improvement over currently available genomic tools for genetic diversity analyses, genome-wide marker-trait association studies, and genetic mapping in sunflower.