Summary 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.

中文翻译：

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着丝粒是芒果染色体倒位和育种性状的热点


摘要 染色体倒位可以通过抑制重组来保留有利等位基因的组合。同时，它们降低了纯化选择的有效性，使有害等位基因得以积累。本研究探讨了低重组区域，包括着丝粒区域和染色体倒位，如何导致澳大利亚芒果育种计划的 225 个 Mangifera indica 基因组中有害和有利基因座的积累。在这里，我们鉴定了 17 个染色体倒位，覆盖了 7.7% （29.7 Mb） 的 M. indica 基因组：8 个着丝粒周围（倒位包括着丝粒）和 9 个近着丝粒（倒位位于染色体的一个臂上）。我们的结果表明，这些大的着丝粒周围倒置正在积累有害的基因座，而旁着丝粒倒置显示出高于和低于全基因组平均值的有害水平。我们发现，尽管染色体倒置具有有害负荷，但它们包含与关键育种性状变异相关的小效应位点。这些结果表明，染色体倒置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育种等位基因的有利组合具有重要意义。