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Journal ArticleDOI

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.
Citations
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Journal ArticleDOI
TL;DR: The studied models were characterized by good detection performance and high specificity and reliability of predictions, with special regard to oestrogen receptor alpha (ERα) and cytochrome P450 (CYP19) aromatase genotypes.
Abstract: The aim of this study was to check the effectiveness of classification and regression trees (CART), support vector machines (SVM) and generalized linear model (GLZ) in the detection of difficult calvings in the Polish Holstein-Friesian Black-and-White heifers and to identify the most influential predictors of such calvings with special regard to oestrogen receptor alpha (ERα) and cytochrome P450 (CYP19) aromatase genotypes. A total of 529 calving records containing four continuous and four categorical predictors were analysed. Calving category (difficult vs. easy) was a dependent variable. The most significant predictors were as follows: gestation length, body condition score index and calving age (for CART), as well as ERα genotype (for GLZ). Sensitivity (percentage of correctly diagnosed difficult calvings) and specificity (percentage of correctly diagnosed easy calvings) on a test set were 70.0% and 94.7% (for CART) as well as 50.0% and 99.0% (for SVM and GLZ), respectively. The studied models were cha...

12 citations

Journal ArticleDOI
TL;DR: The results suggest that for the carcass traits of Japanese Black cattle, a maximum of half of the total additive genetic variance may be explained by SNPs between 100 several tens to several 100s.
Abstract: Genomic selection using high-density single nucleotide polymorphism (SNP) genotype data may accelerate genetic improvements in livestock animals. In this study, we attempted to estimate the variance components of six carcass traits in fattened Japanese Black steers using SNP genotype data. Six hundred and seventy-three steers were genotyped using an Illumina Bovine SNP50 BeadChip and phenotyped for cold carcass weight, ribeye area, rib thickness, subcutaneous fat thickness, estimated yield percent and marbling score. Additive polygenic variance and the variance attributable to a set of SNPs that had statistically significant effects on the trait were estimated via Gibbs sampling with two models: (i) a model with the chosen SNPs and the additive polygenic effects; and (ii) a model with the polygenic effects alone. The proportion of the estimated variance attributable to the SNPs became higher as the number of SNP effects that fit increased. High correlations between breeding values estimated with the model containing the polygenic effect alone and those estimated by chosen SNPs were obtained. No fraction of the total genetic variance was explained by SNPs associated with the trait at P ≥ 0.1. Our results suggest that for the carcass traits of Japanese Black cattle, a maximum of half of the total additive genetic variance may be explained by SNPs between 100 several tens to several 100s.

11 citations

Dissertation
17 Dec 2012
TL;DR: This work illustrated both the existing genetic variation for resistance to H. contortus and the associated complexity of gene expression and gene expression interactions and identified regions of the ovine genome affecting resistance to gastro-intestinal nematodes.
Abstract: Les strongles gastro-intestinaux, dont Haemonchus contortus constituent un probleme majeur pour l'elevage des ovins allaitants. Ils entrainent des pertes de production et le recours aux anthelminthiques est remis en question par l'apparition de souches de vers resistantes. La selection d'ovins plus resistants fait partie des strategies complementaires de lutte les plus serieuses. Cependant sa mise en oeuvre requiert une meilleure comprehension des mecanismes sous-jacents. Cette these vise a identifier les regions du genome ovin impliquees dans la resistance aux strongles gastro-intestinaux. Une analyse statistique d'association entre des marqueurs genetiques et des mesures de resistance d'un troupeau d'ovins croises Martinik Black-belly x Romane a mis en evidence un nombre limite de regions d'interet. Parmi celles-ci, un segment du chromosome 12 a ete choisi pour effectuer des accouplements raisonnes et valider son role dans la resistance a H. contortus. L'effet de cette region a ete valide chez les descendants issus d'accouplements assistes par marqueurs genetiques. Cette region semble limiter fertilite des vers femelles tout en contribuant a une reponse immunitaire plus forte. Le role d'une region du chromosome 21 dans la variation de concentration plasmatique en pepsinogene, un marqueur de lesions abomasales, a egalement ete confirme. Un gene candidat sous-jacent est en cours de sequencage et l'analyse des polymorphismes devrait contribuer a la validation de son role. Deux autres genes tres proches pourraient egalement etre impliques et meriteraient une consideration future. Ces travaux illustrent a la fois la variation genetique disponible pour les caracteres de resistance a H. contortus et la complexite des mecanismes mis en jeu. Des etudes complementaires de sequencage et d'etude d'expression par sequencage devrait contribuer a une meilleure comprehension des fonctions des genes impliques et de leurs interactions. ABSTRACT : Gastro-intestinal nematodes, among which Haemonchus contortus are a major threat to the meat sheep industry. They are responsible for production losses and the apparition of worm populations resistant to drugs limits their use as worm control strategy. Breeding more resistant sheep is among the most practicable alternative strategy. However its implementation requires a deeper understanding of underlying mechanisms. This PhD aims at identifying regions of the ovine genome affecting resistance to gastro-intestinal nematodes. A statistical analysis of existing associations between genetic markers and resistance traits of a Martinik Black-belly x Romane cross-bred sheep flock unraveled a limited number of key players. Among these, a fragment of the chromosome 12 was chosen to perform marker-assisted matings and to validate its role in resistance to H. contortus. The effect of this region was validated in the progenies born from matings. It seems this chromosomic fragment limits female worms fertility and is associated to a stronger immune response. The putative role played by a fragment of the chromosome 21 in plasmatic pepsinogen concentration (a biomarker of abomasal lesions) was also confirmed in this work. A candidate gene underlying this region has been sequenced and the analysis of the detected polymorphisms should confirm its role. Further, two other genes in its vicinity could also play a role in this biological phenomenon and they should also deserve future considerations. This work illustrated both the existing genetic variation for resistance to H. contortus and the associated complexity of underlying mechanisms. Additional sequencing and gene expression sequencing studies should help understanding gene functions and interactions.

