The availability of high-density SNP assays including the BovineSNP50 (50 K) enables the identification of novel quantitative trait loci (QTL) and improvement of the resolution of the locations of ...previously mapped QTL. We performed a series of genome-wide association studies (GWAS) using 50 K genotypes scored in 18,274 animals from 10 US beef cattle breeds with observations for twelve body weights, calving ease and carcass traits.
A total of 159 large-effects QTL (defined as 1-Mb genome windows explaining more than 1% of additive genetic variance) were identified. In general, more QTL were identified in analyses with bigger sample sizes. Four large-effect pleiotropic or closely linked QTLs located on BTA6 at 37-42 Mb (primarily at 38 Mb), on BTA7 at 93 Mb, on BTA14 at 23-26 Mb (primarily at 25 Mb) and on BTA20 at 4 Mb were identified in more than one breed. Several breed-specific large-effect pleiotropic or closely linked QTL were also identified. Some identified QTL regions harbor genes known to have large effects on a variety of traits in cattle such as PLAG1 and MSTN and others harbor promising candidate genes including NCAPG, ARRDC3, ERGIC1, SH3PXD2B, HMGA2, MSRB3, LEMD3, TIGAR, SEPT7, and KIRREL3. Gene ontology analysis revealed that genes involved in ossification and in adipose tissue development were over-represented in the identified pleiotropic QTL. Also, the MAPK signaling pathway was identified as a common pathway affected by the genes located near the pleiotropic QTL.
This largest GWAS ever performed in beef cattle, led us to discover several novel across-breed and breed-specific large-effect pleiotropic QTL that cumulatively account for a significant percentage of additive genetic variance (e.g. more than a third of additive genetic variance of birth and mature weights; and calving ease direct in Hereford). These results will improve our understanding of the biology of growth and body composition in cattle.
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.
Genomic selection is a recently developed technology that is beginning to revolutionize animal breeding. The objective of this study was to estimate marker effects to derive prediction equations for ...direct genomic values for 16 routinely recorded traits of American Angus beef cattle and quantify corresponding accuracies of prediction.
Deregressed estimated breeding values were used as observations in a weighted analysis to derive direct genomic values for 3570 sires genotyped using the Illumina BovineSNP50 BeadChip. These bulls were clustered into five groups using K-means clustering on pedigree estimates of additive genetic relationships between animals, with the aim of increasing within-group and decreasing between-group relationships. All five combinations of four groups were used for model training, with cross-validation performed in the group not used in training. Bivariate animal models were used for each trait to estimate the genetic correlation between deregressed estimated breeding values and direct genomic values.
Accuracies of direct genomic values ranged from 0.22 to 0.69 for the studied traits, with an average of 0.44. Predictions were more accurate when animals within the validation group were more closely related to animals in the training set. When training and validation sets were formed by random allocation, the accuracies of direct genomic values ranged from 0.38 to 0.85, with an average of 0.65, reflecting the greater relationship between animals in training and validation. The accuracies of direct genomic values obtained from training on older animals and validating in younger animals were intermediate to the accuracies obtained from K-means clustering and random clustering for most traits. The genetic correlation between deregressed estimated breeding values and direct genomic values ranged from 0.15 to 0.80 for the traits studied.
These results suggest that genomic estimates of genetic merit can be produced in beef cattle at a young age but the recurrent inclusion of genotyped sires in retraining analyses will be necessary to routinely produce for the industry the direct genomic values with the highest accuracy.
BACKGROUND: In national evaluations, direct genomic breeding values can be considered as correlated traits to those for which phenotypes are available for traditional estimation of breeding values. ...For this purpose, estimates of the accuracy of direct genomic breeding values expressed as genetic correlations between traits and their respective direct genomic breeding values are required. METHODS: We derived direct genomic breeding values for 2239 registered Limousin and 2703 registered Simmental beef cattle genotyped with either the Illumina BovineSNP50 BeadChip or the Illumina BovineHD BeadChip. For the 264 Simmental animals that were genotyped with the BovineHD BeadChip, genotypes for markers present on the BovineSNP50 BeadChip were extracted. Deregressed estimated breeding values were used as observations in weighted analyses that estimated marker effects to derive direct genomic breeding values for each breed. For each breed, genotyped individuals were clustered into five groups using K-means clustering, with the aim of increasing within-group and decreasing between-group pedigree relationships. Cross-validation was performed five times for each breed, using four groups for training and the fifth group for validation. For each trait, we then applied a weighted bivariate analysis of the direct genomic breeding values of genotyped animals from all five validation sets and their corresponding deregressed estimated breeding values to estimate variance and covariance components. RESULTS: After minimizing relationships between training and validation groups, estimated genetic correlations between each trait and its direct genomic breeding values ranged from 0.39 to 0.76 in Limousin and from 0.29 to 0.65 in Simmental. The efficiency of selection based on direct genomic breeding values relative to selection based on parent average information ranged from 0.68 to 1.28 in genotyped Limousin and from 0.51 to 1.44 in genotyped Simmental animals. The efficiencies were higher for 323 non-genotyped young Simmental animals, born after January 2012, and ranged from 0.60 to 2.04. CONCLUSIONS: Direct genomic breeding values show promise for routine use by Limousin and Simmental breeders to improve the accuracy of predicted genetic merit of their animals at a young age and increase response to selection. Benefits from selecting on direct genomic breeding values are greater for breeders who use natural mating sires in their herds than for those who use artificial insemination sires. Producers with unregistered commercial Limousin and Simmental cattle could also benefit from being able to identify genetically superior animals in their herds, an opportunity that has in the past been limited to seed stock animals.
