Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Abo-Ismail, Mohammed; Voort, Gordon Vander; Squires, J.; Swanson, K. C.; Mandell, I. B.; Liao, Xiaoping; Stothard, Paul; Moore, S. S.; Plastow, Graham; Miller, Stephen

doi:10.1186/1471-2156-15-14

Cited by 49 publications

(41 citation statements)

References 63 publications

(64 reference statements)

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“…Olfactory transduction pathways act in the perception of odor through olfactory receptors and biochemical signaling events, which influence food consumption (Ma 2007). This pathway has also been identified as overrepresented in studies assessing feed efficiency and performance in crossbred beef cattle (Abo-ismail et al 2014) and residual feed intake in pigs (Do et al 2014). Plasma membranes isolated from the bovine olfactory epithelium containing large numbers of olfactory receptor cells are characterized by high lipid content, especially phospholipid.…”

Section: Functional Analysismentioning

confidence: 99%

Association study between copy number variation and beef fatty acid profile of Nellore cattle

et al. 2018

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The aim of this study was to analyze the association between the copy number variation regions (CNVRs) and fatty acid profile phenotypes for saturated (SFA), monosaturated (MUFA), polyunsaturated (PUFA), ω6 and ω3 fatty acids, PUFA/SFA and ω6/ω3 ratios, as well as for their sums, in Nellore cattle (Bos primigenius indicus). A total of 963 males were finished in feedlot and slaughtered with approximately 2 years of age. Animals were genotyped with the BovineHD BeadChip (Illumina Inc., San Diego, CA, USA). The copy number variation (CNV) detection was performed using the PennCNV algorithm. Log R ratio (LRR) and allele B frequency (BAF) were used to estimate the CNVs. The association analyses were done using the CNVRuler software and applying a logistic regression model. The phenotype was adjusted using a linear model considering the fixed effects of contemporary group and the animal age at slaughter. The fatty acid profile was analyzed on samples of longissimus thoracis muscle using gas chromatography with a 100-m capillary column. For the association analysis, the adjusted phenotypic values were considered for the traits, while the data was adjusted for the effects of the farm and year of birth, management groups at birth, weaning, and superannuation. A total of 186 CNVRs were significant for SFA (43), MUFA (42), PUFA (66), and omega fatty acid (35) groups, totaling 278 known genes. On the basis of the results, several genes were associated with several fatty acids of different saturations. Olfactory receptor genes were associated with C12:0, C14:0, and C18:0 fatty acids. The SAMD8 and BSCL2 genes, both related to lipid metabolic process, were associated with C12:0. The RAPGEF6 gene was found to be associated with C18:2 cis-9 cis-12 n-6, and its function is related to regulation of GTPase activity. Among the results, we highlighted the olfactory receptor activity (GO:0004984), G-protein-coupled receptor activity (GO:0004930), potassium:proton antiporter activity (GO:0015386), sodium:proton antiporter activity (GO:0015385), and odorant-binding (GO:0005549) molecular functions. A large number of genes associated with fatty acid profile within the CNVRs were identified in this study. These findings must contribute to better elucidate the genetic mechanism underlying the fatty acid profile of intramuscular fat in Nellore cattle.

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Section: Functional Analysismentioning

confidence: 99%

Association study between copy number variation and beef fatty acid profile of Nellore cattle

et al. 2018

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“…The study and improvement of feed efficiency in beef cattle has primarily focused on host-related genetic improvement technologies; however, host genetic contributions to feed efficiency in beef cattle have been difficult to identify (Saatchi et al 2014 ; Sherman et al 2010 ; Abo-Ismail et al 2014 ). The gastrointestinal tract (GIT) contains complex and dynamic microbial communities, which have long been regarded as essential in structure, function, and overall health of the host (Fujimura et al 2010 ).…”

