scholarly journals Genetic gain of pure line selection and combined crossbred purebred selection with constrained inbreeding

2001 ◽  
Vol 72 (2) ◽  
pp. 225-232 ◽  
Author(s):  
P. Bijma ◽  
J.A. Woolliams ◽  
J.A.M. van Arendonk
Keyword(s):  
Genetic Gain ◽  
Selection Index ◽  
Computing Time ◽  
Genetic Correlations ◽  
Pure Line ◽  
Selection Strategies ◽  
Line Selection ◽  
Breeding Schemes ◽  
Estimated Breeding Values ◽  
Genetic Contributions

AbstractUsing deterministic methods, rates of genetic gain (Δ G) and inbreeding (Δ F) were compared between pure line selection (PLS) and combined crossbred purebred selection (CCPS), for the sire line of a three-way crossbreeding scheme. Purebred performance and crossbred performance were treated as genetically correlated traits assuming the infinitesimal model. Breeding schemes were compared at a fixed total number of purebred selection candidates, i.e. including crossbred information did not affect the size of the purebred nucleus. Selection was by truncation on estimated breeding values for crossbred performance. Rates of genetic gain were predicted using a pseudo-BLUP selection index. Rates of inbreeding were predicted using recently developed methods based on long-term genetic contributions. Results showed that changing from PLS to CCPS may increase ΔF by a factor of 2·14. In particular with high heritabilities and low purebred-crossbred genetic correlations, CCPS requires a larger number of parents than PLS, to avoid excessive ΔF. The superiority of CCPS over PLS was judged by comparing ΔG from both selection strategies at the same ΔF. At the same ΔF, CCPS was superior to PLS and the superiority of CCPS was only moderately reduced compared with the situation without a restriction on ΔF. This paper shows that the longterm genetic contribution theory can be used to balance ΔF and ΔG in animal breeding schemes within very limited computing time.

scholarly journals Breeding schemes in reindeer husbandry

Rangifer ◽  
2003 ◽  
Vol 23 (2) ◽  
pp. 45 ◽  
Author(s):  
Lars Rönnegård ◽  
J. A. Woolliams ◽  
Öje Danell
Keyword(s):  
Genetic Gain ◽  
Mass Selection ◽  
Effective Population ◽  
Selection Programme ◽  
Breeding Schemes ◽  
The Difference ◽  
Genetic Contributions ◽  
Parameter Values ◽  
Open Nucleus

The objective of the paper was to investigate annual genetic gain from selection (G), and the influence of selection on the inbreeding effective population size (Ne), for different possible breeding schemes within a reindeer herding district. The breeding schemes were analysed for different proportions of the population within a herding district included in the selection programme. Two different breeding schemes were analysed: an open nucleus scheme where males mix and mate between owner flocks, and a closed nucleus scheme where the males in non-selected owner flocks are culled to maximise G in the whole population. The theory of expected long-term genetic contributions was used and maternal effects were included in the analyses. Realistic parameter values were used for the population, modelled with 5000 reindeer in the population and a sex ratio of 14 adult females per male. The standard deviation of calf weights was 4.1 kg. Four different situations were explored and the results showed: 1. When the population was randomly culled, Ne equalled 2400. 2. When the whole population was selected on calf weights, Ne equalled 1700 and the total annual genetic gain (direct + maternal) in calf weight was 0.42 kg. 3. For the open nucleus scheme, G increased monotonically from 0 to 0.42 kg as the proportion of the population included in the selection programme increased from 0 to 1.0, and Ne decreased correspondingly from 2400 to 1700. 4. In the closed nucleus scheme the lowest value of Ne was 1300. For a given proportion of the population included in the selection programme, the difference in G between a closed nucleus scheme and an open one was up to 0.13 kg. We conclude that for mass selection based on calf weights in herding districts with 2000 animals or more, there are no risks of inbreeding effects caused by selection.

