Abstract
Prior to the mechanization of agriculture and labor-intensive tasks, humans used donkeys (Equus africanus asinus) for farm work and packing. However, as mechanization increased, donkeys have been increasingly raised for meat, milk, and fur in China. To maintain the development of the donkey industry, breeding programs should focus on traits related to these new uses. Compared to conventional marker-assisted breeding plans, genome- and transcriptome-based selection methods are more efficient and effective. To analyze the coding genes of the donkey genome, we assembled the transcriptome of donkey white blood cells de novo. Using transcriptomic deep-sequencing data, we identified 264,714 distinct donkey unigenes and predicted 38,949 protein fragments. We annotated the donkey unigenes by BLAST searches against the non-redundant (NR) protein database. We also compared the donkey protein sequences with those of the horse (E. caballus) and wild horse (E. przewalskii), and linked the donkey protein fragments with mammalian phenotypes. As the outer ear size of donkeys and horses are obviously different, we compared the outer ear size-associated proteins in donkeys and horses. We identified three ear size-associated proteins, HIC1, PRKRA, and KMT2A, with sequence differences among the donkey, horse, and wild horse loci. Since the donkey genome sequence has not been released, the de novo assembled donkey transcriptome is helpful for preliminary investigations of donkey cultivars and for genetic improvement.
Highlights
For thousands of years of human history, donkeys were mainly breeded for farm labor or packing goods
Using high-throughput deep sequencing of the transcriptome of white blood cells sampled from the Dezhou donkey, we obtained approximately 129 million clean reads
As the donkey genome has not been published, the de novo assembled donkey white blood cell transcriptome is useful for preliminary investigations of associations between donkey genotypes and phenotypes
Summary
For thousands of years of human history, donkeys were mainly breeded for farm labor or packing goods. In 2000, the world donkey population was estimated at approximately 43.5 million, but only 41 million donkeys existed in 2006 (a 5.7% reduction) [1]. China has the most donkeys, and its domestic donkey population increased from 7.4 million in 1966 to 10.923 million in 1996 [2]; based on the latest population survey, there were only 6.891 million donkeys in 2007 (a 37% reduction) [3]. The accumulation of artificially selected characters important for farm labor over thousands of years are not suited to the modern demands in China for donkey meat, milk, and fur. Cultivating donkey breeds with new traits based on the demands of modern society is essential for the growth of the donkey industry
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