Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq

Z. Du, C.J. Eisley, S.K. Onteru, O. Madsen, M. Groenen, J.W. Ross, M.F. Rothschild

Research output: Contribution to journalArticleAcademicpeer-review

16 Citations (Scopus)

Abstract

Although structural properties of the porcine reproductive system are shared by many placental mammals, some combination of these properties is unique to pigs. To explore whether genomic elements specific to pigs could potentially underlie this uniqueness, we made the first step to identify novel transcripts in two representative pig reproductive tissues by the technique of massively parallel sequencing. To automate the whole process, we built a computational pipeline, which can also be easily extended for similar studies in other species. In total, 5516 and 9061 novel transcripts were found, and 159 and 252 novel transcripts appear to be specific to pigs for the placenta and testis respectively. Furthermore, these novel transcripts were found to be enriched in quantitative trait loci (QTL) regions for reproduction traits in pigs. We validated eight of these novel transcripts by quantitative real-time PCR. With respect to their genomic organization and their functional relationship to reproduction, these transcripts need to be further validated and explored in various pig breeds to better comprehend the relevant aspects of pig physiology that contribute to reproductive performance.
LanguageEnglish
Pages198-204
JournalAnimal Genetics
Volume45
Issue number2
DOIs
Publication statusPublished - 2014

Fingerprint

Swine
RNA
swine
Reproduction
genomics
swine breeds
Reproductive Techniques
High-Throughput Nucleotide Sequencing
reproductive system
tissues
species identification
Quantitative Trait Loci
placenta
quantitative trait loci
reproductive performance
testes
quantitative polymerase chain reaction
Placenta
physiology
Testis

Keywords

  • long noncoding rnas
  • extreme phenotypes
  • human genome
  • litter size
  • disease
  • mechanisms
  • evolution
  • discovery
  • reveals
  • mir-675

Cite this

Du, Z. ; Eisley, C.J. ; Onteru, S.K. ; Madsen, O. ; Groenen, M. ; Ross, J.W. ; Rothschild, M.F. / Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq. In: Animal Genetics. 2014 ; Vol. 45, No. 2. pp. 198-204.
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Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq. / Du, Z.; Eisley, C.J.; Onteru, S.K.; Madsen, O.; Groenen, M.; Ross, J.W.; Rothschild, M.F.

In: Animal Genetics, Vol. 45, No. 2, 2014, p. 198-204.

Research output: Contribution to journalArticleAcademicpeer-review

TY - JOUR

T1 - Identification of species-specific novel transcripts in pig reproductive tissues using RNA-seq

AU - Du, Z.

AU - Eisley, C.J.

AU - Onteru, S.K.

AU - Madsen, O.

AU - Groenen, M.

AU - Ross, J.W.

AU - Rothschild, M.F.

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AB - Although structural properties of the porcine reproductive system are shared by many placental mammals, some combination of these properties is unique to pigs. To explore whether genomic elements specific to pigs could potentially underlie this uniqueness, we made the first step to identify novel transcripts in two representative pig reproductive tissues by the technique of massively parallel sequencing. To automate the whole process, we built a computational pipeline, which can also be easily extended for similar studies in other species. In total, 5516 and 9061 novel transcripts were found, and 159 and 252 novel transcripts appear to be specific to pigs for the placenta and testis respectively. Furthermore, these novel transcripts were found to be enriched in quantitative trait loci (QTL) regions for reproduction traits in pigs. We validated eight of these novel transcripts by quantitative real-time PCR. With respect to their genomic organization and their functional relationship to reproduction, these transcripts need to be further validated and explored in various pig breeds to better comprehend the relevant aspects of pig physiology that contribute to reproductive performance.

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KW - extreme phenotypes

KW - human genome

KW - litter size

KW - disease

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KW - reveals

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