THE USE OF EMPIRICAL BREEDING VALUES TO IMPROVE GENETIC PROGRESS IN HOPS

Genetic and phenotypic trends and parameters were estimated for reproduction, fleece weight and liveweight in a South African Merino population, divergently selected from 1986, either for (H line) or against (L line) maternal multiple rearing ability. Annual reproduction, ewe greasy fleece weight and pre-joining liveweight data were recorded on 809 Merino ewes, from 1986 to 2002. Phenotypic trends indicated divergence in reproduction traits between the H and L lines. The direct additive variance ratio (h2 ± s.e.) for day of lambing was 0.08 ± 0.02. Estimates of h2 for reproduction traits were: 0.10 ± 0.02 for number of lambs born per ewe; 0.04 ± 0.02 for number of lambs weaned per ewe; and 0.04 ± 0.02 for weight of lamb weaned per ewe, corrected for the gender of the lamb. Corresponding h2 estimates for annual production were 0.57 ± 0.06 for greasy fleece weight and 0.48 ± 0.06 for ewe liveweight at joining. Service sire only exerted a significant (P<0.05) effect on day of lambing, but it accounted for merely 2% of the overall phenotypic variation. Ewe permanent environment variance ratios (c2ewe) for the reproduction traits were: 0.07 ± 0.03 for number of lambs born per ewe; 0.11 ± 0.03 for number of lambs weaned per ewe; and 0.11 ± 0.03 for total weight of lamb weaned per ewe. Corresponding c2ewe estimates for annual production traits were 0.14 ± 0.05 for greasy fleece weight and 0.27 ± 0.06 for ewe joining weight. Genetic and ewe permanent environmental correlations between measures of reproduction exceeded 0.7. Genetic correlations of reproduction traits with greasy fleece weight were low and variable in sign. Genetic correlations of reproduction traits with ewe joining weight were positive and particularly high for weight of lamb weaned. Permanent environmental correlations of reproduction traits with greasy fleece weight and joining weight were generally low to moderate. Genetic trends for the H and L lines (derived from averaged direct breeding values within birth years) were divergent (P<0.01) for all reproduction traits. Expressed as percentage of the overall least squares means of the respective traits, breeding values in the H line increased annually, with 1.3% for lambs born per ewe, 1.5% for lambs weaned per ewe and by 1.8% for weight of lamb weaned per ewe. Corresponding trends in the L line were, respectively, –0.6%, –1.0% and –1.2% per year. Substantial genetic progress in annual lamb output was attainable, despite relatively small h2 estimates. This response was achieved without unfavourable genetic changes in wool and liveweight.

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Prevalence and breeding values of elbow dysplasia in the Estrela mountain dog

Veterinární Medicína ◽

10.17221/7033-vetmed ◽

2013 ◽

Vol 58 (No. 9) ◽

pp. 484-490 ◽

Cited By ~ 2

Author(s):

S. Alves-Pimenta ◽

B. Colaco ◽

AM Silvestre ◽

MM Ginja

Keyword(s):

Hip Dysplasia ◽

Mass Selection ◽

Genetic Trend ◽

Genetic Progress ◽

Breeding Values ◽

Elbow Dysplasia ◽

Low Mass ◽

The Mean ◽

Dog Breed ◽

Genetic Trends

The aims of this study were to determine the prevalence and heritability of elbow dysplasia in the Estrela mountain dog breed, to investigate genetic trends over the last 20 years (1990–2009) and to evaluate the association of individual records with breeding values. The elbows of 351 Estrela mountain dogs were examined using the flexed mediolateral radiographic view and evaluated using the International Elbow Working Group scoring system. Heritability and breeding values were estimated using a linear model. Elbow Dysplasia was found in 16.5% (59/351) of the dogs; males (27%, 34/127) were more affected than females (11%, 24/224) (P < 0.05). The heritability was very low (0.065) and the genetic trend showed a slight positive slope with an improvement in 2004 and 2005. The mean breeding values in elbow dysplasia grades were different but the overlap among grades was very pronounced. The prevalence and heritability of elbow dysplasia in the breed are thus low. Mass selection using individual phenotypes may not be effective. Elbow dysplasia genetic trends are similar to trends for hip dysplasia and passive hip laxity, so the use of selection against hip dysplasia may also result in genetic progress for elbow dysplasia.  

