Centromeres are hotspots for chromosomal inversions and breeding traits in mango
Chromosomal inversions can preserve combinations of favorable alleles by suppressing recombination. Simultaneously, they reduce the effectiveness of purifying selection enabling deleterious alleles to accumulate. This study explores how areas of low recombination, including centromeric regions and chromosomal inversions, contribute to the accumulation of deleterious and favorable loci in 225 Mangifera indica genomes from the Australian Mango Breeding Program. Here, we identify 17 chromosomal inversions that cover 7.7% (29.7 Mb) of the M. indica genome: eight pericentric (inversion includes the centromere) and nine paracentric (inversion is on one arm of the chromosome). Our results show that these large pericentric inversions are accumulating deleterious loci, while the paracentric inversions show deleterious levels above and below the genome wide average. We find that despite their deleterious load, chromosomal inversions contain small effect loci linked to variation in crucial breeding traits. These results indicate that chromosomal inversions have likely facilitated the evolution of key mango breeding traits. Our study has important implications for selective breeding of favorable combinations of alleles in regions of low recombination.
Authors
- Daniel Ortíz-Barrientos (ORCID: https://orcid.org/0000-0002-7493-416X)
- I.S.E. Bally (ORCID: https://orcid.org/0000-0002-0169-4070)
- Agnelo Furtado (ORCID: https://orcid.org/0000-0001-6130-9026)
- Asjad Ali (ORCID: https://orcid.org/0000-0002-0415-4598)
- Norman Munyengwa (ORCID: https://orcid.org/0000-0001-9145-3504)
- Natalie Dillon (ORCID: https://orcid.org/0000-0002-9818-6354)
- Robert James Henry (ORCID: https://orcid.org/0000-0002-4060-0292)
- David Kainer (ORCID: https://orcid.org/0000-0001-7271-4676)
- Cassandra Elphinstone (ORCID: https://orcid.org/0000-0002-2968-1431)
- Craig Hardner (ORCID: https://orcid.org/0000-0001-7134-2524)
- Wijesundara Wasala Wijesundara (ORCID: https://orcid.org/0000-0002-9869-8608)
- Matthew Webb (ORCID: https://orcid.org/0000-0001-7014-936X)
- Kathleen McLay (ORCID: https://orcid.org/0009-0002-6074-6931)
Institutions
- Australian Research Council (AU)
- University of British Columbia (CA)
- The University of Queensland (AU)
- Agriculture and Food (AU)
- ARC Centre of Excellence for Plant Success in Nature and Agriculture (AU)
- Department of Primary Industries (AU)
Publication Details
- Journal
- New Phytologist
- Published
- 2024-11-15
- DOI
- https://doi.org/10.1111/nph.20252
- Citations
- 11
- Primary Topic
- Plant Virus Research Studies
- Type
- article
- Field-Weighted Citation Impact
- 6.60
Funders
- Hort Innovation
- Australian Research Council Centre of Excellence for Plant Success in Nature and Agriculture