Abstract
Chilli veinal mottle virus (ChiVMV) is a serious potyvirus affecting chilli cultivation in India causing economic yield losses. Breeding resistant varieties/ hybrids is best advocated strategy for viral management. Molecular mapping and markers development greatly facilitates accelerated breeding. Genotyping-by-sequencing was employed for marker discovery and simultaneous genotyping of F2 population developed using contrast parents. Total 6628 single nucleotide polymorphisms (SNP) and 18,125 silicoDArT markers were determined. The SNPs and silicoDArT markers ranged from 280 on chromosome 8 to 625 on chromosome 3 and 857 on chromosome 8 to 1753 on chromosome 3, respectively. Genome wide association study (GWAS) detected 17 SNPs and 21 silicoDArT markers associated with ChiVMV resistance. A major genomic region on chromosome 9 was identified as major candidate loci for ChiVMV resistance. A cluster of defense related genes and elongation translation factors (eIFLE) responsible for disease resistance were predicted within the GWAS regions. A cleaved amplified polymorphic sequence ChiVMVR9_2 CAPS marker was developed for the major resistant locus which was physically mapped at 2,458,715 bp on chromosome 9. This marker can be used in marker-assisted breeding and genomic selection. Further fine mapping of the identified region will facilitate precise marker assisted selection for resistance.
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