Statistical tools to select for robustness and milk quality

2013 ◽  
Vol 4 (3) ◽  
pp. 606-611 ◽  
Author(s):  
E. Strandberg ◽  
M. Felleki ◽  
W. F. Fikse ◽  
J. Franzén ◽  
H. A. Mulder ◽  
...  
Keyword(s):  
Genetic Variation ◽  
Dairy Cattle ◽  
Field Data ◽  
Milk Quality ◽  
Large Field ◽  
Residual Variance ◽  
Progeny Testing ◽  
Environment Interaction ◽  
Environmental Sensitivity ◽  
Highly Correlated

This work was part of the EU RobustMilk project. In this work package, we have focused on two aspects of robustness, micro- and macro-environmental sensitivity and applied these to somatic cell count (SCC), one aspect of milk quality. We showed that it is possible to combine both categorical and continuous descriptions of the environment in one analysis of genotype by environment interaction. We also developed a method to estimate genetic variation in residual variance and applied it to both simulated and a large field data set of dairy cattle. We showed that it is possible to estimate genetic variation in both micro- and macro-environmental sensitivity in the same data, but that there is a need for good data structure. In a dairy cattle example, this would mean at least 100 bulls with at least 100 daughters each. We also developed methods for improved genetic evaluation of SCC. We estimated genetic variance for some alternative SCC traits, both in an experimental herd data and in field data. Most of them were highly correlated with subclinical mastitis (>0.9) and clinical mastitis (0.7 to 0.8), and were also highly correlated with each other. We studied whether the fact that animals in different herds are differentially exposed to mastitis pathogens could be a reason for the low heritabilities for mastitis, but did not find strong evidence for that. We also created a new model to estimate breeding values not only for the probability of getting mastitis but also for recovering from it. In a progeny-testing situation, this approach resulted in accuracies of 0.75 and 0.4 for these two traits, respectively, which means that it is possible to also select for cows that recover more quickly if they get mastitis.

scholarly journals Causal relationships between milk quality and coagulation properties in Italian Holstein-Friesian dairy cattle

2015 ◽  
Vol 47 (1) ◽  
Author(s):  
Francesco Tiezzi ◽  
Bruno D Valente ◽  
Martino Cassandro ◽  
Christian Maltecca
Keyword(s):  
Dairy Cattle ◽  
Milk Quality ◽  
Causal Relationships ◽  
Holstein Friesian

scholarly journals Genomic Analysis, Progress and Future Perspectives in Dairy Cattle Selection: A Review

Animals ◽  
2021 ◽  
Vol 11 (3) ◽  
pp. 599
Author(s):  
Miguel A. Gutierrez-Reinoso ◽  
Pedro M. Aponte ◽  
Manuel Garcia-Herreros
Keyword(s):  
Dairy Cattle ◽  
Production Efficiency ◽  
Association Studies ◽  
Phenotypic Traits ◽  
Progeny Testing ◽  
Genome Wide Association Studies ◽  
Genetic Progress ◽  
Breeding Programs ◽  
Increased Risk ◽  
Selection Of

Genomics comprises a set of current and valuable technologies implemented as selection tools in dairy cattle commercial breeding programs. The intensive progeny testing for production and reproductive traits based on genomic breeding values (GEBVs) has been crucial to increasing dairy cattle productivity. The knowledge of key genes and haplotypes, including their regulation mechanisms, as markers for productivity traits, may improve the strategies on the present and future for dairy cattle selection. Genome-wide association studies (GWAS) such as quantitative trait loci (QTL), single nucleotide polymorphisms (SNPs), or single-step genomic best linear unbiased prediction (ssGBLUP) methods have already been included in global dairy programs for the estimation of marker-assisted selection-derived effects. The increase in genetic progress based on genomic predicting accuracy has also contributed to the understanding of genetic effects in dairy cattle offspring. However, the crossing within inbred-lines critically increased homozygosis with accumulated negative effects of inbreeding like a decline in reproductive performance. Thus, inaccurate-biased estimations based on empirical-conventional models of dairy production systems face an increased risk of providing suboptimal results derived from errors in the selection of candidates of high genetic merit-based just on low-heritability phenotypic traits. This extends the generation intervals and increases costs due to the significant reduction of genetic gains. The remarkable progress of genomic prediction increases the accurate selection of superior candidates. The scope of the present review is to summarize and discuss the advances and challenges of genomic tools for dairy cattle selection for optimizing breeding programs and controlling negative inbreeding depression effects on productivity and consequently, achieving economic-effective advances in food production efficiency. Particular attention is given to the potential genomic selection-derived results to facilitate precision management on modern dairy farms, including an overview of novel genome editing methodologies as perspectives toward the future.

