Dataset Information

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

ABSTRACT:

Background

This study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the effects of detected SNPs on carcass traits to avoid undesirable correlated effects on these economically important traits when selecting for feed efficiency; and (4) map the genes to biological mechanisms and pathways. A total number of 339 SNPs corresponding to 180 genes were tested for association with phenotypes using a single locus regression (SLRM) and genotypic model on 726 and 990 crossbred animals for feed efficiency and carcass traits, respectively.

Results

Strong evidence of associations for RFI were located on chromosomes 8, 15, 16, 18, 19, 21, and 28. The strongest association with RFI (P = 0.0017) was found with a newly discovered SNP located on BTA 8 within the ELP3 gene. SNPs rs41820824 and rs41821600 on BTA 16 within the gene HMCN1 were strongly associated with RFI (P = 0.0064 and P = 0.0033, respectively). A SNP located on BTA 18 within the ZNF423 gene provided strong evidence for association with RFI (P = 0.0028). Genomic estimated breeding values (GEBV) from 98 significant SNPs were moderately correlated (0.47) to the estimated breeding values (EBVs) from a mixed animal model. The significant (P < 0.05) SNPs (98) explained 26% of the genetic variance for RFI. In silico functional analysis for the genes suggested 35 and 39 biological processes and pathways, respectively for feed efficiency traits.

Conclusions

This study identified several positional and functional candidate genes involved in important biological mechanisms associated with feed efficiency and performance. Significant SNPs should be validated in other populations to establish their potential utilization in genetic improvement programs.

SUBMITTER: Abo-Ismail MK

PROVIDER: S-EPMC3927660 | biostudies-literature | 2014 Jan

REPOSITORIES: biostudies-literature

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Publications

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

Abo-Ismail Mohammed K MK Vander Voort Gordon G Squires James J JJ Swanson Kendall C KC Mandell Ira B IB Liao Xiaoping X Stothard Paul P Moore Stephen S Plastow Graham G Miller Stephen P SP

BMC genetics 20140130

<h4>Background</h4>This study was conducted to: (1) identify new SNPs for residual feed intake (RFI) and performance traits within candidate genes identified in a genome wide association study (GWAS); (2) estimate the proportion of variation in RFI explained by the detected SNPs; (3) estimate the effects of detected SNPs on carcass traits to avoid undesirable correlated effects on these economically important traits when selecting for feed efficiency; and (4) map the genes to biological mechanis ...[more]

PMID: 24476087

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Project description:BackgroundGeneral, breed- and diet-dependent associations between feed efficiency in beef cattle and single nucleotide polymorphisms (SNPs) or haplotypes were identified on a population of 1321 steers using a 50 K SNP panel. Genomic associations with traditional two-step indicators of feed efficiency - residual feed intake (RFI), residual average daily gain (RADG), and residual intake gain (RIG) - were compared to associations with two complementary one-step indicators of feed efficiency: efficiency of intake (EI) and efficiency of gain (EG). Associations uncovered in a training data set were evaluated on independent validation data set. A multi-SNP model was developed to predict feed efficiency. Functional analysis of genes harboring SNPs significantly associated with feed efficiency and network visualization aided in the interpretation of the results.ResultsFor the five feed efficiency indicators, the numbers of general, breed-dependent, and diet-dependent associations with SNPs (P-value?<?0.0001) were 31, 40, and 25, and with haplotypes were six, ten, and nine, respectively. Of these, 20 SNP and six haplotype associations overlapped between RFI and EI, and five SNP and one haplotype associations overlapped between RADG and EG. This result confirms the complementary value of the one and two-step indicators. The multi-SNP models included 89 SNPs and offered a precise prediction of the five feed efficiency indicators. The associations of 17 SNPs and 7 haplotypes with feed efficiency were confirmed on the validation data set. Nine clusters of Gene Ontology and KEGG pathway categories (mean P-value?<?0.001) including, 9nucleotide binding; ion transport, phosphorous metabolic process, and the MAPK signaling pathway were overrepresented among the genes harboring the SNPs associated with feed efficiency.ConclusionsThe general SNP associations suggest that a single panel of genomic variants can be used regardless of breed and diet. The breed- and diet-dependent associations between SNPs and feed efficiency suggest that further refinement of variant panels require the consideration of the breed and management practices. The unique genomic variants associated with the one- and two-step indicators suggest that both types of indicators offer complementary description of feed efficiency that can be exploited for genome-enabled selection purposes.

