Dataset Information

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.

SUBMITTER: Horodyska J

PROVIDER: S-EPMC5467825 | biostudies-literature | 2017

REPOSITORIES: biostudies-literature

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

Horodyska Justyna J Hamill Ruth M RM Varley Patrick F PF Reyer Henry H Wimmers Klaus K

PloS one 20170612 6

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 lin ...[more]

PMID: 28604785

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Project description:Residual feed intake (RFI) is a complex trait that is economically important for livestock production; however, the genetic and biological mechanisms regulating RFI are largely unknown in pigs. Therefore, the study aimed to identify single nucleotide polymorphisms (SNPs), candidate genes and biological pathways involved in regulating RFI using Genome-wide association (GWA) and pathway analyses. A total of 596 Yorkshire boars with phenotypes for two different measures of RFI (RFI1 and 2) and 60k genotypic data was used. GWA analysis was performed using a univariate mixed model and 12 and 7 SNPs were found to be significantly associated with RFI1 and RFI2, respectively. Several genes such as xin actin-binding repeat-containing protein 2 (XIRP2),tetratricopeptide repeat domain 29 (TTC29),suppressor of glucose, autophagy associated 1 (SOGA1),MAS1,G-protein-coupled receptor (GPCR) kinase 5 (GRK5),prospero-homeobox protein 1 (PROX1),GPCR 155 (GPR155), and FYVE domain containing the 26 (ZFYVE26) were identified as putative candidates for RFI based on their genomic location in the vicinity of these SNPs. Genes located within 50 kbp of SNPs significantly associated with RFI and RFI2 (q-value ≤ 0.2) were subsequently used for pathway analyses. These analyses were performed by assigning genes to biological pathways and then testing the association of individual pathways with RFI using a Fisher's exact test. Metabolic pathway was significantly associated with both RFIs. Other biological pathways regulating phagosome, tight junctions, olfactory transduction, and insulin secretion were significantly associated with both RFI traits when relaxed threshold for cut-off p-value was used (p ≤ 0.05). These results implied porcine RFI is regulated by multiple biological mechanisms, although the metabolic processes might be the most important. Olfactory transduction pathway controlling the perception of feed via smell, insulin pathway controlling food intake might be important pathways for RFI. Furthermore, our study revealed key genes and genetic variants that control feed efficiency that could potentially be useful for genetic selection of more feed efficient pigs.

Project description:A major objective of pork producers is to reduce production cost. Feeding may account for over 75% of pork production costs. Thus, selecting pigs for feed efficiency (FE) traits is a priority in pig breeding programs. While in the Americas, pigs are typically fed high-input diets, based on corn and soybean meal (CS); in Western Europe, pigs are commonly fed diets based on wheat and barley with high amounts of added protein-rich coproducts (WB), e.g., from milling and seed-oil industries. These two feeding scenarios provided a realistic setting for investigating a specific type of genotype by environment interaction; thus, we investigated the genotype by feed interaction (GxF). In the presence of a GxF, different feed compositions should be considered when selecting for FE. This study aimed to 1) verify the presence of a GxF for FE and growth performance traits in different growth phases (starter, grower, and finisher) of 3-way crossbred growing-finishing pigs fed either a CS (547 boars and 558 gilts) or WB (567 boars and 558 gilts) diet; and 2) to assess and compare the expected responses to direct selection under the 2 diets and the expected correlated responses for one diet to indirect selection under the other diet. We found that GxF did not interfere in the ranking of genotypes under both diets for growth, protein deposition, feed intake, energy intake, or feed conversion rate. Therefore, for these traits, we recommend changing the diet of growing-finishing pigs from high-input feed (i.e., CS) to feed with less valuable ingredients, as WB, to reduce production costs and the environmental impact, regardless of which diet is used in selection. We found that GxF interfered in the ranking of genotypes and caused heterogeneity of genetic variance under both diets for lipid deposition (LD), residual energy intake (REI), and residual feed intake (RFI). Thus, selecting pigs under a diet different from the diet used for growing-finishing performance could compromise the LD in all growth phases, compromise the REI and RFI during the starter phase, and severely compromise the REI during the grower phase. In particular, when pigs are required to consume a WB diet for growing-finishing performance, pigs should be selected for FE under the same diet. Breeding pigs for FE under lower-input diets should be considered, because FE traits will become more important and lower-input diets will become more widespread in the near future.

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Project description:Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions amongst causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc - 80 SNPs, Landrace - 146 SNPs) and high feed efficient group (Duroc - 198 SNPs, Landrace - 232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.

Dataset Information

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

Publications

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

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