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Genes2022; 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.

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 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 single nucleotide polymorphisms were also identified. The rate of single nucleotide polymorphisms was 2.21 × 10 in the mule from the parent-offspring trio. This rate is obviously higher than the natural mutation rate for , 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 parent-offspring trio improved our knowledge of the consequences of the integration of parental genomes in mules.
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Publication Date: 2022-11-23 PubMed ID: 36553455PubMed Central: PMC9778318DOI: 10.3390/genes13122188Google Scholar: Lookup
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  • Journal Article
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  • Non-U.S. Gov't

Summary

This research summary has been generated with artificial intelligence and may contain errors and omissions. Refer to the original study to confirm details provided. Submit correction.

This research study investigated the genomic characteristics of a mule, a hybrid offspring of a horse and a donkey, by analyzing its whole-genome sequence along with those of its parents. The researchers found genetic variations in the mule that were not inherited from the parents, suggesting a higher mutation rate in hybrid animals.

Study Methodology and Data Generation

  • The scientists used Illumina sequencing technology to analyze the entire genomes of a parent-offspring trio, which included a horse, a donkey, and their mule offspring.
  • They generated comprehensive sequence data with coverage depths between 40.38× and 46.21× for the horse, mule, and donkey genomes.
  • Approximately 24.86 million distinct variations, or alleles, were found when compared to a reference genome.

Analysis of Genetic Variation

  • The researchers used single nucleotide polymorphisms (SNPs), which are variations at a single position in the DNA sequence, to track which alleles were inherited from which parent.
  • In the mule’s genome, they discovered 25,703 SNPs that did not follow typical Mendelian inheritance patterns—in other words, these variants were not directly inherited from the horse or donkey parent.
  • In addition to these, they identified 555 other SNPs of special interest.

Implications of the Findings

  • The rate of these special SNPs was significantly higher in the mule than the natural mutation rate for other species. This suggests that hybrid offspring, such as mules, might have a greater mutation rate than non-hybrids.
  • Genes associated with these unique SNPs were mainly involved in various important biological functions, including immune response, DNA repair, and cancer-related processes.
  • These findings enhance our understanding of the genomic consequences of hybridization. This improved knowledge could be important for species conservation efforts, breeding programs, and the study of evolutionary biology.

Cite This Article

APA
Ren X, Liu Y, Zhao Y, Li B, Bai D, Bou G, Zhang X, Du M, Wang X, Bou T, Shen Y, Dugarjaviin M. (2022). Analysis of the Whole-Genome Sequences from an Equus Parent-Offspring Trio Provides Insight into the Genomic Incompatibilities in the Hybrid Mule. Genes (Basel), 13(12), 2188. https://doi.org/10.3390/genes13122188

Publication

Genes
ISSN: 2073-4425
NlmUniqueID: 101551097
Country: Switzerland
Language: English
Volume: 13
Issue: 12
PII: 2188

Researcher Affiliations

Ren, Xiujuan
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Liu, Yuanyi
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Zhao, Yiping
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Li, Bei
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Bai, Dongyi
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Bou, Gerelchimeg
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Zhang, Xinzhuang
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Du, Ming
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Wang, Xisheng
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Bou, Tugeqin
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Shen, Yingchao
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.
Dugarjaviin, Manglai
  • Equine Research Center, College of Animal Science, Inner Mongolia Agricultural University, 306 Zhaowuda Road, Hohhot 010018, China.

MeSH Terms

  • Horses / genetics
  • Animals
  • Equidae / genetics
  • Genome
  • Genomics
  • Polymorphism, Single Nucleotide / genetics
  • Hybridization, Genetic

Conflict of Interest Statement

The authors declare no conflict of interest.

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