Use of SNP markers by KASP assay for MAS studies in sunflower against Plasmopara halstedii

Abstract

Downy mildew is a fungal disease caused by Plasmopara halstedii and leads to loss of yield up to 100% in sunflower. Disease control is performed mostly through chemical seed treatment and breeding. Due to the time consuming nature of conventional breeding, it is supported by biotechnological approaches. Marker-assisted selection (MAS) is a strategic approach in molecular breeding using molecular markers. Single nucleotide polymorphisms (SNPs) such as insertions, deletions, and base-pair substitutions are more advantageous than other molecular markers. The abundance and biallelic nature of SNPs in a genome provide flexibility in the choosing of SNPs at the desired loci. Competitive allele-specific PCR (KASP) is a genotyping technology for screening of trait-specific SNP markers. In this study, SNP markers (NSA002867, NSA006138; NSA000052, NSA000354; NSA002220, NSA002251) linked with the downy mildew resistance genes Plarg,Pl13, and Pl8, respectively, were analyzed via KASP in three parental crosses (RHA-419 × Colombi, RHA-419 × P64LC53, RHA-419 × Oliva) for Plarg, one parental cross (HA-R5 × P64LC53) for Pl13, one parental cross (P64LC53 × HA-89) for Pl8, and 140 F2 individuals. According to the allelic discrimination results, NSA002867 and NSA006138 markers were discriminative in all crosses for Plarg, NSA000354 marker was discriminative for Pl13, and NSA002220 and NSA002251 markers were discriminative for Pl8. This study has revealed the potential use of SNP markers in combination with KASP assay for MAS studies, particularly downy mildew resistance in sunflower.