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Genomic Prediction of Average Daily Gain, Back-Fat Thickness, and Loin Muscle Depth Using Different Genomic Tools in Canadian Swine Populations

Frontiers in Genetics ◽

10.3389/fgene.2021.665344 ◽

2021 ◽

Vol 12 ◽

Author(s):

Siavash Salek Ardestani ◽

Mohsen Jafarikia ◽

Mehdi Sargolzaei ◽

Brian Sullivan ◽

Younes Miar

Keyword(s):

Genomic Prediction ◽

Performance Test ◽

Average Daily Gain ◽

Accurate Method ◽

Single Step ◽

Prediction Methods ◽

Genetic Progress ◽

Breeding Values ◽

Fat Thickness ◽

Daily Gain

Improvement of prediction accuracy of estimated breeding values (EBVs) can lead to increased profitability for swine breeding companies. This study was performed to compare the accuracy of different popular genomic prediction methods and traditional best linear unbiased prediction (BLUP) for future performance of back-fat thickness (BFT), average daily gain (ADG), and loin muscle depth (LMD) in Canadian Duroc, Landrace, and Yorkshire swine breeds. In this study, 17,019 pigs were genotyped using Illumina 60K and Affymetrix 50K panels. After quality control and imputation steps, a total of 41,304, 48,580, and 49,102 single-nucleotide polymorphisms remained for Duroc (n = 6,649), Landrace (n = 5,362), and Yorkshire (n = 5,008) breeds, respectively. The breeding values of animals in the validation groups (n = 392–774) were predicted before performance test using BLUP, BayesC, BayesCπ, genomic BLUP (GBLUP), and single-step GBLUP (ssGBLUP) methods. The prediction accuracies were obtained using the correlation between the predicted breeding values and their deregressed EBVs (dEBVs) after performance test. The genomic prediction methods showed higher prediction accuracies than traditional BLUP for all scenarios. Although the accuracies of genomic prediction methods were not significantly (P > 0.05) different, ssGBLUP was the most accurate method for Duroc-ADG, Duroc-LMD, Landrace-BFT, Landrace-ADG, and Yorkshire-BFT scenarios, and BayesCπ was the most accurate method for Duroc-BFT, Landrace-LMD, and Yorkshire-ADG scenarios. Furthermore, BayesCπ method was the least biased method for Duroc-LMD, Landrace-BFT, Landrace-ADG, Yorkshire-BFT, and Yorkshire-ADG scenarios. Our findings can be beneficial for accelerating the genetic progress of BFT, ADG, and LMD in Canadian swine populations by selecting more accurate and unbiased genomic prediction methods.

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Analysis of an open nucleus breeding programme for Djallonkè sheep in the Ivory Coast. 2. Response to selection on body weights

Animal Science ◽

10.1017/s1357729800015873 ◽

1997 ◽

Vol 64 (2) ◽

pp. 301-307 ◽

Cited By ~ 7

Author(s):

C. V. Yapi-Gnaorè ◽

J. E. O. Rege ◽

A. Oya ◽

Nega Alemayehu

Keyword(s):