Project description:The objectives of the present study were to estimate genetic parameters for several feeding behavior traits in growing cattle, as well as the genetic associations among and between feeding behavior and both performance and feed efficiency traits. An additional objective was to investigate the use of feeding behavior traits as predictors of genetic merit for feed intake. Feed intake and live-weight data on 6,088 growing cattle were used of which 4,672 had ultrasound data and 1,548 had feeding behavior data. Feeding behavior traits were defined based on individual feed events or meal events (where individual feed events were grouped into meals). Univariate and bivariate animal linear mixed models were used to estimate (co)variance components. Heritability estimates (± SE) for the feeding behavior traits ranged from 0.19 ± 0.08 for meals per day to 0.61 ± 0.10 for feeding time per day. The coefficient of genetic variation per trait varied from 5% for meals per day to 22% for the duration of each feed event. Genetically heavier cattle, those with a higher daily energy intake (MEI), or those that grew faster had a faster feeding rate, as well as a greater energy intake per feed event and per meal. Better daily feed efficiency (i.e., lower residual energy intake) was genetically associated with both a shorter feeding time per day and shorter meal time per day. In a validation population of 321 steers and heifers, the ability of estimated breeding values (EBV) for MEI to predict (adjusted) phenotypic MEI was demonstrated; EBVs for MEI were estimated using multi-trait models with different sets of predictor traits such as liveweight and/or feeding behaviors. The correlation (± SE) between phenotypic MEI and EBV for MEI marginally improved (P < 0.001) from 0.64 ± 0.03 to 0.68 ± 0.03 when feeding behavior phenotypes from the validation population were included in a genetic evaluation that already included phenotypic mid-test metabolic live-weight from the validation population. This is one of the largest studies demonstrating that significant exploitable genetic variation exists in the feeding behavior of young crossbred growing cattle; such feeding behavior traits are also genetically correlated with several performance and feed efficiency metrics. Nonetheless, there was only a marginal benefit to the inclusion of time-related feeding behavior phenotypes in a genetic evaluation for MEI to improve the precision of the EBVs for this trait.

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Project description:Single nucleotide polymorphism (SNP) arrays for domestic cattle have catalyzed the identification of genetic markers associated with complex traits for inclusion in modern breeding and selection programs. Using actual and imputed Illumina 778K genotypes for 3887 U.S. beef cattle from 3 populations (Angus, Hereford, SimAngus), we performed genome-wide association analyses for feed efficiency and growth traits including average daily gain (ADG), dry matter intake (DMI), mid-test metabolic weight (MMWT), and residual feed intake (RFI), with marker-based heritability estimates produced for all traits and populations.Moderate and/or large-effect QTL were detected for all traits in all populations, as jointly defined by the estimated proportion of variance explained (PVE) by marker effects (PVE???1.0%) and a nominal P-value threshold (P???5e-05). Lead SNPs with PVE???2.0% were considered putative evidence of large-effect QTL (n?=?52), whereas those with PVE???1.0% but?<?2.0% were considered putative evidence for moderate-effect QTL (n?=?35). Identical or proximal lead SNPs associated with ADG, DMI, MMWT, and RFI collectively supported the potential for either pleiotropic QTL, or independent but proximal causal mutations for multiple traits within and between the analyzed populations. Marker-based heritability estimates for all investigated traits ranged from 0.18 to 0.60 using 778K genotypes, or from 0.17 to 0.57 using 50K genotypes (reduced from Illumina 778K HD to Illumina Bovine SNP50). An investigation to determine if QTL detected by 778K analysis could also be detected using 50K genotypes produced variable results, suggesting that 50K analyses were generally insufficient for QTL detection in these populations, and that relevant breeding or selection programs should be based on higher density analyses (imputed or directly ascertained).Fourteen moderate to large-effect QTL regions which ranged from being physically proximal (lead SNPs???3Mb) 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. Bovine positional candidate genes for these traits were functionally conserved across vertebrate species.

Project description:The objective of this study was to develop and validate a customized cost-effective single nucleotide polymorphism (SNP) panel for genetic improvement of feed efficiency in beef cattle. The SNPs identified in previous association studies and through extensive analysis of candidate genomic regions and genes, were screened for their functional impact and allele frequency in Angus and Hereford breeds used as validation candidates for the panel. Association analyses were performed on genotypes of 159 SNPs from new samples of Angus (n = 160), Hereford (n = 329), and Angus-Hereford crossbred (n = 382) cattle using allele substitution and genotypic models in ASReml. Genomic heritabilities were estimated for feed efficiency traits using the full set of SNPs, SNPs associated with at least one of the traits (at P ? 0.05 and P < 0.10), as well as the Illumina bovine 50K representing a widely used commercial genotyping panel. A total of 63 SNPs within 43 genes showed association (P ? 0.05) with at least one trait. The minor alleles of SNPs located in the GHR and CAST genes were associated with decreasing effects on residual feed intake (RFI) and/or RFI adjusted for backfat (RFIf), whereas minor alleles of SNPs within MKI67 gene were associated with increasing effects on RFI and RFIf. Additionally, the minor allele of rs137400016 SNP within CNTFR was associated with increasing average daily gain (ADG). The SNPs genotypes within UMPS, SMARCAL, CCSER1, and LMCD1 genes showed significant over-dominance effects whereas other SNPs located in SMARCAL1, ANXA2, CACNA1G, and PHYHIPL genes showed additive effects on RFI and RFIf. Gene enrichment analysis indicated that gland development, as well as ion and cation transport are important physiological mechanisms contributing to variation in feed efficiency traits. The study revealed the effect of the Jak-STAT signaling pathway on feed efficiency through the CNTFR, OSMR, and GHR genes. Genomic heritability using the 63 significant (P ? 0.05) SNPs was 0.09, 0.09, 0.13, 0.05, 0.05, and 0.07 for ADG, dry matter intake, midpoint metabolic weight, RFI, RFIf, and backfat, respectively. These SNPs contributed to genetic variation in the studied traits and thus can potentially be used or tested to generate cost-effective molecular breeding values for feed efficiency in beef cattle.

Dataset Information

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

Background

Results

Conclusions

Publications

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

Similar Datasets

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