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. 2022 Nov 23;13(12):2188.
doi: 10.3390/genes13122188.

Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule

Xiujuan Ren  1 , Yuanyi Liu  1 , Yiping Zhao  1 , Bei Li  1 , Dongyi Bai  1 , Gerelchimeg Bou  1 , Xinzhuang Zhang  1 , Ming Du  1 , Xisheng Wang  1 , Tugeqin Bou  1 , Yingchao Shen  1 , Manglai Dugarjaviin  1
Affiliations

Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule

Xiujuan Ren et al. Genes (Basel). .

Abstract

Interspecific hybridization often shows negative effects on hybrids. However, only a few multicellular species, limited to a handful of plants and animals, have shown partial genetic mechanisms by which hybridization leads to low fitness in hybrids. Here, to explore the outcome of combining the two genomes of a horse and donkey, we analyzed the whole-genome sequences from an Equus parent-offspring trio using Illumina platforms. We generated 41.39× and 46.21× coverage sequences for the horse and mule, respectively. For the donkey, a 40.38× coverage sequence was generated and stored in our laboratory. Approximately 24.86 million alleles were discovered that varied from the reference genome. Single nucleotide polymorphisms were used as polymorphic markers for assigning alleles to their parental genomic inheritance. We identified 25,703 Mendelian inheritance error single nucleotide polymorphisms in the mule genome that were not inherited from the parents through Mendelian inheritance. A total of 555 de novo single nucleotide polymorphisms were also identified. The rate of de novo single nucleotide polymorphisms was 2.21 × 10-7 in the mule from the Equus parent-offspring trio. This rate is obviously higher than the natural mutation rate for Equus, which is also consistent with the previous hypothesis that interracial crosses may have a high mutation rate. The genes associated with these single nucleotide polymorphisms are mainly involved in immune processes, DNA repair, and cancer processes. The results of the analysis of three genomes from an Equus parent-offspring trio improved our knowledge of the consequences of the integration of parental genomes in mules.

Keywords: Mendelian inheritance error; equus; genomic incompatibility; heterogeneous hybridization.

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Figure 1
Figure 1
Analysis of non-Mendelian inheritance SNPs. Classification of non-Mendelian inheritance SNPs. When variant alleles were identified only in the mule, they were classified as [I] de novo SNPs. MIE SNPs were classified into [II] inherited from the donkey and [III] inherited from the horse.
Figure 2
Figure 2
The statistics of SNP distribution.
Figure 3
Figure 3
Integrated pathway network analysis of point mutation genes involved in antigen processing and presentation in the mule genome. Green and red represent pathways; pink represents genes.
See this image and copyright information in PMC

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