Maximizing genetic response in crossbreds using both purebred and crossbred information

1994 ◽  
Vol 59 (3) ◽  
pp. 401-413 ◽  
Author(s):  
Ming Wei ◽  
J. H. J. van der Werf
Keyword(s):  
Selection Index ◽  
Index Theory ◽  
Pure Line ◽  
Fixed Number ◽  
Genetic Response ◽  
Optimal Response ◽  
Line Selection ◽  
The Difference ◽  
Actual Response ◽  
Better Than

AbstractA combined crossbred and purebred selection (CCPS) method, i.e. using crossbred and purebred information, was proposed to achieve genetic response in crossbred animals. Selection index theory was applied to establish a CCPS index. The CCPS was compared with pure-line selection (PLS) and crossbred selection (CS) methods. The genetic correlation between purebred and crossbred performance (rpc) and crossbred heritability (hc2) are crucial factors in the comparison. The CCPS is always better than PLS or CS when a fixed number of purebred progeny is tested. With a fixed total number of purebred and crossbred tested progeny, CCPS is only worse than PLS for very high values of rpc (>0·8). Superiority of CCPS over PLS increases and over CS decreases with decreasing rpc. The larger hc2 is, relative to purebred heritability (hc2 the more response CS and CCPS will achieve. The robustness of CCPS against inappropriate assumptions on rpc and hc2 values was investigated. The expected response is always an overestimate, and the actual response is smaller than the optimal response when rpc is assumed one but the true rpc is smaller. The difference between actual and optimal response increases as rpc decreases but it is small for large rpc values (e.g. <3% for rpc >0·7). The expected response is smaller than the actual response when rpc is large and hc2> hp2 Finally, the actual response to CCPS is larger than the optimal response to PLS for positive values for rpc. The main conclusions are: (1) CCPS method is optimal for obtaining genetic response in crossbreds; and (2) CCPS with inappropriate assumptions on rpc and hc2 values (e.g. recognizing crossbreds as purebreds) achieves more genetic response than PLS for common values of rpc and crossbred heritability.

Growth performance, genetic parameters and selection index of pure and crossbred populations of Red Sokoto and West African Dwarf goats

2020 ◽  
Vol 42 (1) ◽  
pp. 11-18
Author(s):  
E. N. Nwachukwu ◽  
O. C. Nkemakolam ◽  
A. I. Adeolu
Keyword(s):  
Body Weight ◽  
Growth Performance ◽  
Growth Traits ◽  
Selection Index ◽  
Genetic Correlations ◽  
Pure Line ◽  
West African ◽  
Male And Female ◽  
West African Dwarf ◽  
Indigenous Goat

In 2008, a breeding programme was designed to develop hybrid goat suitable for the rainforest agro-ecological zone of South-Eastern, Nigeria. Two indigenous goat breeds namely, Red Sokoto (RS) and West African Dwarf (WAD) goats were utilized and mated in a main (RS x WAD), reciprocal (WAD x RS) and pure line (RS x RS and WAD x WAD) fashion. A total of 74 progenies were generated from the matings and were evaluated for 12week growth performance. As part of the ranking procedure, a selection index was constructed based on two major body components namely body weight (BWT) and heart girth (HGT) to objectively determine the genetic worth of the growing pure and crossbred progenies of Red Sokoto and West African Dwarf kids. The results showed that average body weight (BWT) of RS x RS (5.29±0.13kg) and RS x WAD (5.14±0.21kg) buck kids were similar but significantly (P< 0.05) heavier than that of their WAD x RS (4.84 + 0.17kg) and WAD x WAD (4.79 + 0.17kg) counterparts. The performance of crossbred RS x WAD compared to WAD x RS and WAD x WAD buck kids indicate that the main crossbred kids sired by Red Sokoto bucks but nursed by WAD dams received superior sets of genes from their large-sized sire. The RS x WAD buck kids in particular, had significantly longer body length (BLT), height-at-withers (HWT) and HGT than WAD x RS and WAD x WAD kids. The phenotypic and genetic correlations of BWT and HGT in both sexes for the different genotypes were high and positive which were indicative of the nature of association between these conformation traits in goats. Heritability estimates (h2) for BWT and HGT in males and females kids ranged from 0.31 – 0.36 versus 0.28 – 0.30, respectively in most of the growing kids. The relative economic values (REV) of chosen traits were generally higher for male kids compared to their female counterparts. Phenotypic variances for BWT and HGT in male and female kids ranged from 0.65 – 0.80. The selection index values were highest in male and female kids of RS x RS, followed by RS x WAD, while WAD x RS kids ranked low and WAD x WAD kids ranked the least. Thus, indicating that selection and improvement of growth traits in these pure and crossbred kids would be in favour of the RS x RS and RS x WAD individuals.

