Chickpea (Cicer arietinum L.) is one of the main sources of plant proteins in the Indian subcontinent and West Asia, where two different morphotypes, desi and kabuli, are grown. Despite the progress in genome mapping and sequencing, the knowledge of the chickpea genome at the chromosomal level, including the long-range molecular chromosome organization, is limited. Earlier cytogenetic studies in chickpea suffered from a limited number of cytogenetic landmarks and did not permit to identify individual chromosomes in the metaphase spreads or to anchor pseudomolecules to chromosomes in situ. In this study, we developed a system for fast molecular karyotyping for both morphotypes of cultivated chickpea. We demonstrate that even draft genome sequences are adequate to develop oligo-fluorescence in situ hybridization (FISH) barcodes for the identification of chromosomes and comparative analysis among closely related chickpea genotypes. Our results show the potential of oligo-FISH barcoding for the identification of structural changes in chromosomes, which accompanied genome diversification among chickpea cultivars. Moreover, oligo-FISH barcoding in chickpea pointed out some problematic, most probably wrongly assembled regions of the pseudomolecules of both kabuli and desi reference genomes. Thus, oligo-FISH appears as a powerful tool not only for comparative karyotyping but also for the validation of genome assemblies.

Centre of Excellence in Genomics and Systems Biology International Crops Research Institute for the Semi Arid Tropics Hyderabad India

Centre of the Region Hana for Biotechnological and Agricultural Research Institute of Experimental Botany of the Czech Academy of Sciences Olomouc Czechia

Department of Cell Biology and Genetics Faculty of Science Palacký University Olomouc Czechia

State Agricultural Biotechnology Centre Centre for Crop and Food Innovation Murdoch University Murdoch WA Australia

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Dryad
10.5061/dryad.66t1g1k32