Chickpea (Cicer arietinum L.) is the second most important grain legume in the world, grown on about 15 million hectares worldwide. The 1990s marked a significant turning point in genetic research on chickpea. In 1991, researchers at Muenster University unveiled the mRNA sequence responsible for an isoflavone oxidoreductase, which was the first sequence available for this species (X60755; Genbank, NCBI). As the new century unfolded, the nucleotide database accumulated over 265 accessions for chickpea. The availability of these new sequences was closely linked to the development of genetic maps. Throughout the 1990s and early 2000s, numerous studies explored populations resulting from crosses between cultivated C. arietinum and wild-sampled accessions of C. reticulatum and C. echinospermum (Benko-Iseppon et al. 2003; Gaur and Slinkard 1990; Gaur and Stinkard 1990; Kazan et al. 1993; Pfaff and Kahl 2003; Radhika et al. 2007; Rakshit et al. 2003; Ratnaparkhe, Tekeoglu, and Muehlbauer 1998; Santra et al. 2000; Simon and Muehibauer 1997; Tekeoglu, Santra, et al. 2000; Tekeoglu, Tullu, et al., 2000; Tekeoglu, Rajesh, and Muehlbauer 2002; Winter et al. 1999, 2000).
The following advance in genetic maps was represented by those primarily constructed using narrow crosses, focusing on two distinct chickpea types: “desi” and “kabuli”. Molecular markers had played a crucial role in uncovering that kabuli and desi types possessed contrasting genetic backgrounds (Chowdhury, Vandenberg, and Warkentin 2002; Iruela et al. 2002). As a result, the majority of genetic maps developed during this period were derived from crosses between kabuli and desi chickpea cultivars (Cho et al. 2002; Cho, Chen, and Muehlbauer 2004; Cobos et al. 2005, 2007; Iruela et al. 2006, 2007; Lichtenzveig et al. 2006; Millan et al. 2003; Sharma et al. 2004; Tar'an et al. 2007; Udupa and Baum 2003).
The development of microsatellite markers (SSR) expedited the identification of markers closely linked to traits of interest (Choudhary et al. 2006, 2009; Hüttel et al. 1999; Lichtenzveig et al. 2005; Sethy, Choudhary, et al. 2006; Sethy, Shokeen, et al. 2006; Winter et al. 1999). However, the valuable information and resources provided by these maps could only be fully utilized when direct comparisons were made using common SSR markers. Although the marker-linkage group assignments in different populations generally agreed, discrepancies between maps arose due to variations in population type and size, mark