scholarly journals Investigations on breeding plans for organic dairy cattle

2004 ◽  
Vol 47 (2) ◽  
pp. 129-139 ◽  
Author(s):  
B. Harder ◽  
W. Junge ◽  
J. Bennewitz ◽  
E. Kalm
Keyword(s):  
Natural Selection ◽  
Population Size ◽  
Artificial Insemination ◽  
Genetic Gain ◽  
Selection Response ◽  
Breeding Program ◽  
Production Traits ◽  
Cattle Breeding ◽  
Economic Weights ◽  
The Impact

Abstract. facilities in Germany, different alternative breeding plans for organic cattle breeding were developed using the computer program ZPLAN. First the impact of the population size on the parameters of success was analysed. A conventional cattle breeding program was compared with an organic breeding program. The results indicate that the selection response increased with increasing population size due to improved selection of bull sires. The EU Regulations on organic farming say that the proportion of artificial insemination has to be reduced as much as possible. According to this, the influence of different proportions of artificial insemination on the monetary genetic gain was investigated. The reduction of artificial insemination below 50% led to high losses in the discounted profit. The influence of higher economic weights for functional traits on the natural selection response was investigated. An increase of the economic weights by 50% led to tolerable decreases in the natural selection response of production traits with regard to a more ecological orientated breeding goal. The effect of the variation of the test capacity and the number of test bulls on the monetary genetic gain was analysed. The optimum for the monetary genetic gain was located at a test capacity of 50%, 30 test bulls and 99 daughters per test bull.

scholarly journals Industrial perspective: capturing the benefits of genomics to Irish cattle breeding

2012 ◽  
Vol 52 (3) ◽  
pp. 172 ◽  
Author(s):  
B. W. Wickham ◽  
P. R. Amer ◽  
D. P. Berry ◽  
M. Burke ◽  
S. Coughlan ◽  
...  
Keyword(s):  
Genomic Selection ◽  
Artificial Insemination ◽  
Genetic Gain ◽  
Selection Index ◽  
Breeding Program ◽  
Training Population ◽  
Genetic Progress ◽  
Cattle Breeding ◽  
Program Costs ◽  
The Cost

Genomics is a technology for increasing the accuracy with which the genetic merit of young potential breeding animals can be determined. It enables earlier selection decisions, thus reducing generation intervals and gives rise to more rapid annual rates of genetic gain. Recently, the cost of genomics has reduced to the point where it enables breeding-program costs to be reduced substantially. Ireland has been a rapid adopter of genomics technology in its dairy-cattle breeding program, with 40% of dairy-cow artificial inseminations in 2010 being from bulls evaluated using genomic information. This rapid adoption has been facilitated by a comprehensive database of phenotypes and genotypes, strong public funding support for applied genomics research, an international network of collaborators, a short path between research and implementation, an overall selection index which farmers use in making breeding decisions, and a motivated and informed breeding industry. The shorter generation interval possible with genomic selection strategies also allows exploitation of the already accelerating rate of genetic progress in Ireland, because elite young dairy bulls are considerably superior to the small numbers of bulls that entered progeny test 6 years ago. In addition, genomics is having a dramatic impact on the artificial-insemination industry by substantially reducing the cost of entry, the cost of operation, and shifting the focus of breeding from bulls to cows. We believe that the current industry structures must evolve substantially if Irish cattle farmers are to realise the full benefits of genomics and be protected from related risks. Our model for future dairy breeding envisages a small number of ‘next generation research herds’, 1000 ‘bull breeder herds’ and an artificial-insemination sector using 30 new genomically selected bulls per year to breed the bulk of replacements in commercial milk-producing herds. Accurate imputation from a low-density to a higher-density chip is a key element of our strategy to enable dairy farmers to afford access to genomics. This model is capable of delivering high rates of genetic gain, realising cost savings, and protecting against the risks of increased inbreeding and suboptimal breeding goals. Our strategy for exploiting genomic selection for beef breeding is currently focussed on genotyping, using a high-density chip, a training population of greater than 2000 progeny-tested bulls representing all the main beef breeds in Ireland. We recognise the need for a larger training population and are seeking collaboration with organisations in other countries and populations.

scholarly journals Claw health and feed efficiency as new selection criteria in the Czech Holstein cattle Krupová Z., Wolfová M., Krupa E., Přibyl J., Zavadilová L.