Maximizing genetic gain for the sire line of a crossbreeding scheme utilizing both purebred and crossbred information

1998 ◽  
Vol 66 (2) ◽  
pp. 529-542 ◽  
Author(s):  
P. Bijma ◽  
J. A. M. van Arendonk
Keyword(s):  
Linkage Disequilibrium ◽  
Selection Index ◽  
Optimum Number ◽  
Linear Unbiased Prediction ◽  
Index Procedure ◽  
Breeding Goal ◽  
Breeding Schemes ◽  
Best Linear Unbiased ◽  
Estimated Breeding Values ◽  
Selection Intensities

AbstractA selection index procedure which utilizes both, purebred and crossbred information was developed for the sire line of a three-path crossbreeding scheme in pigs, to predict response to best linear unbiased prediction (BLUP) selection with an animal model. Purebred and crossbred performance were treated as correlated traits. The breeding goal was crossbred performance but methods can be applied to other goals. A hierarchical mating structure was used. Sires were mated to purebred dams to generate replacements and to F^ from the dam line to generate fattening pigs. Generations were discrete, inbreeding was ignored. The selection index included purebred and crossbred phenotypic information of the current generation and estimated breeding values for purebred and crossbred performance of parents and mates of parents from the previous generation. Reduction of genetic variance due to linkage disequilibrium and reduction of selection intensity due to finite population size and due to correlated index values was accounted for. Selection was undertaken until asymptotic responses were reached. The index was used to optimize the number of selected parents per generation and the number of offspring tested per litter, and to make inferences on the value of crossbred information when the breeding goal was crossbred performance. It was optimal to test a maximum number of offspring per litter, mainly due to increased female selection intensities. Maximum response reductions due to linkage disequilibrium and correlated index values were 32% and 29% respectively. Correcting for correlated index values changed ranking of breeding schemes. Benefit of crossbred information was largest when the genetic correlation between purebred and crossbred performance was low. Due to high correlations between index values in that case, the optimum number of selected sires increased considerably when crossbred information was included.

scholarly journals Mendelian sampling terms as a selective advantage in optimum breeding schemes with restrictions on the rate of inbreeding

2004 ◽  
Vol 83 (1) ◽  
pp. 55-64 ◽  
Author(s):  
S. AVENDAÑO ◽  
J. A. WOOLLIAMS ◽  
B. VILLANUEVA
Keyword(s):  
Genetic Variation ◽  
Genetic Gain ◽  
Selective Advantage ◽  
Breeding Values ◽  
Truncation Selection ◽  
Joint Management ◽  
Breeding Schemes ◽  
Estimated Breeding Values ◽  
Available Information ◽  
Mendelian Sampling

Quadratic indices are a general approach for the joint management of genetic gain and inbreeding in artificial selection programmes. They provide the optimal contributions that selection candidates should have to obtain the maximum gain when the rate of inbreeding is constrained to a predefined value. This study shows that, when using quadratic indices, the selective advantage is a function of the Mendelian sampling terms. That is, at all times, contributions of selected candidates are allocated according to the best available information about their Mendelian sampling terms (i.e. about their superiority over their parental average) and not on their breeding values. By contrast, under standard truncation selection, both estimated breeding values and Mendelian sampling terms play a major role in determining contributions. A measure of the effectiveness of using genetic variation to achieve genetic gain is presented and benchmark values of 0·92 for quadratic optimisation and 0·5 for truncation selection are found for a rate of inbreeding of 0·01 and a heritability of 0·25.

