Abstract
Comparative cytogenetic mapping is a powerful approach to gain insights into genome organization of orphan crops, lacking a whole sequenced genome. To investigate the cytogenomic evolution of important Vigna and Phaseolus beans, we built a BAC-FISH (fluorescent in situ hybridization of bacterial artificial chromosome) map of Vigna aconitifolia (Vac, subgenus Ceratotropis), species with no sequenced genome, and compared with V. unguiculata (Vu, subgenus Vigna) and Phaseolus vulgaris (Pv) maps. Seventeen Pv BACs, eight Vu BACs, and 5S and 35S rDNA probes were hybridized in situ on the 11 Vac chromosome pairs. Five Vac chromosomes (Vac6, Vac7, Vac9, Vac10, and Vac11) showed conserved macrosynteny and collinearity between V. unguiculata and P. vulgaris. On the other hand, we observed collinearity breaks, identified by pericentric inversions involving Vac2 (Vu2), Vac4 (Vu4), and Vac3 (Pv3). We also detected macrosynteny breaks of translocation type involving chromosomes 1 and 8 of V. aconitifolia and P. vulgaris; 2 and 3 of V. aconitifolia and P. vulgaris; and 1 and 5 of V. aconitifolia and V. unguiculata. Considering our data and previous BAC-FISH studies, six chromosomes (1, 2, 3, 4, 5, and 8) are involved in major karyotype divergences between genera and five (1, 2, 3, 4, and 5) between Vigna subgenera, including mechanisms such as duplications, inversions, and translocations. Macrosynteny breaks between Vigna and Phaseolus suggest that the major chromosomal rearrangements have occurred within the Vigna clade. Our cytogenomic comparisons bring new light on the degree of shared macrosynteny and mechanisms of karyotype diversification during Vigna and Phaseolus evolution.
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Abbreviations
- BAC:
-
Bacterial artificial chromosome
- Chr:
-
Chromosome
- DAPI:
-
4,6-Diamidino-2-phenylindole
- FISH:
-
Fluorescence in situ hybridization
- LG:
-
Linkage group
- Mya:
-
Million years ago
- rDNA:
-
Ribosomal DNA
- Pl :
-
Phaseolus lunatus
- Pm :
-
Phaseolus microcarpus
- Pv :
-
Phaseolus vulgaris
- Vac :
-
Vigna aconitifolia
- Vm :
-
Vigna mungo
- Vum :
-
Vigna umbellata
- Vu :
-
Vigna unguiculata
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Acknowledgments
The authors thank Embrapa Meio-Norte (Teresina, Brazil), Embrapa Arroz e Feijão (Santo Antônio de Goiás, Brazil), and IPK (Institute of Plant Genetics and Crop Plant Research, Gatersleben, Germany) for supplying the seeds; Paul Gepts (University of California, Davis, United States) for supplying the BAC clones from P. vulgaris; and Valérie Geffroy (Université Paris-Sud, Orsay Cedex, France) for the bacteriophage SJ19.12 from P. vulgaris.
Funding
This study received financial support and fellowships from CNPq (Conselho Nacional de Desenvolvimento Científico e Tecnológico), CAPES (Coordenação de Pessoal de Nível Superior: Finance Code001; InterSys Network, BioComputational Program), and FACEPE (Fundação de Amparo a Ciência e Tecnologia do Estado de Pernambuco).
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ARSO: performed BAC-FISH, constructed comparative maps and figures, and wrote the manuscript. LVM: performed BAC-FISH and helped to write the manuscript. FOB: helped to carry out the experiments and to write the manuscript. APH: doctorate co-supervisor of ARSO, discussed the experiments and results, maintained and provided P. vulgaris BAC clones. MMA: maintained and provided V. unguiculata BAC clones. TC: maintained and provided V. unguiculata BAC clones. AMBI: doctorate co-supervisor of ARSO and discussed the results. AFC: performed seed multiplication. ACBV: doctorate supervisor of ARSO, designed and directed the research, and corrected the manuscript. All authors read, discussed, and approved the final version of the manuscript.
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Key message
Vigna aconitifolia, V. unguiculata, and Phaseolus vulgaris karyotypes share partial macrosynteny, with evidences of major chromosomal rearrangements (inversions, duplications and translocations) related to the Vigna and Phaseolus (Phaseolineae subtribe) diversification.
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Oliveira, A.R.d.S., Martins, L.d., Bustamante, F.d.O. et al. Breaks of macrosynteny and collinearity among moth bean (Vigna aconitifolia), cowpea (V. unguiculata), and common bean (Phaseolus vulgaris). Chromosome Res 28, 293–306 (2020). https://doi.org/10.1007/s10577-020-09635-0
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DOI: https://doi.org/10.1007/s10577-020-09635-0