Molecular Breeding Development of molecular markers tightly linked to Pvr 4 gene in pepper using next generation sequencing

Abstract: It is imperative to identify highly polymorphic and tightly linked markers of a known trait for molecular marker assisted selection (MAS). Potyvirus resistance 4 (Pvr4) locus in pepper confers resistance to three pathotypes of Potato Virus Y (PVY) and to pepper mottle virus (PepMoV). We describe the use of next generation sequencing technology to generate molecular markers tightly linked to Pvr4. Initially, comparative genomics was carried out and a syntenic region of tomato on chromosome ten was used to generate PCR-based markers and map Pvr4. Subsequently, the genomic sequence of pepper was used and more than 5000 single nucleotide variants (SNVs) were identified within the interval. In addition, we identified nucleotide-binding siteleucine-rich repeat (NB-LRR) type disease resistance genes within the interval. Several of these SNVs were converted to molecular markers desirable for large-scale molecular breeding programmes.