Centromeres are hotspots for chromosomal inversions and breeding traits in mango

IF 8.3 1区生物学 Q1 PLANT SCIENCES New Phytologist Pub Date : 2024-11-15 DOI:10.1111/nph.20252

Melanie J. Wilkinson, Kathleen McLay, David Kainer, Cassandra Elphinstone, Natalie L. Dillon, Matthew Webb, Upendra K. Wijesundara, Asjad Ali, Ian S. E. Bally, Norman Munyengwa, Agnelo Furtado, Robert J. Henry, Craig M. Hardner, Daniel Ortiz-Barrientos

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Abstract

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.

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中心粒是芒果染色体倒位和育种性状的热点

染色体倒位可以通过抑制重组来保存有利等位基因的组合。本研究探讨了在澳大利亚芒果育种计划的 225 个 Mangifera indica 基因组中，低重组区域（包括中心粒区域和染色体倒位）如何导致有害和有利基因座的积累。在这里，我们发现了 17 个染色体倒位，覆盖了籼芒果基因组的 7.7% （29.7 Mb）：8 个包心（倒位包括中心体）和 9 个旁心（倒位在染色体的一个臂上）。我们的研究结果表明，这些大的同心倒位正在积累有害基因位点，而旁中心倒位则显示出高于和低于全基因组平均水平的有害水平。我们发现，尽管存在有害负载，染色体倒位仍包含与关键育种性状变异有关的小效应位点。这些结果表明，染色体倒位很可能促进了芒果关键育种性状的进化。我们的研究对于在低重组区域选择性培育有利的等位基因组合具有重要意义。

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来源期刊

New Phytologist 生物-植物科学

自引率

5.30%

发文量

728

期刊介绍： New Phytologist is an international electronic journal published 24 times a year. It is owned by the New Phytologist Foundation, a non-profit-making charitable organization dedicated to promoting plant science. The journal publishes excellent, novel, rigorous, and timely research and scholarship in plant science and its applications. The articles cover topics in five sections: Physiology & Development, Environment, Interaction, Evolution, and Transformative Plant Biotechnology. These sections encompass intracellular processes, global environmental change, and encourage cross-disciplinary approaches. The journal recognizes the use of techniques from molecular and cell biology, functional genomics, modeling, and system-based approaches in plant science. Abstracting and Indexing Information for New Phytologist includes Academic Search, AgBiotech News & Information, Agroforestry Abstracts, Biochemistry & Biophysics Citation Index, Botanical Pesticides, CAB Abstracts®, Environment Index, Global Health, and Plant Breeding Abstracts, and others.