Development of an integrated intraspecific map of chickpea (Cicer arietinum L.) using two recombinant inbred line populations.

A composite intraspecific linkage map of chickpea was developed by integrating individual maps developed from two F(8:9) RIL populations with one common parent. Different molecular markers viz. RAPD, ISSR, RGA, SSR and ASAP were analyzed along with three yield related traits: double podding, seeds per pod and seed weight. A total of 273 markers and 186 RILs were used to generate the map with eight linkage groups at a LOD score of >/=3.0 and maximum recombination fraction of 0.4. The map spanned 739.6 cM with 230 markers at an average distance of 3.2 cM between markers. The predominantly used SSR markers facilitated identification of homologous linkage groups from the previously published interspecific linkage map of chickpea and confirmed conservation of the SSR markers across the two maps as well as the variation in terms of marker distance and order. The double podding gene was tagged by the markers NCPGR33 and UBC249z at 2.0 and 1.1 cM, respectively. Whereas, seeds per pod, was tagged by the markers TA2x and UBC465 at 0.1 and 1.8 cM, respectively. Eight QTLs were identified that influence seed weight. The joint map approach allowed mapping a large number of markers with a moderate coverage of the chickpea genome and few linkage gaps.