Mapping physiological traits in Carica papaya using microsatellite markers

Abstract

Different varieties of papaya (Carica papaya L.) vary in the phenotypic expression of agronomically important traits. Genetic loci responsible for these differences can be mapped using DNA markers to genotype a segregating progeny population derived from a controlled cross between parents having different phenotypes. Two unique varieties of papaya, Khak dam and 2H94, were chosen as parental materials based on their widely varied phenotypic expression of fruit size, shape, and flesh color. These varieties were used to produce an F2 population that was surveyed for DNA polymorphisms using microsatellite markers. The 100 female and hermaphrodite F2 individuals segregating for flesh color were scored for this trait. Flesh color segregated in a 3:1 ratio with yellow flesh color being dominant suggesting that flesh color is a single gene controlled trait. All of the 137 hermaphrodite individuals in the F2 population were scored for fruit weight, length, and width. Fruit phenotype data was analyzed by constructing histograms to assess the distribution of these traits. Normal distribution was detected for length and width suggesting quantitative inheritance for these traits. Fruit weight may segregate as a mix of normal and bimodal distribution suggesting involvement of a major gene modified by quantitative trait loci (QTL). A total of 1497 microsatellite markers screened for polymorphisms between AU9 female and Sunup hermaphrodite parents showed 607 of them to be polymorphic. Of these, 199 SSR markers were used to genotype the F2 progeny population in order to construct a preliminary genetic linkage map. From this map, a total of 38 markers spaced, on average, 25cM apart across 16 linkage groups were found to also be polymorphic between Khak dam and 2H94 and chosen for genotype screening. To identify major gene loci and QTLs controlling these traits, analysis of variance and MapQTL® 5.0 were used. The map location of markers correlating to QTLs involved in expression of fruit size, or weight, fruit shape, or length and width, and the major gene locus for flesh color were estimated. Significant QTLs affecting weight mapped to linkage group 6, QTLs affecting length to linkage group 7, QTLs affecting width to linkage group 6 and QTLs affecting shape to linkage group 7. The location for the gene affecting flesh color was determined to be located close to marker P3K132 on linkage group I. These sequence specific DNA markers linked to target traits will be fine mapped for exact location and used for marker-assisted breeding system in the future.