De Novo Assembly of the Donkey White Blood Cell Transcriptome and a Comparative Analysis of Phenotype-Associated Genes between Donkeys and Horses.
Authors: Xie Feng-Yun, Feng Yu-Long, Wang Hong-Hui, Ma Yun-Feng, Yang Yang, Wang Yin-Chao, Shen Wei, Pan Qing-Jie, Yin Shen, Sun Yu-Jiang, Ma Jun-Yu
Journal: PloS one
Summary
# Editorial Summary Donkeys are increasingly valued for meat, milk, and fibre production in commercial settings, yet genetic improvement programmes lag behind those for horses owing to limited genomic resources. Researchers sequenced white blood cell transcriptomes de novo and identified over 264,000 distinct donkey genes, predicting 38,949 protein fragments—establishing a foundational reference for the donkey genome when complete sequencing data remained unavailable. Comparative analysis with horses and Przewalski's horses revealed three proteins (HIC1, PRKRA, and KMT2A) associated with outer ear size that showed notable sequence variation across these equid species, suggesting these loci may underpin the phenotypic differences observed clinically. These findings enable more sophisticated transcriptome-based and genome-informed selection strategies for donkey breeding programmes, moving beyond conventional marker-assisted approaches to identify animals with desirable production traits. For practitioners working with donkeys—particularly in regions developing intensive breeding initiatives—understanding these genetic markers provides a foundation for future breeding decisions and may eventually support selection for traits affecting health and performance characteristics relevant to donkey-specific uses.
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Practical Takeaways
- •This genomic resource enables more sophisticated breeding selection for donkeys beyond traditional phenotypic assessment, particularly relevant as donkey use shifts toward meat, milk, and fiber production
- •The identified protein variants could support selective breeding programs targeting specific traits, though practical implementation requires further validation studies
- •Comparative equine genomic data helps clarify species-specific genetic architecture, supporting more targeted breeding decisions in mixed equine operations
Key Findings
- •De novo assembly identified 264,714 distinct donkey unigenes and 38,949 predicted protein fragments from white blood cell transcriptome
- •Three ear size-associated proteins (HIC1, PRKRA, KMT2A) showed sequence differences between donkey, horse, and wild horse species
- •Transcriptome-based selection methods offer more efficient genetic improvement compared to conventional marker-assisted breeding