Ivory Coast ◽

Live Weight ◽

Genetic Progress ◽

Annual Fluctuation ◽

Breeding Values ◽

Male Individual ◽

Nucleus Breeding ◽

Set Up ◽

System Selection ◽

Open Nucleus

AbstractA selection programme was set up in 1983 in the Ivory Coast to improve the growth and live weight of the indigenous Djallonkè sheep using an open nucleus breeding system. Selection was based on male individual weights at 80, 180 and 365 days of age. Multiple sires were used in farmers' flocks. Individual animal model, using average numerator relationship was used to estimate breeding values from which genetic trends were derived. This paper reports results of the analyses of 10 417 records of 80-day weights (WT80) of lambs born between 1984 and 1992 from 29 participating farmers, and 1978 and 849 records on 180- (WT180) and 365- (WT365) day weights, respectively, of lambs from the nucleus. Phenotypic trends exhibited substantial annual fluctuation during the study period. The heaviest weights were obtained in 1986 (10·1 kg) for WT80, 1984 (23·3 kg) for WT180 and 1985 (33·7 kg) for WT365. There was an annual decline of 152 g (P<0·05) in WT80 mainly (–180 g/year) due to negative environmental trend. The phenotypic and environmental trends for WT180 were –703 and –721 g/year, respectively, while the corresponding values for WT365 were –931 and –956 g/year. Overall mean weights of the ram lambs at the three ages were 9·9, 23·3 and 33·7 kg, respectively in the base year and 9·3, 17·8 and 28·2 kg, respectively in the final year. Breeding values increased by 28, 11 and 14 g/year for WT80, WT180 and WT365, respectively. Results of this study indicate that genetic progress can be made in growth performance of Djallonkè sheep if reasonable levels of animal management as well as selection pressure are maintained.

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13 Genetic selection using pooled semen

Journal of Animal Science ◽

10.1093/jas/skaa278.011 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 6-6

Author(s):

Ithalo Coelho de Sousa ◽

Rohan Fernando ◽

Jack C Dekkers ◽

Moysés Nascimento ◽

Richard J Leach ◽

...

Keyword(s):

Standard Procedure ◽

Genetic Selection ◽

Equal Probability ◽

Relationship Matrix ◽

Response To Selection ◽

Swine Industry ◽

Genetic Progress ◽

Complete Dominance ◽

Breeding Values ◽

Pedigree Relationship

Abstract The use of pooled semen (PS), standard procedure at the commercial level of the swine industry, limits genetic progress, since the offspring parentage is unknown. Literature suggests that some boars have a greater number of progeny than others in the same litter when PS is used. The objective of this study was to evaluate different pedigree-relationship matrices for selection purposes when PS is used. Data on a trait with heritability of 0.4 were simulated 1,000 times for 12 scenarios: combination of sires per pool (2 or 3), number of phenotyped progeny (1 or 12), and three boar dominance levels: no dominance (equal probability of parentage), medium dominance, and complete dominance (all progeny from one boar). Ten pools were created for each scenario based on 5 sires and used for 5 dams each. Breeding values (BV) of the progeny were estimated (EBV) using three relationship matrices: known parents (A), using equal probabilities of parentage (E), and probabilities based on known boar dominance (D). Results for each relationship matrix were compared using the average of the true BV (TBV) of the 10% best animals selected based on EBV. Results are presented as percentage TBV of the selected animals compared to using A (Table). In general, D resulted in better results than E as boar dominance increased. Similar results between E and D were obtained when 12 progenies were phenotyped. When one was phenotyped, D was superior than E in the presence of boar dominance. Knowing the probability of each sire contributing to the progeny increases response to selection when pooled semen is used.

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Substantial Genetic Progress in the International Apis mellifera carnica Population Since the Implementation of Genetic Evaluation

Insects ◽

10.3390/insects11110768 ◽

2020 ◽

Vol 11 (11) ◽

pp. 768

Author(s):

Andreas Hoppe ◽

Manuel Du ◽

Richard Bernstein ◽

Friedrich-Karl Tiesler ◽

Martin Kärcher ◽

...

