Comparative karyotype analysis in chickpea (Cicer arietinum L.) using oligo painting FISH

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 chickpea genome at chromosomal level,
including the long-range molecular chromosome organization is limited.
Earlier cytogenetic studies in chickpea suffered from 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-FISH barcodes for identification of chromosomes and comparative
analysis among closely related chickpea genotypes. Our results show the
potential of oligo-FISH barcoding for 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
painting appears as a powerful tool not only for comparative karyotyping,
but also for validation of genome assemblies.