Mapping of gene-specific markers on the genetic map of chickpea ( Cicer arietinum L.)

Abstract

With the exception of the fact that it is made up of eight different chromosomes, the physical organization of the 738-Mb genome of the important legume crop chickpea (Cicer arietinum L.) is unknown. In an attempt to increase our knowledge of the basic structure of this genome, we determined the map positions of a series of genes involved in plant defence responses (DR) by genetic linkage analysis. Exploiting the sequence data available in GenBank, we selected genes known to be induced in chickpea and other plants by pathogen attack. Gene-specific primers were designed based on conserved regions, and used to detect the corresponding gene sequences in a segregating population derived from an interspecific cross between Cicer arietinum and C. reticulatum. Forty-seven gene-specific markers were integrated into an existing map based on STMS, AFLP, DAF and other anonymous markers. The potential of this approach is discussed.

Integration of novel SSR and gene-based SNP marker loci in the chickpea genetic map and establishment of new anchor points with Medicago truncatula genome

“…Seventy-one of these genes contained SNPs that could be converted to reliable genotyping assays using either CAPS or SNaPshot protocols (Table 3). Two additional gene-based markers, P40 and chitinase II, were also used for genetic analysis; these genes were previously mapped in chickpea by Pfaff and Kahl (2003), while their putative orthologs have been mapped in M. truncatula by Choi et al (2004a). …”

“…The inter-specific cross between ICC 4958 × PI 489777 is maintained as an advanced recombinant inbred population that has been used in numerous genetic studies (Huettel et al 2002; Pfaff and Kahl 2003; Winter et al 2000). Although the number of markers previously analyzed in this population is relatively large (407 loci), a high percentage of the markers are anonymous sequences (e.g., RFLP) and/or exhibit dominant patterns of inheritance (e.g., AFLP).…”

“…We note that the bottom of CaLG2 harbors numerous active resistance genes against two of the most important diseases of chickpea ( Fusarium wilt and Ascochyt a blight). At present, no RGHs have been reported mapped close to these resistance phenotypes (Winter et al 2000; Pfaff and Kahl 2003; Sharma et al 2004). Moreover, the low frequency of comparative molecular markers around these R gene regions in both M. truncatula and chickpea complicate precise statements regarding the relationship of these genome regions.

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“…In addition, marker genotyping data for 407 marker loci were compiled (Huettel et al 2002; Pfaff and Kahl 2003; Tekeoglu et al 2000; Winter et al 1999, 2000). …”

Advancing the STMS genomic resources for defining new locations on the intraspecific genetic linkage map of chickpea (Cicer arietinum L.)

“…Nevertheless, microsatellites which are known to be abundant and uniformly distributed in the chickpea genome have been used to develop a genotyping kit for chickpea [19], analyze genetic relationships among Cicer species [23,27] and assess levels of cross-transferability [28,29]. Further, these markers have been applied for the construction of intraspecific [30-36] and interspecific [21,26,37-39] genetic linkage maps and for mapping genes of agronomic importance such as disease resistance [37,39,40] and yield related traits [30,41,42], thereby demonstrating that SSRs are ideal tools for broad applications in basic and applied plant biology [43,44]. However, all these studies have repeatedly used only the limited set of available STMS markers and not more than 120 STMS markers have been mapped on the intraspecific linkage maps currently available [30,34,35].…”