Proteome analysis revealed the key genes and major pathways that social genetic effects influence pig RFI
Ontology highlight
ABSTRACT:
ORGANISM(S): Sus Scrofa Domesticus
SUBMITTER: 
Zhenjian Zhao
PROVIDER: PXD046715 | iProX | Tue Nov 07 00:00:00 GMT 2023
REPOSITORIES: iProX
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Project description:microbiota of pigs with low and high residual feed intake
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Project description:Transcriptional profiling in skeletal muscle of 15 pigs of 20 kg body weight from lines divergently selected for residual feed intake (RFI): low-RFI pigs (RFIneg), high-RFI pigs (RFIpl) .
2014-01-01 | GSE47768 | GEO
Project description:The selection of cattle with high feed efficiency is of paramount importance with regard to reducing feed costs in the beef industry. Global gene expression patterns in metabolically important tissues can be used to identify genes that are potentially involved in regulating feed efficiency. We identified 5 genes (p<0.001;FDR <0.1) to be differentially expressed in skeletal skeletal muscle between high and low residual feed intake heifers with all 5 transcripts being upregulated in the low residual feed intake phenotype. Among these differentially expressed genes, all transcripts were related to oxidative phosphorylation and mitochondrial homeostasis. A total of 11 genes (p<0.001;FDR <0.1) were differentially expressed in hepatic tissue tissue between high and low residual feed intake bulls with 8 transcripts being upregulated and 3 being downregulated in the low residual feed intake phenotype. These differentially expressed genes were related to oxidative response, protein mediation and cell signalling. Pathway analysis on the RNAseq data indicates a relationship between oxidative phosphorylation and residual feed intake in skeletal muscle and aldosterone signalling and NRF2 mediated oxidative stress in hepatic tissue.
2021-05-05 | GSE112793 | GEO
Project description:The objective of this study was to decipher the molecular basis of feed efficiency in meat-type chicken using duodenum tissues from a chicken population divergently selected for residual feed intake (RFI). Residual feed intake is the deviation of expected feed intake from actual feed intake. Chickens that consume less feed than expected are efficient (LRFI) and chickens that consume more feed than expected are inefficient (HRFI). A divergent selection for RFI was undertaken using an unselected random bred chicken population. RFI at day 35-42 was used as a criterion for selecting low (LRFI) and high (HRFI) RFI. Duodenum tissues were collected from 16 male chickens under sterile conditions experimentation. Tissues were collected from 4 males at days 35 and 42 in each line. Duodenum at 35 and 42 days from a chicken population divergently selected for residual feed intake were utilized for RNA extraction and hybridization on Affymetrix microarrays.
2012-08-01 | E-GEOD-39824 | biostudies-arrayexpress
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.
2020-03-23 | GSE144064 | GEO
Project description:The objective of this study was to decipher the molecular basis of feed efficiency in meat-type chicken using duodenum tissues from a chicken population divergently selected for residual feed intake (RFI). Residual feed intake is the deviation of expected feed intake from actual feed intake. Chickens that consume less feed than expected are efficient (LRFI) and chickens that consume more feed than expected are inefficient (HRFI). A divergent selection for RFI was undertaken using an unselected random bred chicken population. RFI at day 35-42 was used as a criterion for selecting low (LRFI) and high (HRFI) RFI. Duodenum tissues were collected from 16 male chickens under sterile conditions experimentation. Tissues were collected from 4 males at days 35 and 42 in each line.
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