An intersection network based on combining SNP coassociation and RNA coexpression networks for feed utilization traits in Japanese Black cattle

Daigo Okada, Satoko Endo, Hirokazu Matsuda, Shinichiro Ogawa, Yukio Taniguchi, Tomohiro Katsuta, Toshio Watanabe, Hiroaki Iwaisaki

Research output: Contribution to journalArticlepeer-review

3 Citations (Scopus)

Abstract

Genome-wide association studies (GWAS) of quantitative traits have detected numerous genetic associations, but they encounter difficulties in pinpointing prominent candidate genes and inferring gene networks. The present study used a systems genetics approach integrating GWAS results with external RNA-expression data to detect candidate gene networks in feed utilization and growth traits of Japanese Black cattle, which are matters of concern. A SNP coassociation network was derived from significant correlations between SNPs with effects estimated by GWAS across 7 phenotypic traits. The resulting network genes contained significant numbers of annotations related to the traits. Using bovine transcriptome data from a public database, an RNA coexpression network was inferred based on the similarity of expression patterns across different tissues. An intersection network was then generated by superimposing the SNP and RNA networks and extracting shared interactions. This intersection network contained 4 tissue-specific modules: nervous system, reproductive system, muscular system, and glands. To characterize the structure (topographical properties) of the 3 networks, their scale-free properties were evaluated, which revealed that the intersection network was the most scale-free. In the subnetwork containing the most connected transcription factors (URI1, ROCK2, and ETV6), most genes were widely expressed across tissues, and genes previously shown to be involved in the traits were found. Results indicated that the current approach might be used to construct a gene network that better reflects biological information, providing encouragement for the genetic dissection of economically important quantitative traits.

Original languageEnglish
Pages (from-to)2553-2566
Number of pages14
JournalJournal of animal science
Volume96
Issue number7
DOIs
Publication statusPublished - 2018 Jul 1

Keywords

  • Feed utilization efficiency
  • Gene network
  • Japanese Black cattle
  • RNA coexpression
  • SNP coassociation

ASJC Scopus subject areas

  • Food Science
  • Animal Science and Zoology
  • Genetics

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