Tools
ToolsHiggins, Janet, Osorio-Guarín, Jaime Andrés, Olave-Achury, Carolina, Toloza-Moreno, Deisy Lisseth, Enriquez, Ayda, Palma, Federica Di, Yockteng, Roxana and De Vega, Jose J. (2024) Characterizing subgenome recombination and chromosomal imbalances in banana varietal lineages. Annals of Botany, 133 (2). pp. 349-364. ISSN 0305-7364
Preview |
PDF (mcad192)
- Published Version
Available under License Creative Commons Attribution. Download (2MB) | Preview |
Abstract
Background: Bananas and plantains (Musa spp.) are among the most important crops worldwide. The cultivated varieties are vegetatively propagated, so their genetic diversity is essentially fixed over time. Musa acuminata, M. balbisiana and M. schizocarpa have provided the named A, B and S subgenomes that predominantly constitute these varieties. Here we aimed to characterize intergenetic recombination and chromosomal imbalances between these A/B/S subgenomes, which often result in copy-number variants (CNVs) leading to changes in gene dosage and phenotype, in a diverse panel of bananas and plantains. This will allow us to characterize varietal lineages better and identify sources of genetic variation. Methods We delimited population structure and clonal lineages in a diverse panel of 188 banana and plantain accessions from the most common cultivars using admixture, principal component and phylogenetic analyses. We used new scalable alignment-based methods, Relative Averaged Alignment (RAA) and Relative Coverage, to infer subgenome composition (AA, AAB, etc.) and interspecific recombination. Results In our panel, we identified ten varietal lineages composed of somatic clones, plus three groups of tetraploid accessions. We identified chromosomal exchanges resulting in gains/losses in chromosomal segments (CNVs), particularly in AAB and ABB varieties. Conclusions We demonstrated alignment-based RAA and Relative Coverage can identify subgenome composition and introgressions with similar results to more complex approaches based on single nucleotide polymorphism (SNP) databases. These ab initio species-agnostic methods can be used without sequencing a panel of wild ancestors to find private SNPs, or in recently diverged pools where private SNPs are uncommon. The extensive A/B/S exchanges and the variation in the length of some introgressions between lineages further support multiple foundational events of hybridization and residual backcrossing. Imbalances between A/B/S may have resulted in CNVs and gene dosage variation. Since most edible banana genomes are fixed on time, these CNVs are stable genetic variations probably associated with phenotypic variation for future genetic studies.
| Item Type: | Article |
|---|---|
| Additional Information: | DATA AVAILABILITY: Germplasm is held in AGROSAVIA’s collection (MGIS: COL004) and is available on request. All sequence data used in this paper have been deposited as study PRJEB62882 in the European Nucleotide Archive at https://www.ebi.ac.uk/ena/browser/view/PRJEB62882. A step by step guide to calculate and plot RAA and RC metrics is included (Supplementary Data File S7). Additionally, this step by step guide and all scripts and code used in the computational analyses are available in a Github repository at https://github.com/jjdevega/Structural-diversity-in-banana-cultivars FUNDING: J.H. and J.D.V. received funding from the Biotechnology and Biology Sciences Research Council (BBSRC)’s Global Challenge Research Fund (BB/P028098/1 and BB/P028098/2), and from the BBSRC Core Strategic Programme Grant (Genomes to Food Security) BB/CSP1720/1 and its constituent work package BBS/E/T/000PR9818 (WP1 Signatures of Domestication and Adaptation), as well as BB/X011089/1. |
| Uncontrolled Keywords: | banana,chromosomal imbalances,homoeologous,introgressions,musa,plantains,recombination,tools,medicine(all) ,/dk/atira/pure/subjectarea/asjc/2700 |
| Faculty \ School: | Faculty of Science > School of Biological Sciences |
| Related URLs: | |
| Depositing User: | LivePure Connector |
| Date Deposited: | 20 Aug 2025 16:30 |
| Last Modified: | 20 Aug 2025 16:30 |
| URI: | https://ueaeprints.uea.ac.uk/id/eprint/100188 |
| DOI: | 10.1093/aob/mcad192 |
Downloads
Downloads per month over past year
Actions (login required)
 |
View Item |