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BMC genomics2012; 13; 473; doi: 10.1186/1471-2164-13-473

Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq.

Abstract: Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes derived from transcriptomes. Results: We present a large-scale analysis of whole transcriptome data. We sequenced the whole mRNA from the blood and muscle tissues of six thoroughbred horses before and after exercise. By comparing current genome annotations, we identified 32,361 unigene clusters spanning 51.83 Mb that contained 11,933 (36.87%) annotated genes. More than 60% (20,428) of the unigene clusters did not match any current equine gene model. We also identified 189,973 single nucleotide variations (SNVs) from the sequences aligned against the horse reference genome. Most SNVs (171,558 SNVs; 90.31%) were novel when compared with over 1.1 million equine SNPs from two SNP databases. Using differential expression analysis, we further identified a number of exercise-regulated genes: 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle. Six of 28 previously-known exercise-related genes were over-expressed in the muscle after exercise. Among the differentially expressed genes, there were 91 transcription factor-encoding genes, which included 56 functionally unknown transcription factor candidates that are probably associated with an early regulatory exercise mechanism. In addition, we found interesting RNA expression patterns where different alternative splicing forms of the same gene showed reversed expressions before and after exercising. Conclusions: The first sequencing-based horse transcriptome data, extensive analyses results, deferentially expressed genes before and after exercise, and candidate genes that are related to the exercise are provided in this study.
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Publication Date: 2012-09-12 PubMed ID: 22971240PubMed Central: PMC3472166DOI: 10.1186/1471-2164-13-473Google Scholar: Lookup
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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 involves a large-scale analysis of whole transcriptome data from six thoroughbred horses. It focuses on the impact of exercise on their genes and identifies unique variations and differential expressions which contribute to the understanding of muscle-associated genetics in horses.

Transcriptome Analysis

  • This research builds on prior genome mapping work by performing a functional annotation using expressed genes sourced from transcriptomes. This broader and deeper exploration helps to highlight areas the genome mapping may have overlooked.
  • The study involved taking mRNA samples from the blood and muscle tissues of six thoroughbred horses, both before and after exercise, and sequencing the whole mRNA to create a transcriptome – a set of all RNA molecules, including mRNA, rRNA, tRNA, and other non-coding RNA. This transcriptome provides massive data for genetic analysis.
  • The researchers compared the transcriptome output to existing genome annotations and identified 32,361 unigene clusters meaning a set of genes from a single locus. More than half of these clusters did not match any current equine gene model.

Single Nucleotide Variations (SNVs)

  • From the sequenced data, researchers identified 189,973 SNVs which are essentially errors in DNA replication. This discovery was significant in that over 90% of these variants were novel when compared with two current equine SNP (Single-nucleotide polymorphism) databases. SNPs are the most common type of genetic variation among people.

Exercise-Regulated Genes

  • Employing differential expression analysis, the researchers identified a number of genes affected by exercise. These included 62 up-regulated and 80 down-regulated genes in the blood, and 878 up-regulated and 285 down-regulated genes in the muscle tissues. The up-regulated genes are more active, and the down-regulated genes are less active after exercise.
  • Notably, six of 28 previously known exercise-related genes were over-expressed in the muscle after exercise.
  • The identified differentially expressed genes provided valuable data for subsequent research in equine exercise physiology and could potentially inform treatment for muscle-related diseases in horses.

Transcription factor-encoding genes and Alternative Splicing Patterns

  • Among the differentially expressed genes before and after exercise, the researchers discovered 91 transcription factor-encoding genes. These are involved in regulating the transcription of genetic information from DNA to mRNA. These included 56 functionally unknown transcription factor candidates, perhaps associated with early regulatory exercise mechanisms.
  • Furthermore, researchers noted interesting RNA expression patterns where alternative splicing forms of the same gene showed opposite expressions before and after exercise. This may hint at more complex gene regulation mechanisms in response to exercise.

Conclusion and Significance

  • The study provides the first sequencing-based horse transcriptome data, extensive analysis results, and identifies differentially expressed genes before and after exercise, as well as candidate genes related to exercise. These findings do not only contribute to understanding the exercise-related genes, their expressions, and regulation in race horses but can also be useful in improving their performance and in treating muscle-related diseases.

Cite This Article

APA
Park KD, Park J, Ko J, Kim BC, Kim HS, Ahn K, Do KT, Choi H, Kim HM, Song S, Lee S, Jho S, Kong HS, Yang YM, Jhun BH, Kim C, Kim TH, Hwang S, Bhak J, Lee HK, Cho BW. (2012). Whole transcriptome analyses of six thoroughbred horses before and after exercise using RNA-Seq. BMC Genomics, 13, 473. https://doi.org/10.1186/1471-2164-13-473

Publication

BMC genomics
ISSN: 1471-2164
NlmUniqueID: 100965258
Country: England
Language: English
Volume: 13
Pages: 473

Researcher Affiliations

Park, Kyung-Do
  • Department of Biotechnology, Hankyong National University, Anseong, Republic of Korea.
Park, Jongsun
    Ko, Junsu
      Kim, Byung Chul
        Kim, Heui-Soo
          Ahn, Kung
            Do, Kyoung-Tag
              Choi, Hansol
                Kim, Hak-Min
                  Song, Sanghoon
                    Lee, Sunghoon
                      Jho, Sungwoong
                        Kong, Hong-Sik
                          Yang, Young Mok
                            Jhun, Byung-Hak
                              Kim, Chulhong
                                Kim, Tae-Hyung
                                  Hwang, Seungwoo
                                    Bhak, Jong
                                      Lee, Hak-Kyo
                                        Cho, Byung-Wook

                                          MeSH Terms

                                          • Animals
                                          • Gene Expression Profiling / methods
                                          • Horses / genetics
                                          • Horses / physiology
                                          • Physical Conditioning, Animal / physiology
                                          • RNA / genetics

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