Journal ArticleDOI
Candidate genes and single nucleotide polymorphisms associated with variation in residual feed intake in beef cattle
B. K. Karisa,Jennifer M. Thomson,Jennifer M. Thomson,Zhiqiang Wang,Paul Stothard,Stephen S. Moore,Stephen S. Moore,Graham Plastow +7 more
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TLDR
The candidate gene approach was used to identify genes associated with residual feed intake (RFI) in beef steers and indicated that the significant genes were involved in biological pathways such as lipid, protein and energy metabolism, electron transport and membrane signaling.Abstract:
The candidate gene approach was used to identify genes associated with residual feed intake (RFI) in beef steers The approach uses prior knowledge of gene functions to predict their biological role in the variation observed in a trait It is suited to identify genes associated with complex traits where each gene has a relatively small effect First, positional candidate genes were identified within the genomic positions of previously reported QTL associated with component traits related to RFI such as dry matter intake (DMI), growth, feed conversion ratio (FCR), average daily gain (ADG), and energy balance Secondly, the positional candidate genes were prioritized into functional candidate genes according to their biological functions and their relationship with the biological processes associated with RFI including carbohydrate, fat and protein metabolism, thermoregulation, immunity and muscle activity Single nucleotide polymorphisms (SNPs) located within the functional candidate genes were identified using mRNA sequences and prioritized into functional classes such as non-synonymous (nsSNP), synonymous (sSNP) or intronic SNP A total of 117 nsSNP were considered as functional SNP and genotyped in steers at the University of Alberta ranch in Kinsella Multiple marker association analysis in ASReml was performed using RFI data obtained from 531 beef steers Twenty-five SNP were significantly associated with RFI (P < 005) accounting for 197% of the phenotypic variation Using SIFT program to predict the effect of the SNP on the function of the corresponding protein, 3 of the 25 SNP were predicted to cause a significant effect on protein function (P < 005) One of the 3 SNP was located in the GHR gene and was also associated with a significant effect on the tertiary structure of the GHR protein (P < 005) as modeled using SWISSModel software Least square means for each genotype were estimated and an over-dominance effect was observed for the SNP located in the GHR, CAST, ACAD11 and UGT3A1 genes In addition, 2 other SNP showed a dominance effect and 3 genes had an additive effect Gene network analysis performed in Ingenuity pathway analysis (IPA) software (Ingenuity Systems, wwwingenuitycom) indicated that the significant genes were involved in biological pathways such as lipid, protein and energy metabolism, electron transport and membrane signaling The genes in this study, if validated in other beef cattle populations, may be useful for marker assisted selection for feed efficiencyread more
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Genome-wide association study for feed efficiency and growth traits in U.S. beef cattle
Christopher M. Seabury,David L. Oldeschulte,Mahdi Saatchi,Jonathan E. Beever,Jared E. Decker,Yvette A. Halley,Eric K. Bhattarai,Maral Molaei,Harvey C. Freetly,Stephanie L. Hansen,Helen Yampara-Iquise,Kristen A. Johnson,Monty S. Kerley,JaeWoo Kim,Daniel D. Loy,E. Marques,Holly L. Neibergs,Robert D. Schnabel,Daniel W Shike,Matthew L Spangler,Robert L. Weaber,Dorian J. Garrick,Dorian J. Garrick,Jeremy F. Taylor +23 more
TL;DR: Fourteen moderate to large-effect QTL regions which ranged from being physically proximal to fully overlapping for RFI, DMI, ADG, and MMWT were detected within and between populations, and included evidence for pleiotropy, proximal but independent causal mutations, and multi-breed QTL.
Journal ArticleDOI
Genome-wide association and systems genetic analyses of residual feed intake, daily feed consumption, backfat and weight gain in pigs
TL;DR: The study detected novel genetic variants and QTLs on SSC 1, 8, 9, 13 and 18 for RFI and indicated significant biological processes and metabolic pathways involved in RFI.
Journal ArticleDOI
Transcriptome profiling of the rumen epithelium of beef cattle differing in residual feed intake
TL;DR: The results suggest that the rumen epithelium of L-RFI (efficient) steers may have increased tissue Morphogenesis that possibly increases paracellular permeability for the absorption of nutrients and increased energy production to support the energetic demands of increased tissue morphogenesis compared to those of H-R FI (inefficient) animals.
Journal ArticleDOI
Identification of Genomic Regions Associated with Feed Efficiency in Nelore Cattle
Priscila S. N. de Oliveira,Aline Silva Mello Cesar,M. L. Nascimento,Amália Saturnino Chaves,Polyana C. Tizioto,Rymer Ramiz Tullio,Dante Pazzanese Duarte Lanna,A. N. Rosa,Tad S. Sonstegard,Gerson Barreto Mourão,James M. Reecy,Dorian J. Garrick,Maurício A. Mudadu,Luiz Lehmann Coutinho,Luciana Correia de Almeida Regitano +14 more
TL;DR: Comparison with published results indicates that different QTLs and genes may be involved in the control of feed efficiency traits in this Nelore cattle population, as compared to Bos taurus cattle.
Journal ArticleDOI
Uncovering Adaptation from Sequence Data: Lessons from Genome Resequencing of Four Cattle Breeds
TL;DR: This study investigated the advantages of sequencing for the detection of adaptive loci in multiple populations, exploiting a recently published data set in cattle and found that sequencing offered an increased detection power and a higher resolution in the localization of selection signatures.
References
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