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

Zobrazit více v PubMed

Abbo S., Berger J., Turner N. C. (2003). Evolution of cultivated chickpea: four bottlenecks limit diversity and constrain adaptation. Funct. Plant Biol. 30 1081–1087. 10.1071/FP03084 PubMed DOI

Albert P. S., Zhang T., Semrau K., Rouillard J. M., Kao Y. H., Wang C. J. R., et al. (2019). Whole-chromosome paints in maize reveal rearrangements, nuclear domains, and chromosomal relationships. Proc. Natl. Acad. Sci. U.S.A. 116 1679–1685. 10.1073/pnas.1813957116 PubMed DOI PMC

Altschul S. F., Gish W., Miller W., Myers E. W., Lipman D. J. (1990). Basic local alignment search tool. J. Mol. Biol. 215 403–410. 10.1016/S0022-2836(05)80360-2 PubMed DOI

Arumuganathan K., Earle E. D. (1991). Nuclear DNA content of some important plant species. Plant Mol. Biol. Rep. 9 208–218. 10.1007/BF02672069 DOI

Barmukh R., Roorkiwal M., Jaba J., Chitikineni A., Mishra S. P., Sagurthi S. R., et al. (2021). Development of a dense genetic map and QTL analysis for pod borer Helicoverpa armigera (Hübner) resistance component traits in chickpea (Cicer arietinum L.). Plant Genome 14:e20071. 10.1002/tpg2.20071 PubMed DOI

Begum K. N., Alam S. S. (2016a). Karyomorphological analysis with differential staining of nine Cicer arietinum L. varieties. Bangladesh J. Bot. 45 327–334.

Begum K. N., Alam S. S. (2016b). Differential fluorescent banding in nine varieties of Cicer arietinum L. Cytologia 81 383–387. 10.1508/cytologia.81.383 DOI

Belser C., Istace B., Denis E., Dubarry M., Baurens F. C., Falentin C., et al. (2018). Chromosome-scale assemblies of plant genomes using nanopore long reads and optical maps. Nat. Plants 4 879–887. 10.1038/s41477-018-0289-4 PubMed DOI

Braz G. T., do Vale Martins L., Zhang T., Albert P. S., Birchler J. A., Jiang J. (2020). A universal chromosome identification system for maize and wild Zea species. Chromosome Res. 28 183–194. 10.1007/s10577-020-09630-5 PubMed DOI

Braz G. T., He L., Zhao H., Zhang T., Semrau K., Rouillard J. M. (2018). Comparative oligo-FISH mapping: an efficient and powerful methodology to reveal karyotypic and chromosomal evolution. Genetics 208 513–523. 10.1534/genetics.117.300344 PubMed DOI PMC

Bredeson J. V., Lyons J. B., Oniyinde I. O., Okereke N. R., Kolade O., Nnabue I., et al. (2021). High contiguity de novo genome sequence of Trifoliate yam (Dioscorea dumetorum) using long read sequencing. bioRxiv [Preprint] bioRxiv 2021.04.14.439117, 10.1101/2021.04.14.439117 DOI

Chen L., Su D., Sun J., Li Z., Han Y. (2020). Development of a set of chromosome-specific oligonucleotide markers and karyotype analysis in the Japanese morning glory Ipomoea nil. Sci. Hortic. 273:109633. 10.1016/j.scienta.2020.109633 DOI

Deokar A., Sagi M., Tar’an B. (2019). Genome-wide SNP discovery for development of high-density genetic map and QTL mapping of ascochyta blight resistance in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 132 1861–1872. 10.1007/s00122-019-03322-3 PubMed DOI PMC

Deschamps S., Zhang Y., Llaca V., Ye L., Sanyal A., King M., et al. (2018). Chromosome-scale assembly of the sorghum genome using nanopore sequencing and optical mapping. Nat. Commun. 9:4844. 10.1038/s41467-018-07271-1 PubMed DOI PMC

do Vale Martins L., de Oliveira Bustamante F., da Silva Oliveira A. R., da Costa A. F., de Lima Feitoza L., Liang Q., et al. (2021). BAC- and oligo-FISH mapping reveals chromosome evolution among Vigna angulatris, V. enguiculata, and Phaseolus vulgaris. Chromosoma 130 133–147. 10.1007/s00412-021-00758-9 PubMed DOI

Doležel J., Doleželová M., Roux N., Van den houwe I. (1998). A novel method to prepare slides for high resolution chromosome studies in Musa spp. Infomusa 7 3–4.

