Genetic analysis of agronomic traits in a wide cross of chickpea

A genetic map composed of 10 linkage groups (LGs) covering 848.1 cM was constructed from a recombinant inbred line population from the cross Cicer arietinum (ICCL81001) × Cicer reticulatum (Cr5-9). The lines were genotyped with random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR) and sequence tagged microsatellite site (STMS) markers, and phenotyped with respect to flowering time, flower colour, growth habit, seed size, seed coat reticulation, seed coat thickness and reaction to infection by two races of fusarium wilt. Segregation distortion was observed for 35% of markers, mainly clustered on LG4, LG7 and two unassigned linkage groups. Rs/rs (seed coat reticulation) together with a quantitative trait locus (QTL) accounted for >50% of the variation for seed coat thickness. Both Hg/hg (growth habit) and a flowering time QTL mapped to LG3A. The STMS marker TA142 was closely linked to this QTL. Two QTL for seed size were detected—one on LG4 linked to STMS markers GAA47 and STMS11, and the other on LG2 linked to STMS TA110. Two tightly linked QTL on LG2 closely linked to STMS marker TA59 controlled the resistance to both races of the pathogen causing fusarium wilt.