Keyword(s):

Apis Mellifera ◽

Large Scale ◽

Genetic Evaluation ◽

Breeding Value ◽

Genetic Progress ◽

Breeding Values ◽

Apis Mellifera Carnica ◽

Inbreeding Coefficients ◽

Year 2000 ◽

Honey Yield

The Apis mellifera carnica subspecies of the honeybee has long been praised for its gentleness and good honey yield before systematic breeding efforts began in the early 20th century. However, before the introduction of modern techniques of genetic evaluation (best linear unbiased prediction, BLUP) and a computerized data management in the mid 1990s, genetic progress was slow. Here, the results of the official breeding value estimation in BeeBreed.eu are analyzed to characterize breeding progress and inbreeding. From about the year 2000 onward, the genetic progression accelerated and resulted in a considerable gain in honey yield and desirable properties without increased inbreeding coefficients. The prognostic quality of breeding values is demonstrated by a retrospective analysis. The success of A. m. carnica breeding shows the potential of BLUP-based breeding values and serves as an example for a large-scale breeding program.

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Development of a synthetic pig sire line by election with immigration 2. Immigration

Animal Science ◽

10.1017/s0003356100030944 ◽

1976 ◽

Vol 22 (2) ◽

pp. 245-254 ◽

Cited By ~ 4

Author(s):

A. J. Webb

Keyword(s):

Native Population ◽

Genetic Progress ◽

Breeding Values ◽

Alternative Systems ◽

Native Pigs ◽

As If

SUMMARYA synthetic sire line has been developed over 11 generations by a process of selection accompanied by immigration. In each generation prospective immigrants of any breed were mated to native pigs already i n the Sire Line, and, ignoring breed, their progeny were given the same opportunity of being selected as the progeny from matings involving natives alone. This method of immigration is shown to be biased as a result of (a) heterosis in crosses of immigrants with natives, and (b) treating natives and immigrants as if they were members of the same population. When affected by both sources of bias, the breeding values of inferior immigrant progeny may be seriously overestimated with the result that inferior genes may enter the native population and hold back genetic progress. Methods of removing the bias and alternative systems of immigration are discussed.

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Responses to selection for growth and backfat in closed nucleus herds of Hampshire and Duroc pigs

Canadian Journal of Animal Science ◽

10.4141/a99-121 ◽

2001 ◽

Vol 81 (1) ◽

pp. 17-23 ◽

Cited By ~ 3

Author(s):

J. P. Gibson ◽

V. M. Quinton ◽

P. Simedrea

Keyword(s):

Selection Index ◽

High Standard ◽

Selection Response ◽

Genetic Trend ◽

Genetic Progress ◽

Breeding Values ◽

Frozen Semen ◽

Key Words Pig ◽

Breeding Selection ◽

Estimated Breeding Values

A herd of purebred Hampshire and a herd of purebred Duroc pigs were created between 1987 and 1989 and subsequently selected on an index of growth rate and backfat from 1989 to 1995. Strict rules were put in place to promote rapid turnover of generations and allow only minimal culling for structural soundness. In 1990, 1991, 1993 and 1994, a number of sows coming from the Hampshire and Duroc selection lines were bred using frozen semen collected from a sample of control boars born in 1988 and 1989. Estimates of genetic trend based on single trait animal model analyses of age at 100 kg and backfat estimated rates of response to selection of approximately –1.4 and –0.4 days and –0.5 and –0.3 mm backfat per annum in Durocs and Hampshires, respectively. These were close to the original predictions based on the index employed for Durocs, but somewhat less than expected for Hampshires. Comparison of progeny of selected versus control boars was consistent with significant selection responses having been achieved, though estimates of the magnitude of the response had high standard errors. During the period of the trial, both the Hampshire and Duroc herds went from slightly below average on the Canadian National Genetic Evaluation Program to become the number one herds within their breed for the sire line index based on backfat and growth. The trial demonstrated that selection indexes based on estimated breeding values can be used effectively to achieve genetic progress. Key words: Pig breeding, selection index, estimated breeding values, selection response

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THE EFFECT OF DIFFERENT NUMERATOR RELATIONSHIP MATRICES ON BREEDING VALUES ESTIMATED FROM MULTIPLE TRAIT BLUP

Canadian Journal of Animal Science ◽

10.4141/cjas87-022 ◽

1987 ◽

Vol 67 (1) ◽

pp. 201-204

Author(s):

R. A. KEMP ◽

J. W. WILTON

Keyword(s):