Galasso I., Pignone D., Frediani M., Maggiani M., Cremonini R. (1996). Chromatin characterization by banding techniques, in situ hybridization, and nuclear DNA content in Cicer L. (Leguminosae). Genome 39 258–265. 10.1139/g96-035 PubMed DOI

Gaur R., Jeena G., Shah N., Gupta S., Pradhan S., Tyagi A. K., et al. (2015). High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea. Sci. Rep. 5:13387. 10.1038/srep13387 PubMed DOI PMC

Gerlach W. L., Bedbrook J. R. (1979). Cloning and characterization of ribosomal RNA genes from wheat and barley. Nucleic Acids Res. 7 1869–1885. 10.1093/nar/7.7.1869 PubMed DOI PMC

Gortner G., Nenno M., Weising K., Zink D., Nagl W., Kahl G. (1998). Chromosomal localization and distribution of simple sequence repeat and the Arabidopsis-type telomere sequence in the genome of Cicer arietinum L. Chromosome Res. 6 97–104. 10.1023/A:1009282828236 PubMed DOI

Gupta S., Nawaz K., Parween S., Roy R., Sahu K., Pole A. K., et al. (2017). Draft genome sequence of Cicer reticulatum L., the wild progenitor of chickpea provides a resource for agronomic trait improvement. DNA Res. 24 1–10. 10.1093/dnares/dsw042 PubMed DOI PMC

Han Y., Zhang T., Thammapichai P., Weng Y., Jiang J. (2015). Chromosome-specific painting in Cucumis species using bulked oligonucleotides. Genetics. 200 771–779. 10.1534/genetics.115.177642 PubMed DOI PMC

Hiremath P. J., Kumar A., Penmetsa R. V., Farmer A., Schlueter J. A., Chamarthi S., et al. (2012). Large-scale development of cost-effective SNP marker assays for diversity assessment and genetic mapping in chickpea and comparative mapping in legumes. Plant Biotechnol. J. 10 716–732. 10.1111/j.1467-7652.2012.00710.x PubMed DOI PMC

Hou L., Xu M., Zhang T., Xu Z., Wang W., Zhang J., et al. (2018). Chromosome painting and its applications in cultivated and wild rice. BMC Plant Biol. 18:110. 10.1186/s12870-018-1325-2 PubMed DOI PMC

Jain M., Misra G., Patel R. K., Priya P., Jhanwar S., Khan A. W., et al. (2013). A draft genome sequence of the pulse crop chickpea (Cicer arietinum L.). Plant J. 74 715–729. 10.1111/tpj.12173 PubMed DOI

Jiang J. (2019). Fluorescence in situ hybridization in plants: recent developments and future applications. Chromosome Res. 27 153–165. 10.1007/s10577-019-09607-z PubMed DOI

Karafiátová M., Hřibová E., Doležel J. (2017). “Cytogenetics of Cicer,” in The Chickpea Genome, eds Varshney R., Thudi M., Muehlbauer F. (Cham: Springer; ), 25–41. 10.1007/978-3-319-66117-9_4 DOI

Li H., Durbin R. (2010). Fast and accurate long-read alignment with burrows–wheeler transform. Bioinformatics 26 589–595. 10.1093/bioinformatics/btp698 PubMed DOI PMC

Liu X., Sun S., Wu Y., Zhou Y., Gu S., Yu H., et al. (2020). Dual-color oligo-FISH can reveal chromosomal variations and evolution in Oryza species. Plant J. 101 112–121. 10.1111/tpj.14522 PubMed DOI

