Identification of QTLs contributing to extremely high pungency in Bhut Jolokia, a ghost pepper landrace of Capsicum chinense

The pungency of Capsicum fruits is determined by groups of compounds called capsaicinoids. In the present study, we developed a genetic linkage map using a BC 1 mapping population generated through interspecific crossed between Bhut Jolokia (BJ: landraces of C. chinense ) and C. annuum cultivar and subsequently used to identify the QTLs for pungency. A set of 424 markers were assigned to 12 linkage groups (LGs) covering 1197.73 cM map distance. High-performance liquid chromatography (HPLC) analysis was performed to estimate the two major capsaicinoids namely, capsaicin and dihydrocapsaicin for F 1 and BC 1 progenies along with the parental lines. A total of eight QTLs (quantitative trait locus) were identified for four pungency-related traits namely capsaicin, dihydrocapsaicin, total capsaicinoids, and ratio of capsaicin/dihydrocapsaicin. Interestingly, a hotspot on LG4 was found to harbor QTLs for all four pungency traits. The hotspot contributes a high value of percentage of variance extended (PVE) making it a promising locus for map-based gene cloning and marker-assisted breeding applications. Most importantly present study revealed that there is a novel locus in BJ over the previously reported Pun1 alleles which controlled the pungency traits in Capsicum .