Section: Introductionmentioning

confidence: 99%

Microbial community profiles of the colon from steers differing in feed efficiency

et al. 2015

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Ruminal microbial fermentation plays an essential role in host nutrition, and as a result, the rumen microbiota have been a major focus of research examining bovine feed efficiency. Microbial communities within other sections of the gastrointestinal tract may also be important with regard to feed efficiency, since it is critical to the health and nutrition of the host. The objective of this study was to characterize the microbial communities of the colon among steers differing in feed efficiency. Individual feed intake (FI) and body weight (BW) gain were determined from animals fed the same ration, within two contemporary groups of steers. Four steers from each contemporary group within each Cartesian quadrant were sampled (n = 16/group) from the bivariate distribution of average daily BW gain and average daily FI. Bacterial 16S rRNA gene amplicons were sequenced from the colon content using next-generation sequencing technology. Within the colon content, UniFrac principal coordinate analyses did not detect any separation of microbial communities, and bacterial diversity or richness did not differ between efficiency groups. Relative abundances of microbial populations and operational taxonomic units did reveal significant differences between efficiency groups. The phylum Firmicutes accounted for up to 70% of the populations within all samples, and families Ruminococcaceae and Clostridiaceae were highly abundant. Significant population shifts in taxa were detected, including the families Ruminococcaceae, Lachnospiraceae, and Sphingomonadaceae, and the genera Butyrivibrio, Pseudobutyrivibrio, Prevotella, Faecalibacterium and Oscillospira. This study suggests the association of the colon microbial communities as a factor influencing feed efficiency at the 16S level.

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“…For backfat thickness, 103 candidate loci within 9 candidate genes were identified in current study. However, only one gene (SLC20A2) was associated with carcass trait [54]. For carcass length, 188 loci and 31 candidate genes were identified.…”

Section: Discussionmentioning

confidence: 99%

Genome-wide scan for runs of homozygosity identifies potential candidate regions associated with growth traits in beef cattle

Zhao

Zhang

Liu

et al. 2020

Preprint

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Background: Runs of homozygosity (ROH) are continuous homozygous regions that generally exist in the DNA sequence of diploid organisms. Identifications of regions of the genome lead to reduction in performance can provide valuable insight into the genetic architecture of complex traits. Here, we evaluated genome-wide patterns of homozygosity and their association with growth traits in a commercial beef cattle population.Results: We identified a total of 29,271 ROH segments with an average number of 63.36 and an average length of 0.98 Mb in this commercial beef cattle population, representing ~2.53% (~63.36Mb) of the genome. To evaluate the enrichment of ROH across genomes, we initially identified 280 ROH regions by merging ROH events identified across all individuals. Of these, nine regions were significantly associated with six growth phenotype traits (body height, chest circumference, fat coverage, backfat thickness, ribeye area, carcass length; P<0.01), which contain 187 candidate genes. Furthermore, we found 26 consensus ROH regions with frequencies exceeding 10%, and several of these consensus overlapped with QTLs which are associated with weight gain, calving difficulty and stillbirth. To precisely locate locus within each ROH for every studied trait, we further utilized loci-based methods for association analysis among these identified regions. Totally, we obtained 9,360 loci within ROH, and 1,631 loci displaying significant association (P<0.01) for eight traits. In addition, we found that 67 genes embedded with homozygous loci. Several identified candidate genes, including EBF2, SLC20A2, SH3BGRL2, HMGA1 and ACSL1, were related to growth traits.Conclusions: This study assessed genome-wide autozygosity pattern and inbreeding level in a commercial beef cattle population. Our study identified many candidate regions and genes with ROH for growth traits in beef cattle, which can provide important insights into investigating homozygosity across genome in other farm animals. Our findings may further be unitized to assist the design of selection mating strategy.

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Single nucleotide polymorphisms for feed efficiency and performance in crossbred beef cattle

Cited by 49 publications

References 63 publications

Association study between copy number variation and beef fatty acid profile of Nellore cattle

Association study between copy number variation and beef fatty acid profile of Nellore cattle

Microbial community profiles of the colon from steers differing in feed efficiency

Genome-wide scan for runs of homozygosity identifies potential candidate regions associated with growth traits in beef cattle

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