Fine mapping and gene silencing pinpoint Capana10g002229 as a strong candidate gene regulating the deciduous character of ripe pepper fruit ( Capsicum spp.)

Key message The pepper S locus, which controls the deciduous character of ripe fruit, was first fine mapped into an interval with a physical length of ~ 38.03 kb on chromosome P10. Capana10g002229 , encoding a polygalacturonase, was proposed as a strong candidate gene based on sequence comparison, expression pattern analysis and virus-induced gene silencing (VIGS). Abstract The deciduous character of ripe fruit, which is controlled by the dominant S locus, is a domesticated trait with potential value in the pepper processing industry ( Capsicum spp.). However, the gene associated with the S locus has not been identified. Here, one major QTL designated S10.1 was detected by using the F 2 population ( n = 155) derived from BA3 ( Capsicum annuum ) × YNXML ( Capsicum frutescens ) and was further verified in an intraspecific backcross population ( n = 254) derived from the cross between BB3 ( C. annuum ) and its wild relative Chiltepin ( C. annuum var. glabriusculum ) with BB3 as the recurrent parent. Then, a large BC 1 F 2 population derived from the self-pollination of BB3 × (BB3 × Chiltepin) individuals and comprising 4217 individuals was used to screen the recombinants, and the S locus was ultimately delimited into a 38.03-kb region on chromosome P10 harbouring four annotated genes. Capana10g002229 , encoding a polygalacturonase (PG), was proposed as the best candidate gene for S based on sequence comparison and expression pattern analyses. Downregulation of Capana10g002229 in fruits through VIGS significantly delayed fruit softening and abscission from the fruit-receptacle junction. Taken together, the results show that Capana10g002229 could be regarded as a strong candidate gene associated with the S locus in pepper. These findings not only lay a foundation for deciphering the molecular mechanisms underlying pepper domestication but also provide a strategy for genetic improvement of the deciduous character of ripe fruit using a marker-assisted selection approach.