2018 ◽  
Vol 63 (No. 10) ◽  
pp. 408-418 ◽  
Author(s):  
Z. Krupová ◽  
M. Wolfová ◽  
E. Krupa ◽  
J. Přibyl ◽  
L. Zavadilová
Keyword(s):  
Feed Intake ◽  
Feed Efficiency ◽  
Disease Incidence ◽  
Selection Index ◽  
Residual Feed Intake ◽  
Selection Response ◽  
Holstein Cattle ◽  
Breeding Objective ◽  
Economic Weights ◽  
The Impact

The objective of this study was to calculate economic weights for ten current breeding objective traits and for four new traits characterising claw health and feed efficiency in Czech Holstein cattle and to investigate the impact of different selection indices on the genetic responses for these traits. Economic weights were estimated using a bio-economic model, while applying actual (2017) and predicted (2025) production and economic circumstances. For the actual situation, the economic weights of claw disease incidence were –100.1 € per case, and those of daily residual feed intake in cows, breeding heifers, and fattened animals were –79.37, –37.16, and –6.33 €/kg dry matter intake per day, respectively. In the predicted situation, the marginal economic weights for claw disease and feed efficiency traits increased on average by 38% and 20%, respectively. The new traits, claw disease incidence and daily residual feed intake, were gradually added to the 17 current Holstein selection index traits to improve the new traits. Constructing a comprehensive index with 21 traits and applying the general principles of the selection index theory, a favourable annual genetic selection response was obtained for the new traits (–0.008 cases of claw disease incidence and –0.006 kg of daily residual feed intake across all cattle categories), keeping the annual selection response of the most important current breeding objective traits at a satisfactory level (e.g., 73 kg of milk yield per lactation, 0.016% of milk fat). Claw health and feed efficiency should be defined as new breeding objectives and new selection index traits of local dairy population.

Selection response in fecal worm egg counts in the Rylington Merino parasite resistant flock

2006 ◽  
Vol 46 (7) ◽  
pp. 809 ◽  
Author(s):  
L. J. E. Karlsson ◽  
J. C. Greeff
Keyword(s):  
Genetic Gain ◽  
Genetic Correlations ◽  
Time Frame ◽  
Selection Response ◽  
Breeding Value ◽  
Selection Line ◽  
Production Traits ◽  
Parasite Resistance ◽  
Component Trait ◽  
Parasite Challenge

The Rylington Merino internal parasite resistant selection line was initiated in 1987 from a wide genetic base of 100 ewe flocks. Selection for parasite resistance was based on selecting animals with a low worm egg count in a natural parasite challenge environment. The realised annual genetic gain for estimated breeding value of worm egg count is 2.7%. The genetic gain in parasite resistance has been achieved without any adverse genetic correlations with the other economically important production traits. There is an unfavourable genetic correlation between worm egg count and scouring traits. The recommendation to industry is to select for both low worm egg count and reduced diarrhoea and combine these traits with other economically important production traits. The relative weighting applied to each component trait will vary according to the local parasite challenge situation and the time frame available to achieve sustainable parasite control.

Economic evaluation of beef cattle breeding schemes incorporating performance testing of young bulls for feed intake

2004 ◽  
Vol 44 (5) ◽  
pp. 393 ◽  
Author(s):  
J. A. Archer ◽  
S. A. Barwick ◽  
H.-U. Graser
Keyword(s):  
Beef Cattle ◽  
Feed Intake ◽  
Genetic Gain ◽  
Selection Criterion ◽  
Performance Testing ◽  
Cattle Breeding ◽  
Commercial Unit ◽  
Base Scenario ◽  
Breeding Schemes ◽  
The Impact

A model beef cattle breeding scheme consisting of a breeding unit and a commercial unit was used to evaluate the impact on genetic gain and profitability of incorporating feed intake measurements as an additional selection criterion in breeding programmes. Costs incurred by the breeding unit were compared with returns generated in the commercial unit, with bulls from the breeding unit being used as sires in the commercial unit. Two different market objectives were considered — a grass-fed product for the Australian domestic market, and a grain-fed product for the Japanese market. Breeding units utilising either artificial insemination or natural service were also considered. A base scenario was modelled incorporating a range of criteria available to Australian cattle breeders. A second scenario incorporated selection of sires for the breeding unit using a 2-stage selection process, with a proportion of bulls selected after weaning for measurement of (residual) feed intake. Measurement of feed intake of bulls improved accuracy of breeding unit sire selection by 14–50% over the equivalent base scenario, and genetic gain in the breeding objective was improved for all scenarios, with gains ranging from 8 to 38% over the base scenario. After accounting for the cost of measuring feed intake ($150–450), additional profit was generated from inclusion of feed intake measurement on a proportion of bulls for all breeding schemes considered. Profit was generally maximised where 10–20% of bulls were selected at weaning for measurement of intake, with improvement in profit ranging from 9 to 33% when optimal numbers of bulls were selected for intake measurement.

