Plant breeders are interested to have molecular markers associated with trait of interest so that they can use these markers to enhance their selection efficiency in chickpea breeding. Basically, chickpea community is interested to develop markers associated with resistance to Fusarium wilt, Ascochyta blight, Helicoverpa armigera, and tolerance to several abiotic stresses like drought, salinity, etc. In recent years, community has shown interest to map nutritional quality traits as well.

During year 2009, interesting attempts to locate or validate resistance genes or quantitative trait loci (QTL) in chickpea genetic map have been achieved. It should be mentioned that most work has been focused either fusarium wilt or ascochyta blight. Besides, a paper related to the location of agromic traits was published.

Collaboration between a Tunisian (INRAT and Unv. Tunis) and Spanish group (UCO) permitted to map a second gene controlling fusarium wilt race 0 (Foc02/foc02) in a cluster of genes sited in LG2 (Halila et al. 2009). Authors used a RIL population derived from an intra-specific cross CA 2139 (kabuli, susceptible) × JG 62 (desi, resistant race 0) evaluated in an infected field. This time resistance was treated as a quantitative trait because in this population the allelic state for both resistance genes could not be reliably determined. The first genes conferring resistance to race 0 (Foc01/foc01) were previously mapped in LG5 (Cobos et al. 2005).

Two research groups from India () in collaboration with CSIRO (Australia) could validate the location in LG2 of resistance genes to races 1, 2 and 3 (Gowda et al 2009). These authors also worked with a RIL population derived from an intraspecific cross: JG 62 (susceptible to races 1-5) × Vijay (resistant). In this population, monogenic inheritance for resistance to the three Foc races was observed. Novel STMS markers were included in this linkage group contributing to the saturation of this important genomic area.

In relation to resistance to ascochyta blight two Indian groups (from ICARDA and Univ Raipur) studied F₂ plants from a narrow cross to locate QTL contributing to resistance to an Indian isolate of ascochyta blight (AB), based on the seedling and adult plant reaction (Kottapalli et al. 2009). In this publication three QTL were reported: QTL1 mapped to LG3, and QTL2 and QTL3 both mapped to LG4. Interestingly, there are coincidences with QTL previously mapped in different genetic backgrounds.

Anbessa et al. (2009) from University of Saskatchewan (Canada) also detected QTL for ascochyta blight resistance in chickpea using four intra-specific populations. QTL were detected in groups 2, 3, 4, 6 and 8. However, QTL showing higher LOD values were placed in LG2 and LG4.

Besides, an attempt to target genomic areas conferring resistance to ascochyta blight and fusarium wilt using RGA was achieved by a Spanish group (Palomino et al. 2009) although not high significant association with any resistance gene have been found. Efforts to find candidate genes for QTL2 has been done by genome walking using SCK13603 as anchored sequence resulting that was located in a region of a putative retrotransposon (Iruela et al. 2009).