Genome-wide association analysis and functional annotation of positional candidate genes for feed conversion efficiency and growth rate in pigs

Abstract

Feed conversion efficiency is a measure of how well an animal converts feed into live weight and it is typically expressed as feed conversion ratio (FCR). FCR and related traits like growth rate (e.g. days to 110 kg—D110) are of high interest for animal breeders, farmers and society due to implications on animal performance, feeding costs and environmental sustainability. The objective of this study was to identify genomic regions associated with FCR and D110 in pigs. A total of 952 terminal line boars, showing an individual variation in FCR, were genotyped using 60K SNP-Chips. Markers were tested for associations with estimated breeding values (EBV) for FCR and D110. For FCR, the largest number of associated SNPs was located on chromosomes 4 (30 SNPs), 1 (25 SNPs), X (15 SNPs) and 6 (12 SNPs). The most prominent genomic regions for D110 were identified on chromosomes 15 (10 SNPs), 1 and 4 (both 9 SNPs). The most significantly associated SNPs for FCR and D110 mapped 129.8 Kb from METTL11B (chromosome 4) and 32Kb from MBD5 (chromosome 15), respectively. A list of positional genes, closest to significantly associated SNPs, was used to identify enriched pathways and biological functions related to the QTL for both traits. A number of candidate genes were significantly overrepresented in pathways of immune cell trafficking, lymphoid tissue structure, organ morphology, endocrine system function, lipid metabolism, and energy production. After resequencing the coding region of selected positional and functional candidate genes, six SNPs were genotyped in a subset of boars. SNPs in PRKDC, SELL, NR2E1 and AKRIC3 showed significant associations with EBVs for FCR/D110. The study revealed a number of chromosomal regions and candidate genes affecting FCR/D110 and pointed to corresponding biological pathways related to lipid metabolism, olfactory reception, and also immunological status.

Weighted single‐step genome‐wide association study and pathway analyses for feed efficiency traits in Nellore cattle

“…This biological mechanism is also related to insulin response (Richardson & Herd, 2004), which supports the relationship between insulin genes and FE, as previously stated. Indeed, several lipid‐related genes were identified, such as SDCBP (Santos, 2018), ACLY (Ji, Osorio, Drackley, & Loor, 2012), OLR1 (Vinsky, Islam, Chen, & Li, 2013), CRTC3 (Raza et al., 2019), PRKDC (Horodyska, Hamill, Varley, Reyer, & Wimmers, 2017), HNRNPA3 (Wang et al., 2018), HTATIP2 (Liao et al., 2014) and NFE2L2 (Wu, Cui, & Klaasen, 2011) genes. The OLR1 and CRTC3 genes were reported associated with body weight, rib eye area and fat thickness in Nellore (Fonseca et al., 2015), and fat deposition in Qinchuan cattle (Raza et al., 2019), respectively.…”

A Genome-Wide Association Study on Feed Efficiency Related Traits in Landrace Pigs

“…The phenotypic measurements of FCR, ADFI, and RFI are difficult and costly which need an automatic feeding system. Besides, the selection of single FE related traits may affect other traits that are valuable for pig production, such as growth rate ( Horodyska et al, 2017 ). This conundrum makes the genetic investigation of FE very important.…”

“…Studies have revealed many potential candidate genes for FE related traits in pigs. For FCR, several researchers reported that significant SNPs and QTLs were mainly located on chromosomes (SSC) 4, 6, 7, 8, 17, and 18 ( Sahana et al, 2013 ; Horodyska et al, 2017 ). Another study identified three QTLs for ADG, which were located on SSC 4, 14, and 15 ( Ji et al, 2019 ).…”

GWAS and eQTL analysis identifies a SNP associated with both residual feed intake and GFRA2 expression in beef cattle

“… 52 when compared to lesser muscled counterparts 52 . DIS3 , a gene nearby to a variant associated with RFI in the current study, encodes a protein involved in RNA metabolism 53 and has been linked with feed conversion efficiency in pigs 54 .…”