Customized selection indices for dairy bulls in Australia

1996 ◽  
Vol 62 (3) ◽  
pp. 393-403 ◽  
Author(s):  
P. J. Bowman ◽  
P. M. Visscher ◽  
M. E. Goddard
Keyword(s):  
Body Weight ◽  
Milk Fat ◽  
Protein Yield ◽  
Production Traits ◽  
Breeding Objective ◽  
Economic Weights ◽  
Wide Range ◽  
Selection Indices ◽  
Dairy Bulls ◽  
The Impact

AbstractCustomized sire selection indices were developed for Australian dairy bulls in order to promote more objective use of estimated breeding values in commercial breeding programmes. It was assumed that the breeding goal for commercial dairy farmers is the profitability of a bull's progeny. Seven characteristics of the progeny were identified as having a major impact on profitability and were included in the breeding objective: milk, fat and protein yield, survival, body weight, milking speed and temperament. Traits in the selection indices used to predict profit were milk, fat and protein yield, survival, milking speed, temperament, size, overall type and fore teat placement. Size was included because of its correlation with body weight, and overall type and front teat placement because of their correlation with survival. To avoid double counting the benefits of milk production traits, temperament and milking speed, the survival trait in the objective was defined as survival independent of voluntary culling for these traits. Customization of the breeding objective was achieved by adjusting the economic weights for traits in the objective to take account of important characteristics of farmers' herds, the milk payment system under which they operate and make allowance for their own value judgements. An assessment of the impact of customization suggested that, even though there is a wide range in the economic weights that are applicable in different areas of Australia, there would be little loss of efficiency in using a single national index. However, customization is still believed to be desirable given that it is likely that a substantial proportion offarmers will be reluctant to use a national index, especially in those states which have quotas and focus on the liquid milk market. The algorithms described in the paper have been incorporated into a user-friendly microcomputer program called $electabull which is now commercially available to farmers.

scholarly journals Differences in local population history at the finest level: the case of the Estonian population

2020 ◽  
Vol 28 (11) ◽  
pp. 1580-1591 ◽  
Author(s):  
Vasili Pankratov ◽  
Francesco Montinaro ◽  
Alena Kushniarevich ◽  
Georgi Hudjashov ◽  
Flora Jay ◽  
...  
Keyword(s):  
Natural Selection ◽  
Genetic Structure ◽  
Population Size ◽  
Effective Population Size ◽  
Local Population ◽  
Population History ◽  
Human Populations ◽  
Effective Population ◽  
The Impact ◽  
Estonian Population

Abstract Several recent studies detected fine-scale genetic structure in human populations. Hence, groups conventionally treated as single populations harbour significant variation in terms of allele frequencies and patterns of haplotype sharing. It has been shown that these findings should be considered when performing studies of genetic associations and natural selection, especially when dealing with polygenic phenotypes. However, there is little understanding of the practical effects of such genetic structure on demography reconstructions and selection scans when focusing on recent population history. Here we tested the impact of population structure on such inferences using high-coverage (~30×) genome sequences of 2305 Estonians. We show that different regions of Estonia differ in both effective population size dynamics and signatures of natural selection. By analyzing identity-by-descent segments we also reveal that some Estonian regions exhibit evidence of a bottleneck 10–15 generations ago reflecting sequential episodes of wars, plague and famine, although this signal is virtually undetected when treating Estonia as a single population. Besides that, we provide a framework for relating effective population size estimated from genetic data to actual census size and validate it on the Estonian population. This approach may be widely used both to cross-check estimates based on historical sources as well as to get insight into times and/or regions with no other information available. Our results suggest that the history of human populations within the last few millennia can be highly region specific and cannot be properly studied without taking local genetic structure into account.

scholarly journals Natural selection constrains neutral diversity across a wide range of species.

2014 ◽  
Author(s):  
Russell B. Corbett-Detig ◽  
Daniel L. Hartl ◽  
Timothy B. Sackton
Keyword(s):  
Genetic Diversity ◽  
Natural Selection ◽  
Population Size ◽  
Neutral Theory ◽  
Genetic Maps ◽  
Modeling Framework ◽  
Neutral Genetic Diversity ◽  
Wide Range ◽  
Census Population Size ◽  
The Impact

