Review: Genetic and genomic selection as a methane mitigation strategy in dairy cattle

High rates of genetic gain can be achieved through (1) accurate predictions of breeding values (2) high intensities of selection and (3) shorter generation intervals. Reliabilities of ~60% are currently achievable using genomic selection in dairy cattle. This breakthrough means that selection of animals can happen at a very early age (i.e. as soon as a DNA sample is available) and has opened opportunities to radically redesign breeding schemes. Most research over the past decade has focussed on the feasibility of genomic selection, especially how to increase the accuracy of genomic breeding values. More recently, how to apply genomic technology to breeding schemes has generated a lot of interest. Some of this research remains the intellectual property of breeding companies, but there are examples in the public domain. Here we review published research into breeding scheme design using genomic selection and evaluate which designs appear to be promising (in terms of rates of genetic gain) and those that may have unfavourable side-effects (i.e. increasing the rate of inbreeding). The schemes range from fairly conservative designs where bulls are screened genomically to reduce numbers entering progeny testing, to schemes where very large numbers of bull calves are screened and used as sires as soon as they reach sexual maturity. More radical schemes that incorporate the use of reproductive technologies (in juveniles) and genomic selection in nucleus herds are also described. The models used are either deterministic and more recently tend to be stochastic, simulating populations of cattle. A key driver of the rate of genetic gain is the generation interval, which could range from being similar to that in conventional testing (~5 years), down to as little as 1.5 years. Generally, the rate of genetic gain is between 12% and 100% more than in conventional progeny testing, while the rate of inbreeding tends to be lower per generation than in progeny testing because Mendelian sampling terms can be estimated more accurately. However, short generation intervals can lead to higher rates of inbreeding per year in genomic breeding programs.

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World experience and perspectives of genomic selection in dairy cattle

The Animal Biology ◽

10.15407/animbiol18.01.117 ◽

2016 ◽

Vol 18 (1) ◽

pp. 117-125 ◽

Cited By ~ 2

Author(s):

S. Ruban ◽

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V. Danshin ◽

O. Fedota ◽

◽

...

Keyword(s):

Dairy Cattle ◽

Genomic Selection

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Genetic Diversity in the Italian Holstein Dairy Cattle Based on Pedigree and SNP Data Prior and After Genomic Selection

Frontiers in Veterinary Science ◽

10.3389/fvets.2021.773985 ◽

2022 ◽

Vol 8 ◽

Author(s):

Michela Ablondi ◽

Alberto Sabbioni ◽

Giorgia Stocco ◽

Claudio Cipolat-Gotet ◽

Christos Dadousis ◽

...

Keyword(s):

Genetic Diversity ◽

Dairy Cattle ◽

Population Size ◽

Genomic Selection ◽

Effective Population Size ◽

Genomic Data ◽

Future Market ◽

Nucleotide Polymorphisms ◽

Effective Population ◽

Snp Data

Genetic diversity has become an urgent matter not only in small local breeds but also in more specialized ones. While the use of genomic data in livestock breeding programs increased genetic gain, there is increasing evidence that this benefit may be counterbalanced by the potential loss of genetic variability. Thus, in this study, we aimed to investigate the genetic diversity in the Italian Holstein dairy cattle using pedigree and genomic data from cows born between 2002 and 2020. We estimated variation in inbreeding, effective population size, and generation interval and compared those aspects prior to and after the introduction of genomic selection in the breed. The dataset contained 84,443 single-nucleotide polymorphisms (SNPs), and 74,485 cows were analyzed. Pedigree depth based on complete generation equivalent was equal to 10.67. A run of homozygosity (ROH) analysis was adopted to estimate SNP-based inbreeding (FROH). The average pedigree inbreeding was 0.07, while the average FROH was more than double, being equal to 0.17. The pattern of the effective population size based on pedigree and SNP data was similar although different in scale, with a constant decrease within the last five generations. The overall inbreeding rate (ΔF) per year was equal to +0.27% and +0.44% for Fped and FROH throughout the studied period, which corresponded to about +1.35% and +2.2% per generation, respectively. A significant increase in the ΔF was found since the introduction of genomic selection in the breed. This study in the Italian Holstein dairy cattle showed the importance of controlling the loss of genetic diversity to ensure the long-term sustainability of this breed, as well as to guarantee future market demands.

