Identification of QTLs conferring resistance to begomovirus isolate of PepYLCIV in Capsicum chinense

Pepper yellow leaf curl disease caused by begomoviruses has emerged as a major limitation to the cultivation of pepper ( Capsicum spp.) production in a number of regions around the world. Although begomovirus resistance has been reported in several accessions, pepy-1 derived from BaPep-5 ( C. annuum ) is the only begomovirus resistance gene cloned to date. In this study, we evaluated the resistance of a C. chinense accession GR1 against pepper yellow leaf curl Indonesia virus (PepYLCIV), which is one of the predominant begomovirus species infecting pepper plants in Indonesia. Infection of PepYLCIV to susceptible Habanero ( C. chinense ) plants induced typical yellowing symptoms, whereas the GR1 plant showed symptoms with very low severity. Moreover, the accumulation of viral DNA was restricted in GR1 compared to Habanero. Phenotypic analyses of F 1 and F 2 populations obtained by crossing Habanero with GR1 inferred that the resistance is a dominant trait controlled by multiple genes. Linkage analysis in the F 2 population using restriction site-associated DNA sequencing data detected two significant quantitative trait loci (QTLs), one on chromosome 4 and another on chromosome 11, which explained 31.6 and 19.7% of the phenotypic variation, respectively. Moreover, QTL-seq conducted using F 3 population partially confirmed the result of F 2 population, which detected QTLs on chromosome 3 and 11, respectively. The QTLs identified for PepYLCIV resistance in this research are novel since no other resistance causing QTLs have ever been reported in these genomic regions. GR1 is a highly valuable genetic resource for the breeding of begomovirus resistance in peppers.