scholarly journals Pre-selection against a lethal recessive allele in breeding schemes with optimum-contribution selection or truncation selection

2021 ◽  
Vol 53 (1) ◽  
Author(s):  
Line Hjortø ◽  
Mark Henryon ◽  
Huiming Liu ◽  
Peer Berg ◽  
Jørn Rind Thomasen ◽  
...  
Keyword(s):  
Genetic Gain ◽  
Recessive Allele ◽  
Selection Strategy ◽  
Carrier Status ◽  
Truncation Selection ◽  
Selection Strategies ◽  
Significant Difference ◽  
Selection Step ◽  
Breeding Schemes ◽  
Male Carriers

Abstract Background We tested the hypothesis that breeding schemes with a pre-selection step, in which carriers of a lethal recessive allele (LRA) were culled, and with optimum-contribution selection (OCS) reduce the frequency of a LRA, control rate of inbreeding, and realise as much genetic gain as breeding schemes without a pre-selection step. Methods We used stochastic simulation to estimate true genetic gain realised at a 0.01 rate of true inbreeding (ΔFtrue) by breeding schemes that combined one of four pre-selection strategies with one of three selection strategies. The four pre-selection strategies were: (1) no carriers culled, (2) male carriers culled, (3) female carriers culled, and (4) all carriers culled. Carrier-status was known prior to selection. The three selection strategies were: (1) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ Δ F true was predicted and controlled using pedigree relationships (POCS), (2) OCS in which $$\Delta {\text{F}}_{{{\text{true}}}}$$ Δ F true was predicted and controlled using genomic relationships (GOCS), and (3) truncation selection of parents. All combinations of pre-selection strategies and selection strategies were tested for three starting frequencies of the LRA (0.05, 0.10, and 0.15) and two linkage statuses with the locus that has the LRA being on a chromosome with or without loci affecting the breeding goal trait. The breeding schemes were simulated for 10 discrete generations (t = 1, …, 10). In all breeding schemes, ΔFtrue was calibrated to be 0.01 per generation in generations t = 4, …, 10. Each breeding scheme was replicated 100 times. Results We found no significant difference in true genetic gain from generations t = 4, …, 10 between breeding schemes with or without pre-selection within selection strategy. POCS and GOCS schemes realised similar true genetic gains from generations t = 4, …, 10. POCS and GOCS schemes realised 12% more true genetic gain from generations t = 4, …, 10 than truncation selection schemes. Conclusions We advocate for OCS schemes with pre-selection against the LRA that cause animal suffering and high costs. At LRA frequencies of 0.10 or lower, OCS schemes in which male carriers are culled reduce the frequency of LRA, control rate of inbreeding, and realise no significant reduction in true genetic gain compared to OCS schemes without pre-selection against LRA.

scholarly journals Effects of Different Strategies for Exploiting Genomic Selection in Perennial Ryegrass Breeding Programs

2020 ◽  
Vol 10 (10) ◽  
pp. 3783-3795
Author(s):  
Hadi Esfandyari ◽  
Dario Fè ◽  
Biructawit Bekele Tessema ◽  
Lucas L. Janss ◽  
Just Jensen
Keyword(s):  
Genomic Selection ◽  
Perennial Ryegrass ◽  
Genetic Gain ◽  
Additive Genetic Variance ◽  
Phenotypic Selection ◽  
Breeding Program ◽  
Breeding Programs ◽  
Traditional Program ◽  
Breeding Schemes ◽  
Estimated Breeding Values