11 citations

DOI
03 Nov 2021
TL;DR: In this article, the authors highlighted the pivotal role of immune function in affecting the severity of metabolic challenges the animals face when approaching calving and suggested that the immune system may play a role in the etiology of metabolic diseases occurring in early lactation.
Abstract: Recent research on the transition period (TP) of dairy cows has highlighted the pivotal role of immune function in affecting the severity of metabolic challenges the animals face when approaching calving. This suggests that the immune system may play a role in the etiology of metabolic diseases occurring in early lactation. Several studies have indicated that the roots of immune dysfunctions could sink way before the “classical” TP (e.g., 3 weeks before and 3 weeks after calving), extending the time frame deemed as “risky” for the development of early lactation disorders at the period around the dry-off. Several distressing events occurring during the TP (i.e., dietary changes, heat stress) can boost the severity of pre-existing immune dysfunctions and metabolic changes that physiologically affect this phase of the lactation cycle, further increasing the likelihood of developing diseases. Based on this background, several operational and nutritional strategies could be adopted to minimize the detrimental effects of immune dysfunctions on the adaptation of dairy cows to the new lactation. A suitable environment (i.e., optimal welfare) and a balanced diet (which guarantees optimal nutrient partitioning to improve immune functions in cow and calf) are key aspects to consider when aiming to minimize TP challenges at the herd level. Furthermore, several prognostic behavioral and physiological indicators could help in identifying subjects that are more likely to undergo a “bad transition”, allowing prompt intervention through specific modulatory treatments. Recent genomic advances in understanding the linkage between metabolic disorders and the genotype of dairy cows suggest that genetic breeding programs aimed at improving dairy cows’ adaptation to the new lactation challenges (i.e., through increasing immune system efficiency or resilience against metabolic disorders) could be expected in the future. Despite these encouraging steps forward in understanding the physiological mechanisms driving metabolic responses of dairy cows during their transition to calving, it is evident that these processes still require further investigation, and that the TP—likely extended from dry-off—continues to be “the final frontier” for research in dairy sciences.

11 citations

Journal ArticleDOI
12 Jul 2021-Animal
TL;DR: In this article, the authors provide perspectives on technologies and practices that contribute most to sustainable production of milk from high-performing dairy cows and herds, where genomic evaluations are utilized for multiple trait selection, welfare is monitored by remote sensing, rations are formulated at micronutrient levels, health care is focused on prevention and reproduction is managed with precision.
Abstract: Milk and dairy products provide highly sustainable concentrations of essential amino acids and other required nutrients for humans; however, amount of milk currently produced per dairy cow globally is inadequate to meet future needs. Higher performing dairy cows and herds produce more milk with less environmental impact per kg than lower performing cows and herds. In 2018, 15.4% of the world's dairy cows produced 45.4% of the world's dairy cow milk, reflecting the global contribution of high-performing cows and herds. In high-performing herds, genomic evaluations are utilized for multiple trait selection, welfare is monitored by remote sensing, rations are formulated at micronutrient levels, health care is focused on prevention and reproduction is managed with precision. Higher performing herds require more inputs and generate more waste products per cow, thus innovations in environmental management on such farms are essential for lowering environmental impacts. Our focus is to provide perspectives on technologies and practices that contribute most to sustainable production of milk from high-performing dairy cows and herds.

11 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

Journal ArticleDOI
01 Apr 2001-Genetics
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

Journal ArticleDOI
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

Journal ArticleDOI
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