A high-resolution intraspecific linkage map of pepper (Capsicum annuum L.) and selection of reduced RIL subsets for fast mapping.

A high resolution intraspecific linkage map of pepper (Capsicum annuum L.) was constructed from a population of 297 recombinant inbred lines. The parents were the large-fruited inbred cultivar 'Yolo Wonder' and the hot pepper line 'Criollo de Morelos 334', which is heavily used as a source of resistance to a number of diseases. A set of 587 markers (507 AFLPs, 40 SSRs, 19 RFLPs, 17 SSAPs and four STSs) were used to generate the map; of these, 489 were assembled into 49 linkage groups (LGs), including 14 LGs with 10 to 60 markers per LG, and 35 with two to nine markers per LG. The framework map covered 1857 cM with an average inter-marker distance of 5.71 cM. It was possible to assign 23 LGs, composed of 69% of the markers and covering 1553 cM, to one of the 12 haploid pepper chromosomes, leaving 26 LGs (304 cM) unassigned. The chromosome framework map built with 250 markers led to a high level of mapping confidence and an average inter-marker distance of 6.54 cM. By applying MapPop software, smaller subsets of 141 or 93 most informative individuals were selected with a view to reducing the time and cost of further mapping and phenotyping. To define the smallest number of individuals sufficient for assigning any new marker to a chromosome, subsets from 12 to 45 individuals, and a set of 13 markers distributed over all 12 chromosomes were screened. In most cases, the markers were correctly assigned to their expected chromosome, but the accuracy of the map position decreased as the number of individuals was reduced.