The neutral theory of molecular evolution predicts that the amount of neutral polymorphisms within a species will increase proportionally with the census population size (Nc). However, this prediction has not been borne out in practice: while the range of Nc spans many orders of magnitude, levels of genetic diversity within species fall in a comparatively narrow range. Although theoretical arguments have invoked the increased efficacy of natural selection in larger populations to explain this discrepancy, few direct empirical tests of this hypothesis have been conducted. In this work, we provide a direct test of this hypothesis using population genomic data from a wide range of taxonomically diverse species. To do this, we relied on the fact that the impact of natural selection on linked neutral diversity depends on the local recombinational environment. In regions of relatively low recombination, selected variants affect more neutral sites through linkage, and the resulting correlation between recombination and polymorphism allows a quantitative assessment of the magnitude of the impact of selection on linked neutral diversity. By comparing whole-genome polymorphism data and genetic maps using a coalescent modeling framework, we estimate the degree to which natural selection reduces linked neutral diversity for 40 species of obligately sexual eukaryotes. We then show that the magnitude of the impact of natural selection is positively correlated with Nc, based on body size and species range as proxies for census population size. These results demonstrate that natural selection removes more variation at linked neutral sites in species with large Nc than those with small Nc, and provides direct empirical evidence that natural selection constrains levels of neutral genetic diversity across many species. This implies that natural selection may provide an explanation for this longstanding paradox of population genetics.

scholarly journals Effects of linked selective sweeps on demographic inference and model selection

2016 ◽  
Author(s):  
Daniel R. Schrider ◽  
Alexander G. Shanku ◽  
Andrew D. Kern
Keyword(s):  
Genetic Variation ◽  
Natural Selection ◽  
Positive Selection ◽  
Population Size ◽  
Natural Populations ◽  
Parameter Estimates ◽  
Selective Sweeps ◽  
Recent Positive Selection ◽  
Demographic Inference ◽  
The Impact

AbstractThe availability of large-scale population genomic sequence data has resulted in an explosion in efforts to infer the demographic histories of natural populations across a broad range of organisms. As demographic events alter coalescent genealogies they leave detectable signatures in patterns of genetic variation within and between populations. Accordingly, a variety of approaches have been designed to leverage population genetic data to uncover the footprints of demographic change in the genome. The vast majority of these methods make the simplifying assumption that the measures of genetic variation used as their input are unaffected by natural selection. However, natural selection can dramatically skew patterns of variation not only at selected sites, but at linked, neutral loci as well. Here we assess the impact of recent positive selection on demographic inference by characterizing the performance of three popular methods through extensive simulation of datasets with varying numbers of linked selective sweeps. In particular, we examined three different demographic models relevant to a number of species, finding that positive selection can bias parameter estimates of each of these models—often severely. Moreover, we find that selection can lead to incorrect inferences of population size changes when none have occurred. We argue that the amount of recent positive selection required to skew inferences may often be acting in natural populations. These results suggest that demographic studies conducted in many species to date may have exaggerated the extent and frequency of population size changes.

scholarly journals Udder and Claw-Related Health Traits in Selection of Czech Holstein Cows

2019 ◽  
Vol 19 (3) ◽  
pp. 647-661
Author(s):  
Zuzana Krupová ◽  
Ludmila Zavadilová ◽  
Marie Wolfová ◽  
Emil Krupa ◽  
Eva Kašná ◽  
...  
Keyword(s):  
Selection Criteria ◽  
Selection Index ◽  
Genetic Selection ◽  
Selection Response ◽  
Clinical Mastitis ◽  
Holstein Cows ◽  
Breeding Objective ◽  
Economic Weights ◽  
The Impact ◽  
Selection Of

AbstractThe aim of the study was to investigate the impact of the implementation of new health traits into the breeding objective and selection criteria for Czech Holstein cows on the genetic selection response in the breeding objective traits. Incidence of overall claw diseases was included into the current breeding objective for cows (11 traits together). Three traits that indicated claw health (incidence of claw diseases overall and infectious and non-infectious claw diseases) and incidence of clinical mastitis were successively added to the current selection criteria in a cow selection index (a maximum of 19 traits). Selection responses in the breeding objective traits were estimated by applying the general principles of the selection index theory. The required genetic variances for the new traits, the economic weights for all breeding objective traits and the genetic correlations among the selection index traits were estimated within this study. The marginal economic weights, which were calculated for two-year-old cows by applying a bioeconomic model with implemented gene flow, were -193 and -168 € per case for clinical mastitis and overall claw disease incidence, respectively. Using the comprehensive selection index with 19 traits, the reduction in the incidence of both udder and claw diseases was calculated to be 0.004 cases per cow per year. At the same time, a more favourable genetic selection response was obtained for other functional traits, e.g., +0.020% for cow conception rate and +0.010 years for productive life of cow (which represented the profit of 67 € and 367 € per herd and per year, respectively) when compared to the current index. Based on this study, a direct selection of cows for claw and udder health is nowadays recommended to improve the health status of herds and economics in production systems.

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