Relationship Matrix ◽

Genetic Progress ◽

Multiple Trait ◽

Breeding Values ◽

Reduced Animal Model ◽

Numerator Relationship Matrix ◽

Best Linear Unbiased ◽

The Mean ◽

Estimated Breeding Values ◽

Accuracy Of Prediction

A numerator relationship matrix (Ac) due to sires and dams was compared with a numerator relationship matrix (Ai) due to sires and maternal grandsires in a multiple-trait-reduced animal model (MT-RAM). Best linear unbiased predictors of estimated breeding values (EBV) for 200-d weight (WW) and postweaning gain (PG) (gain from 200 to 365 d of age) were estimated from data simulating a beef cattle population. As expected, mean EBV and bias (EBV-BV) for both traits were not significantly affected by different relationship matrices. The mean variances of EBV with Ac were larger than those with Ai for both traits. The mean EBV variances were closer to mean BV variances with Ac compared to Ai, which is consistent with increased precision of EBV. Product-moment correlations of EBV and BV (accuracy of prediction) were not equal (P < 0.01) for Ac compared to Ai with WW or PG. The EBV using Ac were more accurate than EBV using Ai. The increased precision and accuracy of EBV from a MT-RAM with Ac would result in greater genetic progress in the population. Key words: Relationship matrices, estimated breeding values, MT-RAM

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9 A comparison of different genomic prediction methods in the Canadian Landrace swine population

Journal of Animal Science ◽

10.1093/jas/skaa278.019 ◽

2020 ◽

Vol 98 (Supplement_4) ◽

pp. 10-10

Author(s):

Siavash Salek Ardestani ◽

Mohsen Jafarikia ◽

Brian Sullivan ◽

Mehdi Sargolzaei ◽

Younes Miar

Keyword(s):

Genomic Prediction ◽

Performance Test ◽

Average Daily Gain ◽

Single Step ◽

Breeding Value ◽

Prediction Methods ◽

Nucleotide Polymorphisms ◽

Economic Traits ◽

Genetic Progress ◽

Breeding Values

Abstract Increasing the accuracy of breeding value prediction can lead to more profitability through accelerating genetic progress for economic traits. The objective of this study was to assess the predictive abilities and unbiasedness of best linear unbiased prediction (BLUP) and popular genomic prediction methods of BayesC, BayesC(π = 0.99), genomic BLUP (GBLUP), and single-step GBLUP (ssGBLUP). Genotypic information (50K and 60K) of 4,890 performance tested Landrace pigs before February 2019 and 471 validation Landrace pigs that both had phenotypic information on backfat thickness (BFT), average daily gain (ADG), and loin muscle depth (LMD) from two Canadian pig breeding companies (AlphaGene and Alliance Genetics Canada) were used. The de-regressed breeding values (DEBV) were employed in GBLUP and Bayesian methods. A total number of 48,580 single nucleotide polymorphisms remained after quality control and imputation steps. The prediction accuracies were calculated using the correlation between predicted breeding values before performance test and DEBVs after performance test. All employed genomic prediction methods showed higher prediction accuracies for BFT (50.80–52.68%), ADG (26.61–34.47%), and LMD (18.25–25.08%) compared to BLUP method (BFT = 28.54%, ADG = 16.41%, LMD = 17.15%). The highest prediction accuracies for BFT and ADG were obtained using ssGBLUP method, and for LMD it was obtained using BayesC(π = 0.99). The BayesC(π = 0.99) showed also the lowest prediction biases across the studied traits (+0.05 for BFT, 0.00 for AGD, and -0.10 for LMD). In conclusion, our results revealed the superiority of ssGBLUP (for BFT and ADG) and BayesC(π = 0.99) (for LMD) over other tested methods in this study. However, the prediction accuracies from the tested genomic prediction methods were not significantly different from each other. Thus, employing these methods can be helpful for accelerating the genetic improvement of BFT, ADG, and LMD in the moderate population size of Canadian Landrace.

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