Genomic selection (GS) is a potential pathway to accelerate genetic gain for perennial ryegrass (Lolium perenne L.). The main objectives of the present study were to investigate the level of genetic gain and accuracy by applying GS in commercial perennial ryegrass breeding programs. Different scenarios were compared to a conventional breeding program. Simulated scenarios differed in the method of selection and structure of the breeding program. Two scenarios (Phen-Y12 and Phen) for phenotypic selection and three scenarios (GS-Y12, GS and GS-SP) were considered for genomic breeding schemes. All breeding schemes were simulated for 25 cycles. The amount of genetic gain achieved was different across scenarios. Compared to phenotypic scenarios, GS scenarios resulted in substantially larger genetic gain for the simulated traits. This was mainly due to more efficient selection of plots and single plants based on genomic estimated breeding values. Also, GS allows for reduction in waiting time for the availability of the superior genetic materials from previous cycles, which led to at least a doubling or a trebling of genetic gain compared to the traditional program. Reduction in additive genetic variance levels were higher with GS scenarios than with phenotypic selection. The results demonstrated that implementation of GS in ryegrass breeding is possible and presents an opportunity to make very significant improvements in genetic gains.

Appropriate selection indices for functional traits in dairy cattle breeding schemes

2018 ◽  
Vol 86 (1) ◽  
pp. 13-18 ◽  
Author(s):  
Arash Chegini ◽  
Navid Ghavi Hossein-Zadeh ◽  
Seyed Hossein Hosseini Moghaddam ◽  
Abdol Ahad Shadparvar
Keyword(s):  
Genetic Gain ◽  
Deterministic Model ◽  
Selection Index ◽  
Index Theory ◽  
Multiple Trait ◽  
Cattle Breeding ◽  
Udder Health ◽  
Selection Indices ◽  
Dairy Cattle Breeding ◽  
Breeding Schemes

AbstractThe objective of this study was to establish different single or multiple trait selection indices to calculate genetic and economic gains by combining some production, reproduction and udder health traits in a population similar to the overall practical situation in Iran, with and without imposing restrictions on genetic change for some traits. The SelAction software was used to perform the analyses based on selection index theory through a deterministic model. Results indicated that among established indices, the index that showed the highest genetic gain for milk yield did not maximize the total genetic and economic gains. Rather, the index that included all production, reproduction and udder health traits yielded the highest genetic and economic gains. When we placed restriction on the selection indices, the economic gain decreased and the amount of reduction depended on the heritability and the correlation of restricted trait(s) with other traits. Generally, regarding the economic genetic gain per generation, the indices based on records of 200 offspring were 4.819% more efficient than those that used information of 100 offspring.

scholarly journals Expected Genetic Contributions and Their Impact on Gene Flow and Genetic Gain

Genetics ◽  
1999 ◽  
Vol 153 (2) ◽  
pp. 1009-1020 ◽  
Author(s):  
J A Woolliams ◽  
P Bijma ◽  
B Villanueva
Keyword(s):  
Gene Flow ◽  
Genetic Gain ◽  
Overlapping Generations ◽  
Predictive Accuracy ◽  
Index Theory ◽  
Previous Theory ◽  
Selection Indices ◽  
Breeding Groups ◽  
Genetic Contributions

Abstract Long-term genetic contributions (ri) measure lasting gene flow from an individual i. By accounting for linkage disequilibrium generated by selection both within and between breeding groups (categories), assuming the infinitesimal model, a general formula was derived for the expected contribution of ancestor i in category q (μi(q)), given its selective advantages (si(q)). Results were applied to overlapping generations and to a variety of modes of inheritance and selection indices. Genetic gain was related to the covariance between ri and the Mendelian sampling deviation (ai), thereby linking gain to pedigree development. When si(q) includes ai, gain was related to E[μi(q)ai], decomposing it into components attributable to within and between families, within each category, for each element of si(q). The formula for μi(q) was consistent with previous index theory for predicting gain in discrete generations. For overlapping generations, accurate predictions of gene flow were obtained among and within categories in contrast to previous theory that gave qualitative errors among categories and no predictions within. The generation interval was defined as the period for which μi(q), summed over all ancestors born in that period, equaled 1. Predictive accuracy was supported by simulation results for gain and contributions with sib-indices, BLUP selection, and selection with imprinted variation.

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