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- Title
Oligo-FISH barcode in beans: a new chromosome identification system.
- Authors
de Oliveira Bustamante, Fernanda; do Nascimento, Thiago Henrique; Montenegro, Claudio; Dias, Sibelle; do Vale Martins, Lívia; Braz, Guilherme Tomaz; Benko-Iseppon, Ana Maria; Jiang, Jiming; Pedrosa-Harand, Andrea; Brasileiro-Vidal, Ana Christina
- Abstract
Key message: An Oligo-FISH barcode system was developed for two model legumes, allowing the identification of all cowpea and common bean chromosomes in a single FISH experiment, and revealing new chromosome rearrangements. The FISH barcode system emerges as an effective tool to understand the chromosome evolution of economically important legumes and their related species. Current status on plant cytogenetic and cytogenomic research has allowed the selection and design of oligo-specific probes to individually identify each chromosome of the karyotype in a target species. Here, we developed the first chromosome identification system for legumes based on oligo-FISH barcode probes. We selected conserved genomic regions between Vigna unguiculata (Vu, cowpea) and Phaseolus vulgaris (Pv, common bean) (diverged ~ 9.7–15 Mya), using cowpea as a reference, to produce a unique barcode pattern for each species. We combined our oligo-FISH barcode pattern with a set of previously developed FISH probes based on BACs and ribosomal DNA sequences. In addition, we integrated our FISH maps with genome sequence data. Based on this integrated analysis, we confirmed two translocation events (involving chromosomes 1, 5, and 8; and chromosomes 2 and 3) between both species. The application of the oligo-based probes allowed us to demonstrate the participation of chromosome 5 in the translocation complex for the first time. Additionally, we detailed a pericentric inversion on chromosome 4 and identified a new paracentric inversion on chromosome 10. We also detected centromere repositioning associated with chromosomes 2, 3, 5, 7, and 9, confirming previous results for chromosomes 2 and 3. This first barcode system for legumes can be applied for karyotyping other Phaseolinae species, especially non-model, orphan crop species lacking genomic assemblies and cytogenetic maps, expanding our understanding of the chromosome evolution and genome organization of this economically important legume group.
- Subjects
COMMON bean; SYSTEM identification; CHROMOSOMES; COWPEA; CHROMOSOME inversions; BEANS; DNA sequencing; LEGUMES
- Publication
Theoretical & Applied Genetics, 2021, Vol 134, Issue 11, p3675
- ISSN
0040-5752
- Publication type
Article
- DOI
10.1007/s00122-021-03921-z