With an objective to understand the linkage and recombination among molecular markers along the linkage groups, molecular markers are used with a variety of mapping populations such as recombinant inbred lines (RILs). Segregation data for markers obtained on these mapping populations are used to understand the recombination among marker loci and genetic maps are prepared. Initial genetic maps in chickpea were prepared using isozyme marker loci on interspecific mapping populations, which were subsequently integrated with SSR markers. In recent years, several genetic maps based on both inter- as well as intra-specific mapping populations have become available. ICRISAT in collaboration with UC-Davis, Uni Frankfurt, GenXPro GmbH and several other partners has developed a high-density genetic map with >1450 marker loci. Similarly, Uni Cordoba and Uni Frankfurt has developed an integrated genetic map.

A new chickpea map based on the inter-specific RIL population derived from the cross Cicer arietinum ICC 4958 × C. reticulatum PI 489777 previously mapped by Winter et al (2002) has been just published (Nayak et al. 2010). This map resulted from an international collaboration, comprise 521 loci organized into eight linkage groups. Gene-based markers provide anchor points for comparing the genomes of Medicago and chickpea, revealed synteny between these two species. This is an outstanding contribution to chickpea community.

Finally, it has been reported a genetic map developed in a inter-specific population where flowering time, flower colour, growth habit, seed size, seed coat reticulation, seed coat thickness and reaction to infection by two races of fusarium wilt were evaluated (Cobos et al. 2009). Phenotipic variation of seed coat thickness was explained by the unmapped locus Rs/rs (seed coat reticulation) and a QTLTt in LG4. Both Hg/hg (growth habit) and a flowering time QTL mapped to LG3A. Two QTL for seed size were detected one on LG4 and the other on LG2. Besides it was confirmed the location of resistance genes to fusarium wilt races 0 and 5 in LG2 closely linked to STMS marker TA59.