Abstract

BackgroundThe feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry. Elucidating the genetic mechanisms underpinning FCR may promote more efficient improvement of FCR through artificial selection. In this study, we integrated a genome-wide association study (GWAS) with transcriptome analyses of different tissues in Yorkshire pigs (YY) with the aim of identifying key genes and signalling pathways associated with FCR.ResultsA total of 61 significant single nucleotide polymorphisms (SNPs) were detected by GWAS in YY. All of these SNPs were located on porcine chromosome (SSC) 5, and the covered region was considered a quantitative trait locus (QTL) region for FCR. Some genes distributed around these significant SNPs were considered as candidates for regulating FCR, including TPH2, FAR2, IRAK3, YARS2, GRIP1, FRS2, CNOT2 and TRHDE. According to transcriptome analyses in the hypothalamus, TPH2 exhibits the potential to regulate intestinal motility through serotonergic synapse and oxytocin signalling pathways. In addition, GRIP1 may be involved in glutamatergic and GABAergic signalling pathways, which regulate FCR by affecting appetite in pigs. Moreover, GRIP1, FRS2, CNOT2, and TRHDE may regulate metabolism in various tissues through a thyroid hormone signalling pathway.ConclusionsBased on the results from GWAS and transcriptome analyses, the TPH2, GRIP1, FRS2, TRHDE, and CNOT2 genes were considered candidate genes for regulating FCR in Yorkshire pigs. These findings improve the understanding of the genetic mechanisms of FCR and may help optimize the design of breeding schemes.

Highlights

  • The feed conversion ratio (FCR) is an important productive trait that greatly affects profits in the pig industry

  • Elucidating the genetic mechanisms underpinning FCR and identifying genes that are significantly associated with FCR could enhance the efficiency of FCR improvement

  • LD block, associated region analysis and candidate genes identified for FCR Several linkage disequilibrium (LD) blocks were detected in the regions where the 61 significantly associated single nucleotide polymorphism (SNP) were located: 3 LD blocks were detected in the region of 33.4–34.5 Mb on SSC5; 3 LD blocks were detected in the region of 36.1–44.3 Mb on SSC5, and 1 LD block was detected in the region of 47.1–47.8 Mb on SSC5 (Fig. 2)

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Summary

Objectives

The objectives of our study were to identify QTLs and to unravel the genetic architecture of FCR in Yorkshire pigs by performing both GWAS and transcriptome analyses in pig tissues that are related to the progress of FCR

Methods
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