Ohri D., Pal M. (1991). The origin of chickpea (Cicer arietinum L.): karyotype and nuclear DNA amount. Heredity 66 367–372. 10.1038/hdy.1991.46 DOI

Parween S., Nawaz K., Roy R., Pole A. K., Suresh B. V., Misra G., et al. (2015). An advanced draft genome assembly of a desi type chickpea (Cicer arietinum L.). Sci. Rep. 5:12806. 10.1038/srep12806 PubMed DOI PMC

Quinlan A. R., Hall I. M. (2010). BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26 841–842. 10.1093/bioinformatics/btq033 PubMed DOI PMC

Rajesh P. N., Sant V. J., Gupta V. S., Muehlbauer F. J., Rajesh P. K. (2003). Genetic relationships among annual and perennial wild species of Cicer using inter simple sequence repeat (ISSR) polymorphism. Euphytica 129 15–23. 10.1023/A:1021567821141 DOI

Redden R. J., Berger J. D. (2007). “History and origin of chickpea,” in Chickpea Breeding and Management, eds Yadav S. S., Redden R. J., Chen W., Sharma B. (Oxfordshire: CAB International; ), 10.1079/9781845932138.001 DOI

Roorkiwal M., Jarquin D., Singh M. K., Gaur P. M., Bharadwaj C., Rathore A., et al. (2018). Genomic-enabled prediction models using multi-environment trials to estimate the effect of genotype× environment interaction on prediction accuracy in chickpea. Sci. Rep. 8 1–11. 10.1038/s41598-018-30027-2 PubMed DOI PMC

Roorkiwal M., von Wettberg E. J., Upadhyaya H. D., Warschefsky E., Rathore A., Varshney R. K. (2014). Exploring germplasm diversity to understand the domestication process in Cicer spp. using SNP and DarT markers. PLoS One 9:e102016. 10.1371/journal.pone.0102016 PubMed DOI PMC

Ruperao P., Chan C. K. K., Azam S., Karafiátová M., Hayashi S., Čížková J., et al. (2014). A chromosomal genomics approach to assess and validate the desi and kabuli draft chickpea genome assemblies. Plant Biotechnol. J. 12 778–786. 10.1111/pbi.12182 PubMed DOI

Schwarzacher T., Heslop-Harrison P. (2000). Practical in Situ Hybridisation. Oxford: BIOS Scientific Publishers Limited, 203.

Sharma P. C., Winter P., Bünger T., Hüttel B., Weising K., Kahl G. (1995). Abundance and polymorphism of di-, tri- and tetra-nucleotide tandem repeats in chickpea (Cicer arietinum L.). Theor. Appl. Genet. 90 90–96. 10.1007/BF00221000 PubMed DOI

Šimoníková D., Němečková A., Čížková J., Brown A., Swennen R., Doležel J., et al. (2020). Chromosome painting in cultivated bananas and their wild relatives (Musa spp.) reveals differences in chromosome structure. Int. J. Mol. 21:7915. 10.3390/ijms21217915 PubMed DOI PMC

Šimoníková D., Němečková A., Karafiátová M., Uwimana B., Swennen R., Doležel J., et al. (2019). Chromosome painting facilitates anchoring reference genome sequence to chromosomes in situ and integrated karyotyping in banana (Musa Spp.). Front. Plant Sci. 10:1503. 10.3389/fpls.2019.01503 PubMed DOI PMC

Staginnus C., Desel C., Schmidt T., Kahl G. (2010). Assembling a puzzle of dispersed retrotransposable sequences in the genome of chickpea (Cicer arietinum L.). Genome 53 1090–1102. 10.1139/G10-093 PubMed DOI

Staginnus C., Huettel B., Desel C., Schmidt T., Kahl G. (2001). A PCR-based assay to detect En/Spm-like transposon sequences in plants. Chromosome Res. 9 591–605. 10.1023/A:1012455520353 PubMed DOI

