Distribution and location of genetic effects for dairy traits
TL;DR: A high-density scan using 38,416 single nucleotide polymorphism markers for 5,285 bulls confirmed 2 previously known major genes on Bos taurus autosomes (BTA) 6 and 14 but revealed few other large effects as discussed by the authors.
About: This article is published in Journal of Dairy Science.The article was published on 2009-06-01 and is currently open access. It has received 224 citations till now. The article focuses on the topics: Quantitative trait locus & Allele.
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01 Jan 2013
TL;DR: The aim of this paper was to review on the application of genomics in animal production for different characteristics associated with both milk and meat production and the current availability of tools of molecular genetics and genomics to predict more precision breeding values of animals from birth, decreasing the generation interval and increasing the intensity of selection.
Abstract: Genetic improvement evaluates and uses genetic variation to maintain and improve quality and quantity of animal production. The identification of high genetic merit animals is complicated by the fact that most traits of economic importance, being quantitative in nature, has controlled continuous variations which several genes interact with the environment. The aim of this paper was to review on the application of genomics in animal production for different characteristics associated with both milk and meat production and the current availability of tools of molecular genetics and genomics to predict more precision breeding values of animals from birth, decreasing the generation interval and increasing the intensity of selection.
2 citations
01 Aug 2017
TL;DR: A genome-wide association study (GWAS) was carried out on Iranian water buffaloes with the objective of detecting genomic regions associated with some morphological traits.
Abstract: A genome-wide association study (GWAS) was carried out on Iranian water buffaloes with the objective of detecting genomic regions associated with some morphological traits. For this propos, a set of 376 water buffalo with phenotypic data from Azeri (N=246), Khuzestani (N=109) and Mazandarani (N=20) breeds were genotyped with Axiom® Buffalo Genotyping Array which contains 89,988 single nucleotide polymorphism (SNP) markers. Detecting genomic regions that associated with type traits was done using GenABEL package in R. In total, 8, 9, 9, 5, 7, 5, 12, 8 and 7genomic regions were detected that maybe associated with body length (BL), heart girth (HG - represented the circumference of the chest just behind the forelimbs), chest depth (CD), height-at-withers (HAW), and hip width (HIW), pin width (PW), hip to pin length (HP) and head size (HS) and horn length (HL) morphological traits, respectively. Annotation of these regions using the UMD3.1 Bostaurus Genome Assembly was performed to find putative candidate genes within the selected regions. Among the candidate genes identified in these regions GRB10, EGR1, ACAT2, SLC25A25, NRP1, FOXC2 and ABR genes are related to biological cell growth pathways and BMP2K, EGR1, CCIN, FRMPD1, ARPC5L, DNM1, FOXC2, ABR and MPP1 are related skeletal bone development biological pathways such as bone mineralization. Further investigation of these regions with additional data is necessary to confirm the associations and fine-map the QTL regions.
Keywords: Genome wide association study, single nucleotide polymorphisms, Azeri, Khuzestaniand Mazandrani buffalo breeds.
2 citations
TL;DR: In this article, the authors compare accuracies of DGV obtained using three different prior distributions of the single-nucleotide polymorphism (SNP) effects (normal, Student's t and double-exponential) in simulated data, to understand the extent of reduction in DGV accuracy when the prior distribution does not match the true distribution of QTL effects.
Abstract: The ideal method to estimate direct genomic values (DGV) would calculate the conditional mean of the breeding value given the genotype of individuals at each quantitative traits locus (QTL). In this study we compare accuracies of DGV obtained using three different prior distributions of the single-nucleotide polymorphism (SNP) effects (normal, Student’s t and double-exponential) in simulated data, to understand the extent of reduction in DGV accuracy when the prior distribution does not match the true distribution of QTL effects. We then apply the methods in a real dataset of 1149 Australian Holstein-Friesian bulls, both to find the prior distribution that is most robust across traits and to make interpretations about the true distribution of QTL effects. Methods using normal and Student’s t prior distributions had fixed hyper-parameters, whereas hyper-parameters for double-exponential prior distribution were conditional to the data. Using the Student’s t distribution for the prior distribution of SNP effects gave the largest estimates of SNP effects in the presence of QTL with large effects in both simulated and real data, and achieved the best accuracies of DGV in both datasets. The double-exponential distribution resulted in higher shrinkage of SNP effect estimates, even when a large true effect was present. The normal distribution resulted in the greatest degree of shrinkage of estimated effects, and gave the lowest accuracies. The amount of information of the data analyzed might still be inadequate to estimate these hyper-parameters accurately. A Student’s t distribution with fixed hyper-parameters was the best approximation of the QTL distribution for the two dairy traits analyzed.
2 citations
01 Jan 2018
TL;DR: It is concluded that the size of the calf does not affect gestation length and the apparent significance of growth and body size related genomic regions for SB and CE, and the lack thereof for GL.
Abstract: Breeding values from 7416 Austrian and German Fleckvieh bulls were used to determine similarities and differences in the genomic architecture of stillbirth (SB), calving ease (CE) and gestation length (GL). The comparison was done using genome wide associations based on 42,041 SNPs after quality control and the full data set. The genomic region on BTA21 (2.4Mb) appeared to be significant for all three traits, containing the UBE3A gene connected to known syndromes impairing reproductive functions. The region on BTA14 (24Mb) was harbouring PLAG1, TGS1, RPS20, LYN and SOX17 connected to growth and body size was also significant for SB and CE, but was far from significance for GL. An additional peak was located on BTA6 (38Mb) significant for CE and approaching significance for SB. The genomic region contained the LCORL gene associated with both intrauterine growth and adult height. Based on the apparent significance of growth and body size related genomic regions for SB and CE, and the lack thereof for GL we concluded that the size of the calf does not affect gestation length. The genomic regions influencing only GL, but not SB or CE were located on BTA4 (9495Mb) and BTA7 (53Mb). Both genomic regions were rich in genes, but without any strong candidates based on the described gene functions. Genes of similar functions appeared in both however, which might provide some lead for further investigations. These included genes connected to immune response, particularly viral resistance, early embryogenesis, myogenesis and prenatal development.