Adaptive sampling of potential-field data: A direct approach to compressive inversion

Geophysics ◽  
2014 ◽  
Vol 79 (1) ◽  
pp. IM1-IM9 ◽  
Author(s):  
Nathan Leon Foks ◽  
Richard Krahenbuhl ◽  
Yaoguo Li
Keyword(s):  
Potential Field ◽  
Adaptive Sampling ◽  
Field Data ◽  
Computational Cost ◽  
Large Field ◽  
Magnetic Data ◽  
Data Sampling ◽  
Data Types ◽  
Data Set ◽  
Potential Field Data

Compressive inversion uses computational algorithms that decrease the time and storage needs of a traditional inverse problem. Most compression approaches focus on the model domain, and very few, other than traditional downsampling focus on the data domain for potential-field applications. To further the compression in the data domain, a direct and practical approach to the adaptive downsampling of potential-field data for large inversion problems has been developed. The approach is formulated to significantly reduce the quantity of data in relatively smooth or quiet regions of the data set, while preserving the signal anomalies that contain the relevant target information. Two major benefits arise from this form of compressive inversion. First, because the approach compresses the problem in the data domain, it can be applied immediately without the addition of, or modification to, existing inversion software. Second, as most industry software use some form of model or sensitivity compression, the addition of this adaptive data sampling creates a complete compressive inversion methodology whereby the reduction of computational cost is achieved simultaneously in the model and data domains. We applied the method to a synthetic magnetic data set and two large field magnetic data sets; however, the method is also applicable to other data types. Our results showed that the relevant model information is maintained after inversion despite using 1%–5% of the data.

scholarly journals Canaryseed (Phalaris canariensis L.) accessions from nineteen countries show useful genetic variation for agronomic traits

2011 ◽  
Vol 91 (1) ◽  
pp. 37-48 ◽  
Author(s):  
M. Cogliatti ◽  
F. Bongiorno ◽  
H. Dalla Valle ◽  
W J Rogers
Keyword(s):  
Genetic Variation ◽  
Grain Yield ◽  
Harvest Index ◽  
Agronomic Traits ◽  
Grain Weight ◽  
Environment Interaction ◽  
Grain Number ◽  
Harvest Maturity ◽  
Phalaris Canariensis ◽  
Late Sowing

Fifty-seven accessions of canaryseed (47 populations and 10 cultivars) from 19 countries were evaluated for agronomic traits in four field trials sown over 3 yr in the province of Buenos Aires, Argentina. Genetic variation was found for all traits scored: grain yield and its components (grain weight, grain number per square meter, grain number per head and head number per square meter), harvest index, percent lodging, and phenological characters (emergence to heading, emergence to harvest maturity and heading to harvest maturity). Although genotype × environment interaction was observed for all traits, the additive differences between accessions were sufficient to enable promising breeding materials to be identified. Accessions superior in performance to the local Argentinean population, which in general gave values close to the overall mean of the accessions evaluated, were identified. For example, a population of Moroccan origin gave good yield associated with elevated values of the highly heritable character grain weight, rather than with the more commonly observed grain number per square meter. This population was also of relatively short stature and resistant to lodging, and, although it performed best when sown within the normal sowing date, tolerated late sowing fairly well. Other accessions were also observed with high grain weight, a useful characteristic in itself, since large grains are desirable from a quality point of view. Regarding phenology, the accessions showed a range of 160 degree days (8 calendar days in our conditions) in maturity, which, while not large in magnitude, may be of some utility in crop rotation management. Some accessions were well adapted to late sowing. Grain yield in general was strongly correlated with grain number per square meter. Principal components analysis (PCA) carried out for all characteristics provided indications of accessions combining useful characteristics and identified three components that explained approximately 70% of the phenotypic variation. Furthermore, a second PCA plus regression showed that approximately 60% of the variation in grain yield could be explained by a component associated with harvest index and grain number per square meter. Pointers were provided to possible future breeding targets.Key words: Phalaris canariensis, canaryseed, accessions, yield, phenology, genetics, breeding

scholarly journals Genetic variation of maize silage ingestibility in dairy cattle

2003 ◽  
Vol 52 (6) ◽  
pp. 489-500 ◽  
Author(s):  
Yves Barrière ◽  
Jean-Claude Emile ◽  
Fabien Surault
Keyword(s):  
Genetic Variation ◽  
Dairy Cattle ◽  
Maize Silage

The use of progeny testing with artificial insemination in dairy cattle

1950 ◽  
Vol 50 (1) ◽  
pp. 21-31 ◽  
Author(s):  
Alan Robertson ◽  
J. M. Rendel
Keyword(s):  
Dairy Cattle ◽  
Artificial Insemination ◽  
Progeny Testing

Breeding and milk quality

1984 ◽  
Vol 9 ◽  
pp. 27-34
Author(s):  
J. R. Mulholland
Keyword(s):  
Dairy Cattle ◽  
Milk Quality ◽  
Dominant Factor ◽  
Probability Curve ◽  
Animal Remains ◽  
Normal Probability ◽  
Payment Schemes ◽  
Long Time ◽  
High Production ◽  
The Relationship