Staginnus C., Winter P., Desel C., Schmidt T., Kahl G. (1999). Molecular structure and chromosomal localization of major repetitive DNA families in the chickpea (Cicer arietinum L.) genome. Plant Mol. Biol. 39 1037–1050. 10.1023/A:1006125430386 PubMed DOI

Sudupak M. A., Akkaya M. S., Kence A. (2002). Analysis of genetic relationships omong perennial and annual Cicer species growing in Turkey using RAPD markers. Theor. Appl. Genet. 105 1220–1228. 10.1007/s00122-003-1505-8 PubMed DOI

Thudi M., Bohra A., Nayak S. N., Varghese N., Shah T. M., Penmetsa R. V., et al. (2011). Novel SSR markers from BAC-end sequences, DArT arrays and a comprehensive genetic map with 1,291 marker loci for chickpea (Cicer arietinum L.). PLoS One 6:e27275. 10.1371/journal.pone.0027275 PubMed DOI PMC

Thudi M., Chitikineni A., Liu X., He W., Roorkiwal M., Yang W. (2016). Recent breeding programs enhanced genetic diversity in both desi and kabuli varieties of chickpea (Cicer arietinum L.). Sci. Rep. 6 1–10. 10.1038/srep38636 PubMed DOI PMC

Upadhyaya H. D., Dwicedi S. L., Baum M., Varshney R. K., Udupa S. M., Gowda C. L., et al. (2008). Genetic structure, diversity, and allelic richness in composite collection and reference set in chickpea (Cicer arietinum L.). BMC Plant Biol. 8:106. 10.1186/1471-2229-8-106 PubMed DOI PMC

Varshney R. K., Song C., Saxena R. K., Azam S., Yu S., Sharpe A. G., et al. (2013). Draft genome sequence of chickpea (Cicer arietinum) provides a resource for trait improvement. Nat. Biotechnol. 31 240–246. 10.1038/nbt.2491 PubMed DOI

Varshney R. K., Thudi M., Roorkiwal M., He W., Upadhyaya H. D., Yang W., et al. (2019). Resequencing of 429 chickpea accessions from 45 countries provides insight into genome diversity, domestication and agronomic traits. Nat. Genet. 51 857–864. 10.1038/s41588-019-0401-3 PubMed DOI

Vláčilová K., Ohri D., Vrána J., Číhalíková J., Kubaláková M., Kahl G., et al. (2002). Development of flow cytogenetics and physical genome mapping in chickpea (Cicer arietinum L.). Chrom. Res. 10 695–706. 10.1023/A:1021584914931 PubMed DOI

Wang J., Liu W., Zhu D., Hong P., Zhang S., Xiao S., et al. (2020). Chromosome-scale genome assembly of sweet cherry (Prunus avium L.) cv. Tieton obtained using long-read and Hi-C seqeuncing. Hortic. Res. 7:122. 10.1038/s41438-020-00343-8 PubMed DOI PMC

Xin H., Zhang T., Han Y., Wu Y., Shi J., Xi M., et al. (2018). Chromosome painting and comparative physical mapping of the sex chromosomes in Populus tomentosa and Populus deltoides. Chromosoma 127 313–321. 10.1007/s00412-018-0664-y PubMed DOI

Zatloukalová P., Hřibová E., Kubaláková M., Suchánková P., Šimková H., Adoración C., et al. (2011). Integration of genetic and physical maps of the chickpea (Cicer arietinum L.) genome using flow-sorted chromosomes. Chromosome Res. 19 729–739. 10.1007/s10577-011-9235-2 PubMed DOI

Zimin A. V., Marçais G., Puiu D., Roberts M., Salzberg S. L., Yorke J. A. (2013). The MaSuRCA genome assembler. Bioinformatics 29 2669–2677. 10.1093/bioinformatics/btt476 PubMed DOI PMC

Zobrazit více v PubMed

Dryad
10.5061/dryad.66t1g1k32