2 citations
Dissertation•
02 Jul 2009
TL;DR: The hypothesis that historic geographic ancestry plays a stronger role in explaining genotypic variation, and haplotype block structure in cattle, than does the more recent selection into breeds with specific agriculture function is supported.
Abstract: COMPUTATIONAL METHODS FOR HAPLOTYPE INFERENCE WITH APPLICATION TO HAPLOTYPE BLOCK CHARACTERIZATION IN CATTLE Rafael Villa Angulo, PhD George Mason University, 2009 Dissertation Director: Prof. John J Grefenstette Genetic haplotype analysis is important in the identification of DNA variations relevant to several common and complex human diseases, and for the identification of Quantitative Trait Loci genes in animal models. Haplotype analysis is now considered one of the most promising methods for studying gene-disease and gene-phenotype association studies. In this dissertation, we address the problem of haplotype inference from cattle genotypes, which has significant differences with human genotype data. Using data derived by the International Bovine HapMap Consortium, we provide the first high-resolution haplotype block characterization in the cattle genome. In addition, a new genetic algorithm method for haplotype inference in large and complex pedigrees was developed. Novel results indicate that cattle and humans share high similarity in linkage disequilibrium and haplotype block structure in the scale of 1-100 kb. Effective populations size estimated from linkage disequilibrium reflects the period of domestication ~12,000 years ago, and the current bottleneck in breeds during the last ~700 years. Analysis of haplotype block density correlation, block boundary discordances, and haplotype sharing show clear differentiation between indicus, African, and composite breed subgroups, but not between dairy and beef subgoups. Our results support the hypothesis that historic geographic ancestry plays a stronger role in explaining genotypic variation, and haplotype block structure in cattle, than does the more recent selection into breeds with specific agriculture function. Another significant contribution from this dissertation is the development of new method for haplotype inference in large and complex cattle pedigrees. A new representation of the search space for valid haplotype configurations was developed, and a genetic algorithm was used to optimize features of the haplotype assignments. The genetic algorithm includes a novel population initialization method, new crossover and mutation operators, and a fitness function that minimizes the inferred recombinations in the pedigree. The new method outperformed the current available methods capable of handling large and complex pedigrees, and has the advantage of being scalable to larger
2 citations
References
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Book•
01 Jan 1981
TL;DR: The genetic constitution of a population: Hardy-Weinberg equilibrium and changes in gene frequency: migration mutation, changes of variance, and heritability are studied.
Abstract: Part 1 Genetic constitution of a population: Hardy-Weinberg equilibrium. Part 2 Changes in gene frequency: migration mutation. Part 3 Small populations - changes in gene frequency under simplified conditions. Part 4 Small populations - less simplified conditions. Part 5 Small populations - pedigreed populations and close inbreeding. Part 6 Continuous variation. Part 7 Values and means. Part 8 Variance. Part 9 Resemblance between relatives. Part 10 Heritability. Part 11 Selection - the response and its prediction. Part 12 Selection - the results of experiments. Part 13 Selection - information from relatives. Part 14 Inbreeding and crossbreeding - changes of mean value. Part 15 Inbreeding and crossbreeding - changes of variance. Part 16 Inbreeding and crossbreeding - applications. Part 17 Scale. Part 18 Threshold characters. Part 19 Correlated characters. Part 20 Metric characters under natural selection.
20,288 citations
TL;DR: It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
Abstract: Recent advances in molecular genetic techniques will make dense marker maps available and genotyping many individuals for these markers feasible. Here we attempted to estimate the effects of ∼50,000 marker haplotypes simultaneously from a limited number of phenotypic records. A genome of 1000 cM was simulated with a marker spacing of 1 cM. The markers surrounding every 1-cM region were combined into marker haplotypes. Due to finite population size (Ne = 100), the marker haplotypes were in linkage disequilibrium with the QTL located between the markers. Using least squares, all haplotype effects could not be estimated simultaneously. When only the biggest effects were included, they were overestimated and the accuracy of predicting genetic values of the offspring of the recorded animals was only 0.32. Best linear unbiased prediction of haplotype effects assumed equal variances associated to each 1-cM chromosomal segment, which yielded an accuracy of 0.73, although this assumption was far from true. Bayesian methods that assumed a prior distribution of the variance associated with each chromosome segment increased this accuracy to 0.85, even when the prior was not correct. It was concluded that selection on genetic values predicted from markers could substantially increase the rate of genetic gain in animals and plants, especially if combined with reproductive techniques to shorten the generation interval.
6,036 citations
TL;DR: Efficient methods for processing genomic data were developed to increase reliability of estimated breeding values and to estimate thousands of marker effects simultaneously, and a blend of first- and second-order Jacobi iteration using 2 separate relaxation factors converged well for allele frequencies and effects.
4,196 citations
TL;DR: Genotypes for 38,416 markers and August 2003 genetic evaluations for 3,576 Holstein bulls born before 1999 were used to predict January 2008 daughter deviations and genomic prediction improves reliability by tracing the inheritance of genes even with small effects.
1,166 citations