The concept of practical theology depends on our idea about action and its relation to theology. The metaphysics of action is a study of the ontological role of action, its position among other ...things, and its relation to other objects. We can deduce a metaphysics of action from a systematic consideration of the works of Allamah Tabatabaei. According to Tabatabaei, action is a kind of movement, a movement that has its origins in the soul. A free agent acts through the mediation of constructed thoughts (conventional objects). Agent's movement does not add anything to the external world, but merely changes the way in which a human being relates to the outside. Every change in the world leads to other changes and consequently to a change in the state of affairs. So, the agent changes the world through constructed thoughts. Any thought that enters the realm of human action, must pass through the filter of conventional objects. It is clear that theology is primarily a theoretical field related to the realm of beliefs. The question is how theology enters this filter and how it becomes the basis and source of action, and in other words how it becomes the source of world change, and what is the advantage of theology over other theoretical principles for action? According to Tabatabaei, religion reminds man of the preferences associated with being and creation. On this basis, the notion of practical theology can be defined as the knowledge of explaining and justifying how the theological origin of action is preferred in the formation of individual and social actions of man.
The availability of high-density single nucleotide polymorphism (SNP) genotypes, such as BoveineHD770K, provides opportunities to identify genomic regions associated with traits in cattle. The ...objective of this study was to identify quantitative trait loci (QTL) associated with growth and body composition traits in Brangus beef cattle using actual and imputed 770K SNP genotypes. A total of 1537 Brangus beef cattle were genotyped with the Bovine50K, GGPHD77K, or BovineHD770K SNP chip and deregressed estimated breeding values were derived and fitted as observations in analyses. BayesB approach was used to map QTL for each trait, and significant windows and SNPs were identified. A total of 18 QTL were identified, in which 7 were associated with more than one trait, while the remained 11 QTL were trait-specific. One pleiotropic QTL of particularly large-effect was identified on chromosome 6 at 38Mb, which influences direct birth weight, weaning weight, and yearling weight, and harbors growth-related genes NCAPG and LCORL. Biological pathways of pleiotropic QTL were also performed using gene ontology term enrichment analysis. The QTL mapping results obtained from this study will aid in better understanding the biological processes accounting for variation in growth and body composition traits in Brangus cattle.
•18 significant QTL were identified associated with growth and body composition traits in Brangus.•7 QTL had pleiotropic effects, in which 4 of them were novel.•11 QTL were trait-specific, in which 2 were novel.
As consumers continue to request food products that have health advantages, it will be important for the livestock industry to supply a product that meet these demands. One such nutrient is fatty ...acids, which have been implicated as playing a role in cardiovascular disease. Therefore, the objective of this study was to determine the extent to which molecular markers could account for variation in fatty acid composition of skeletal muscle and identify genomic regions that harbor genetic variation.
Subsets of markers on the Illumina 54K bovine SNPchip were able to account for up to 57% of the variance observed in fatty acid composition. In addition, these markers could be used to calculate a direct genomic breeding values (DGV) for a given fatty acids with an accuracy (measured as simple correlations between DGV and phenotype) ranging from -0.06 to 0.57. Furthermore, 57 1-Mb regions were identified that were associated with at least one fatty acid with a posterior probability of inclusion greater than 0.90. 1-Mb regions on BTA19, BTA26 and BTA29, which harbored fatty acid synthase, Sterol-CoA desaturase and thyroid hormone responsive candidate genes, respectively, explained a high percentage of genetic variance in more than one fatty acid. It was also observed that the correlation between DGV for different fatty acids at a given 1-Mb window ranged from almost 1 to -1.
Further investigations are needed to identify the causal variants harbored within the identified 1-Mb windows. For the first time, Angus breeders have a tool whereby they could select for altered fatty acid composition. Furthermore, these reported results could improve our understanding of the biology of fatty acid metabolism and deposition.
Background: The identification of genetic markers associated with complex traits that are expensive to record such as feed intake or feed efficiency would allow these traits to be included in ...selection programs. To identify large-effect QTL, we performed a series of genome-wide association studies and functional analyses using 50K and 770K SNP genotypes scored in 5,133 animals from 4 independent beef cattle populations with phenotypes for average daily gain (ADG), dry matter intake (DMI), metabolic mid-test body weight (MBW) and residual feed intake (RFI). Results: A total of 5, 5, 17 and 10 large-effect QTL (defined as 1-Mb genome windows explaining more than 1 % of the additive genetic variance) were identified for ADG, DMI, MBW and RFI, respectively. These QTL had little overlap across the 4 populations. The pleiotropic QTL on BTA 7 at 23 Mb identified in the Angus population harbours a promising candidate gene ACSL6 (acyl-CoA synthetase long-chain family member 6), and was the largest effect QTL associated with DMI and MBW explaining 10.39 % and 14.25 % of the additive genetic variance, respectively. Pleiotropic QTL associated with ADG and MBW were detected on BTA 6 at 38 Mb and BTA 7 at 93 Mb confirming previous reports. No QTL for RFI explained more than 2.5 % of the additive genetic variance in any population. Gene ontology (GO) analyses revealed that genes involved in the metabolism of nitrogen components, fatty acids and carbohydrates were significantly overrepresented in the QTL regions identified for RFI. GO analyses implicate the role of cytokines in the regulation of feed intake in beef cattle. Genes within the PI3K-Akt signaling pathway were enriched for their association with variation in both ADG and DMI. Conclusions: This GWAS study which is the largest performed for feed efficiency and its component traits in beef cattle to date, identified several large-effect QTL that cumulatively explained sufficient additive genetic variance to enable the implementation of genomic selection for feed efficiency. These results enhance our understanding of the biology of growth, feed intake and utilisation in beef cattle.
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