A Genetic Linkage Map of Capsicum baccatum var. pendulum

Capsicum baccatum is one of the five domesticated pepper, but despite its economic and cultural importance this species is less well studied when compared with other Capsicum crops, such as C. annuum and C. chinense. This study reports the construction of a genetic linkage map of C. baccatum (2n = 2x = 24 chromosomes) with 42 SSR, 85 ISSR and 56 RAPD markers using an intraspecific F₂ population of 203 individuals. The segregation of each marker and linkage analysis were performed using JoinMap v4.0 software. The 183 mapped markers were aligned into 12 major linkage groups and four subgroups (1B, 2B, 5B and 7B) at LOD value of 3.0. The total length of the map was 2547.5 cM, with an average marker interval of 14.25 cM. The linkage groups ranged from 110.3 to 321.8 cM in length and included 8 to 27 markers, respectively. Of 152 microsatellites primer pairs of C. annuum tested, 62 identified polymorphism loci in the population the C. baccatum, and 42 were mapped, allowing the introduction of this species in comparative mapping studies. To the best of our knowledge, this is the first report on genetic linkage mapping of C. baccatum and the map developed will be highly useful for anchoring of more loci in future investigations. This linkage map also represents an important step towards understanding the Capsicum genome structure and in order to genetically dissect important agronomic traits, providing a firm basis for the application of a marker-assisted selection breeding strategy in this species.