Karyotype Differentiation in Cultivated Chickpea Revealed by Oligopainting Fluorescence in situ Hybridization.

Alžběta Doležalová,Miroslava Karafiátová,Jaroslav Doležel,Lucia Sládeková,Kateřina Holušová,Denisa Šimoníková,Rajeev K Varshney,Eva Hřibová

doi:10.3389/fpls.2021.791303

Abstract

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.

Highlights

Chickpea (Cicer arietinum L.) is an important legume crop and one of the main sources of dietary proteins in South Asia and sub-Saharan Africa, where two different morphotypes, desi and kabuli, are grown
We have developed two bulked oligopainting probes for chromosome identification in C. arietinum
In silico mapping of oligomers designed for kabuli type of C. arietinum genome to the desi genotype revealed other short regions in the desi genome covered by the low number of kabuli-specific oligomers (Figure 1)

Summary

Introduction

Chickpea (Cicer arietinum L.) is an important legume crop and one of the main sources of dietary proteins in South Asia and sub-Saharan Africa, where two different morphotypes, desi and kabuli, are grown. Draft genome assemblies of both morphotypes were produced recently (Varshney et al, 2013; Ruperao et al, 2014; Parween et al, 2015), establishing a solid foundation for the development of molecular tools to speed-up chickpea breeding. The pseudomolecules were assembled using DNA markers (Thudi et al, 2011; Hiremath et al, 2012) that differed from those used in the desi genome sequence project. The use of a different strategy to order the scaffolds into pseudomolecules resulted in their different orientation between desi and kabuli types (Parween et al, 2015). Neither desi nor kabuli pseudomolecules were anchored to chromosomes

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