SUMMARYThe broad principles of animal breeding are outlined and the ‘normal-probability curve’ is used to illustrate how progress should be made in improving the genetic merit of dairy cattle. The importance of genetically correlated responses is discussed, together with the need to test progeny. The way in which genetic improvement accumulates in dairy cattle is described and the need to use high-production sires with reliable proofs is stressed. Present and proposed milk-quality payment schemes require that selection should be based on the yield of recorded solids as the best indicator of total solids. As cattle breeding involves a long time-scale, it is not always possible to take into account short-term changes in the value of milk constituents. The effect of changing values upon the ranking of bulls is small and, for the foreseeable future, the use of the weight of recorded solids, i.e. the weight of fat plus the weight of protein, as the selection factor, is likely to maximize progress. The relationship between functional type and herd life is examined. It is concluded that there is no obvious relationship between type and herd life; yield is the dominant factor in determining the length of time an animal remains in the herd. Any breeding programme should therefore place maximum emphasis on production.

scholarly journals Selection of a suitable definition of environment for the estimation of genotype × environment interaction in the weaning weight of beef cattle

2008 ◽  
Vol 53 (No. 10) ◽  
pp. 407-417 ◽  
Author(s):  
L. Vostrý ◽  
J. Přibyl ◽  
V. Jakubec ◽  
Z. Veselá ◽  
I. Majzlík
Keyword(s):  
Beef Cattle ◽  
Evaluation Model ◽  
Economic Value ◽  
Information Criterion ◽  
Ratio Test ◽  
Residual Variance ◽  
Environment Interaction ◽  
Weaning Weight ◽  
Genotype Environment Interaction ◽  
And Performance

Genotype by environment interactions for weaning weight in beef cattle were tested using several definitions of environments. Four breeds of beef cattle (Hereford, Aberdeen Angus, Beef Simmental, and Charolais) were represented. The environments were defined according to five criteria: altitude, production areas, economic value of the land, less favourable areas, and performance levels of a breed within herds. Ten mixed models were compared including the effects of direct and maternal genetics, herd-year-season, maternal permanent environmental, breed, environment, genotype × environment interaction, sex of calf, and age of dam. The suitability of the models was tested by Akaike’s Information Criterion, likelihood ratio test, and magnitude of the residual variance. The most suitable definitions of environment were less favoured areas and herd levels of performance. Estimates of direct heritability ranged from 0.07 to 0.19. Genotype × environment interactions should be included in a genetic evaluation model for interbreed comparisons of beef cattle in the Czech Republic.

scholarly journals High differentiation in functional traits but similar phenotypic plasticity in populations of a soil specialist along a climatic gradient

2020 ◽  
Vol 125 (6) ◽  
pp. 969-980 ◽  
Author(s):  
Silvia Matesanz ◽  
Marina Ramos-Muñoz ◽  
Mario Blanco-Sánchez ◽  
Adrián Escudero
Keyword(s):  
Genetic Variation ◽  
Phenotypic Plasticity ◽  
Functional Traits ◽  
Common Garden ◽  
Population Level ◽  
General Purpose ◽  
Climatic Conditions ◽  
Environment Interaction ◽  
Moisture Variation ◽  
Neutral Genetic Variation

Abstract Background and Aims Plants experiencing contrasting environmental conditions may accommodate such heterogeneity by expressing phenotypic plasticity, evolving local adaptation or a combination of both. We investigated patterns of genetic differentiation and plasticity in response to drought in populations of the gypsum specialist Lepidium subulatum. Methods We created an outdoor common garden with rain exclusion structures using 60 maternal progenies from four distinct populations that substantially differ in climatic conditions. We characterized fitness, life history and functional plasticity in response to two contrasting treatments that realistically reflect soil moisture variation in gypsum habitats. We also assessed neutral genetic variation and population structure using microsatellite markers. Key Results In response to water stress, plants from all populations flowered earlier, increased allocation to root tissues and advanced leaf senescence, consistent with a drought escape strategy. Remarkably, these probably adaptive responses were common to all populations, as shown by the lack of population × environment interaction for almost all functional traits. This generally common pattern of response was consistent with substantial neutral genetic variation and large differences in population trait means. However, such population-level trait variation was not related to climatic conditions at the sites of origin. Conclusions Our results show that, rather than ecotypes specialized to local climatic conditions, these populations are composed of highly plastic, general-purpose genotypes in relation to climatic heterogeneity. The strikingly similar patterns of plasticity among populations, despite substantial site of origin differences in climate, suggest past selection on a common norm of reaction due to similarly high levels of variation within sites. It is thus likely that plasticity will have a prevalent role in the response of this soil specialist to further environmental change.

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