Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes

Abstract

Cultivated chickpea is the third most important legume after field bean and garden pea worldwide. Despite considerable breeding towards improved yield and resistance to biotic and abiotic stresses, the production of chickpea remained stagnant, but molecular tools are expected to increase the impact of current improvement programs. As a first step towards this goal, various genetic linkage maps have been established and markers linked to resistance genes been identified. However, until now, only one linkage group (LG) has been assigned to a specific chromosome. In the present work, mitotic chromosomes were sorted using flow cytometry and used as template for PCR with primers designed for genomic regions flanking microsatellites. These primers amplify sequence-tagged microsatellite site markers. This approach confirmed the assignment of LG8 to the smallest chromosome H. For the first time, LG5 was linked to the largest chromosome A, LG4 to a medium-sized chromosome E, while LG3 was anchored to the second largest chromosome B. Chromosomes C and D could not be flow-sorted separately and were jointly associated to LG6 and LG7. By the same token, chromosomes F and G were anchored to LG1 and LG2. To establish a set of preferably diagnostic cytogenetic markers, the genomic distribution of various probes was verified using FISH. Moreover, a partial genomic bacterial artificial chromosome (BAC) library was constructed and putative single/low-copy BAC clones were mapped cytogenetically. As a result, two clones were identified localizing specifically to chromosomes E and H, for which no cytogenetic markers were yet available.

Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement

“…The 74-bp tandem repeats were organized 'head to tail' with multiple copies within a previously identified LTR 16 that we conclude was misannotated. The fluorescence in situ hybridization (FISH) experiments with oligonucleotide probes for the 100-bp tandem repeat revealed centromeric and pericentromeric distribution on pro-metaphase chromosomes in agreement with previous reports 16,17 . The 74-bp tandem repeats are distributed along all chromosomes but excluded from regions containing the 100-bp tandem repeat (Supplementary Fig.…”

Impact of Genomic Technologies on Chickpea Breeding Strategies

“…A pioneer work towards integration of genetic-and chromosome-based physical maps has been done recently by Zatloukalová et al, [98]. They have been able to assign linkage groups (LG) in chickpea to different chromosomes using flow cytometry and PCR-based primers that amplify sequence-tagged microsatellite site markers.…”

Comparative Analysis of Kabuli Chickpea Transcriptome with Desi and Wild Chickpea Provides a Rich Resource for Development of Functional Markers

“…A considerable progress has been made in the development of genetic linkage maps of chickpea as well [13]–[18]. Further, the genetic and physical maps of chickpea genome have been integrated to assign the genetic linkage groups to particular chromosomes [19]. A significant progress in the chickpea improvement is expected to be made in coming years based on these genomic resources.…”