Identification of a Major-Effect Quantitative Trait Loci Associated with Begomovirus Resistance in

Begomoviruses, viz. squash leaf curl China virus and tomato leaf curl New Delhi virus causative diseases are major concerns of quantitative and qualitative losses in pumpkin () worldwide. Punjab Agricultural University (PAU) in India has identified a resistant source (PVR-1343) against mixed infection (MI-Sq/To) of these begomoviruses. Introgression of resistance in diverse genetic backgrounds requires the identification of quantitative trait loci (QTLs) associated with MI-Sq/To resistance. Phenotyping of 229 F progenies derived from the PVR-1343 × P-135 cross revealed digenic recessive inheritance against MI-Sq/To resistance in PVR-1343. To identify the genomic region, resistant and susceptible bulks were subjected to whole-genome resequencing along with their parents. The whole-genome resequence analysis of parents and bulks using QTLseq/QTLseqr approaches identified an overlapping 1.52 Mb region on chromosome 7 (), while chromosomal region spanning 0.87 Mb on chromosome17 () was additionally identified by QTLseqr. However, the highest peak value on chromosome 7 with three algorithms {G', ∆(SNP-index) and -log ( value)} highlighted the major contribution of in MI-Sq/To resistance. Nine polymorphic SNPs identified within the highly significant region were converted into KASP markers. KASP genotyping of F individuals narrowed down the interval to 103 kb region flanked by two markers, Cmo3914729 and Cmo4018182, which contained 16 annotated genes and accounted for 59.84% of phenotypic variation. The Cmo4018182 KASP marker accurately predicted disease reaction in 91% of diverse genotypes and showed nonsynonym substitutions in the coding region of putative candidate gene. These findings pave the way for marker-assisted breeding and elucidating the underlying mechanism of begomovirus resistance in .