De Novo Assembly of the Donkey White Blood Cell Transcriptome and a Comparative Analysis of Phenotype-Associated Genes between Donkeys and Horses.
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.
Publication Date: 2015-07-24 PubMed ID: 26208029PubMed Central: PMC4514889DOI: 10.1371/journal.pone.0133258Google Scholar: Lookup
The Equine Research Bank provides access to a large database of publicly available scientific literature. Inclusion in the Research Bank does not imply endorsement of study methods or findings by Mad Barn.
- Journal Article
- Research Support
- 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.
The research article is an investigation into the unique genetic attributes of donkeys, focusing on white blood cells, in comparison to horses, to better understand donkey breeding for new uses such as producing meat, milk, and fur.
Overview and Objective of the Study
- The study sought to analyze the coding genes of the donkey genome, with the intent of aiding the further development of the donkey industry, specifically in China where donkeys are increasingly being raised for meat, milk, and fur.
- The researchers used a method called de novo transcriptome assembly of donkey white blood cells to identify the unique proteins and genes in donkeys. A transcriptome represents all the genes that are active in a cell at a certain point in time.
- The purpose of this research was to move beyond traditional breeding plans and harness the power of genomics and transcriptomics to create more effective ways of breeding donkeys for specific traits.
Methodology and Findings
- The researchers carried out transcriptomic deep-sequencing, a method used to examine the RNA molecules, to identify 264,714 distinct donkey unigenes and predicted 38,949 protein fragments.
- They then annotated these unigenes by comparing them against a non-redundant protein database through Basic Local Alignment Search Tool (BLAST) searches.
- For further comparison, they linked the protein fragments of donkeys with mammalian phenotypes and compared the protein sequences with those of the horse and wild horse.
Significant Discoveries
- The major analysis centered on the difference in ear size between donkeys and horses.
- The researchers were able to identify three proteins (HIC1, PRKRA, and KMT2A) associated with ear size, which showed sequence differences across the donkey, horse, and wild horse species.
- This understanding of the underlying genetic differences between these close species provides a foundation for more refined and targeted breeding programs for donkeys.
Conclusions and Impact of the Study
- This study provides essential preliminary research for donkey genome sequence, which has not yet been released.
- The transcriptome assembled in this study could be highly beneficial for future investigations of donkey cultivars and for developing genetic improvements in breeding programs.
- The research has broader implications for animal breeding and genetics and can potentially deepen our understanding of donkey physiology and adaptability to different environments or uses.
Cite This Article
APA
Xie FY, Feng YL, Wang HH, Ma YF, Yang Y, Wang YC, Shen W, Pan QJ, Yin S, Sun YJ, Ma JY.
(2015).
De Novo Assembly of the Donkey White Blood Cell Transcriptome and a Comparative Analysis of Phenotype-Associated Genes between Donkeys and Horses.
PLoS One, 10(7), e0133258.
https://doi.org/10.1371/journal.pone.0133258 Publication
Researcher Affiliations
- Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Black Donkey Research Institute, Shandong Dongeejiao Company Limited, Liaocheng, Shandong, 252000, China.
- Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Black Donkey Research Institute, Shandong Dongeejiao Company Limited, Liaocheng, Shandong, 252000, China.
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
- Black Donkey Research Institute, Shandong Dongeejiao Company Limited, Liaocheng, Shandong, 252000, China.
- Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
- Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
- Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
- College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
- Institute of Reproductive Science, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; Key Laboratory of Animal Reproduction and Germplasm Enhancement in Universities of Shandong, Qingdao Agricultural University, Qingdao, Shandong, 266109, China; College of Animal Science and Technology, Qingdao Agricultural University, Qingdao, Shandong, 266109, China.
MeSH Terms
- Animals
- Databases, Protein
- Equidae / genetics
- Equidae / metabolism
- Horses / genetics
- Horses / metabolism
- Leukocytes / metabolism
- Phenotype
- Transcriptome
Conflict of Interest Statement
The authors have declared that no competing interests exist.
References
This article includes 21 references
Citations
This article has been cited 0 times.Use Nutrition Calculator
Check if your horse's diet meets their nutrition requirements with our easy-to-use tool Check your horse's diet with our easy-to-use tool
Talk to a Nutritionist
Discuss your horse's feeding plan with our experts over a free phone consultation Discuss your horse's diet over a phone consultation
Submit Diet Evaluation
Get a customized feeding plan for your horse formulated by our equine nutritionists Get a custom feeding plan formulated by our nutritionists