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Relevance of genomic evaluation for egg quality traits in layers

10.1101/704742 ◽

2019 ◽

Author(s):

David Picard Druet ◽

Amandine Varenne ◽

Florian Herry ◽

Frédéric Hérault ◽

Sophie Allais ◽

...

Keyword(s):

Dairy Cattle ◽

Genomic Selection ◽

Egg Quality ◽

Pure Line ◽

Genetic Evaluation ◽

Evaluation Methodology ◽

Quality Traits ◽

Genomic Evaluation ◽

Cattle Breeding ◽

Dairy Cattle Breeding

AbstractBackgroundGenomic evaluation, based on thousands of genetic markers, has become the standard evaluation methodology in dairy cattle breeding programs over the past few years. Despite the many differences between dairy cattle breeding and poultry breeding, genomic selection seems very promising for the avian sector, and studies are currently being conducted to optimize avian selection schemes. In this optimization perspective, one of the key parameters is to properly predict the accuracy of genomic evaluation in pure line layers.MethodsBoth genetic evaluation and genomic evaluation were performed on three candidate populations (male and female), using different sizes of phenotypic records on five egg quality traits and at two different ages. The methodologies used were BLUP & ssGBLUP, and variance-covariance matrices were estimated through REML. To estimate evaluation accuracy, the LR method was implemented. Four statistics were used to assess the relative accuracy of the estimated breeding values of candidates, their bias and dispersion, as well as the differences between genetic evaluation and genomic evaluation.ResultsIt was observed that genomic evaluation, whether performed on males or females, always proved more accurate than genetic evaluation. The gain was higher when phenotypic information was narrowed and an augmentation of the size of the reference population led to an increase in accuracy prediction, for what regards genomic evaluation. By taking into account the increase of selection intensity and the decrease of the generation interval induced by genomic selection, the expected annual genetic gain would be higher with ancestry-based genomic evaluation of male candidates than with genetic evaluation based on collaterals. This advantage of genomic selection over genetic selection requires to be studied in more details for female candidates.ConclusionsIn conclusion, in the population studied, genomic evaluation for egg quality traits of breeding birds at birth seems a promising strategy, at least for what regards males selection.

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Impact of genomic selection on health improvement of high-yielding cows

Veterinaria i kormlenie ◽

10.30917/att-vk-1814-9588-2021-6-12 ◽

2021 ◽

Author(s):

O.A. Skachkova ◽

A.V. Brigida

Keyword(s):

Dairy Cattle ◽

Genomic Selection ◽

Animal Health ◽

Economic Value ◽

Reproductive Function ◽

Resistance Breeding ◽

Health Improvement ◽

Phenotypic Traits ◽

Milk Productivity ◽

Wide Range

The use of selection in dairy cattle breeding, focused for many decades on increasing milk productivity and technological properties of milk (fats and proteins), has led to the health problems of cows, including a decrease in the reproductive function, the prevalence of lameness, metritis, mastitis, infectious lesions of hooves, ketosis, milk fever and others (on average, from 30,0 % to 70,0 %). Calves, which are born by high-yielding cows in their early postnatal period, are characterized by a high mortality rate due to diarrhea (56,0 %) and respiratory diseases (47,0 %). The mortality of young animals and the forced culling of cows are global problems in the world of dairy farming. As a result, there is an interest in disease resistance breeding of dairy cattle, given that only healthy animals have an economic value, being effective and profitable. The purpose of this article was to provide some information on the global trends in the selection of dairy cattle. It is shown that genomic selection, which is originally used among bulls for their assessment and selection based on the productivity of offspring, is currently used to select female cattle by predicting their own further productivity. At the same time, the current direction of selection is a new group of economically significant breeding traits related, inter alia, to animal health, when all traits are assessed together (milk productivity, fat production, protein production, number of live calves produced, incidence of mastitis, lameness, metritis and other signs). The level of genomic selection's reliability is shown, which is 49,0 %, achieved as a result of developments begun in 2016 on the use of genomic selection, taking into account the indicated signs of health. The task is to improve the reliability of estimates for a wide range of phenotypic traits that contribute to the profitability resulting from keeping dairy cows throughout their productive life.

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