scholarly journals Purebred and Crossbred Genomic Evaluation and Mate Allocation Strategies To Exploit Dominance in Pig Crossbreeding Schemes

2020 ◽  
Vol 10 (8) ◽  
pp. 2829-2841
Author(s):  
David González-Diéguez ◽  
Llibertat Tusell ◽  
Alban Bouquet ◽  
Andres Legarra ◽  
Zulma G. Vitezica
Keyword(s):  
Variance Components ◽  
Genetic Variance ◽  
Sources Of Information ◽  
Genomic Evaluation ◽  
Multiple Trait ◽  
Genetic Value ◽  
Additive Genetic Effects ◽  
Positive Heterosis ◽  
Allocation Strategies ◽  
Qtl Effects

We investigated the effectiveness of mate allocation strategies accounting for non-additive genetic effects to improve crossbred performance in a two-way crossbreeding scheme. We did this by computer simulation of 10 generations of evaluation and selection. QTL effects were simulated as correlated across purebreds and crossbreds, and (positive) heterosis was simulated as directional dominance. The purebred-crossbred correlation was 0.30 or 0.68 depending on the genetic variance component used. Dominance and additive marker effects were estimated simultaneously for purebreds and crossbreds by multiple trait genomic BLUP. Four scenarios that differ in the sources of information (only purebred data, or purebred and crossbred data) and mate allocation strategies (mating at random, minimizing expected future inbreeding, or maximizing the expected total genetic value of crossbred animals) were evaluated under different cases of genetic variance components. Selecting purebred animals for purebred performance yielded a response of 0.2 genetic standard deviations of the trait “crossbred performance” per generation, whereas selecting purebred animals for crossbred performance doubled the genetic response. Mate allocation strategy to maximize the expected total genetic value of crossbred descendants resulted in a slight increase (0.8%, 4% and 0.5% depending on the genetic variance components) of the crossbred performance. Purebred populations increased homozygosity, but the heterozygosity of the crossbreds remained constant. When purebred-crossbred genetic correlation is low, selecting purebred animals for crossbred performance using crossbred information is a more efficient strategy to exploit heterosis and increase performance at the crossbred commercial level, whereas mate allocation did not improve crossbred performance.

scholarly journals SNP-based mate allocation strategies to maximize total genetic value in pigs

2019 ◽  
Vol 51 (1) ◽  
Author(s):  
David González-Diéguez ◽  
Llibertat Tusell ◽  
Céline Carillier-Jacquin ◽  
Alban Bouquet ◽  
Zulma G. Vitezica
Keyword(s):  
Inbreeding Depression ◽  
Genetic Gain ◽  
Variance Components ◽  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Genetic Effects ◽  
Breeding Values ◽  
Genetic Merit ◽  
Additive Genetic Effects ◽  
Allocation Strategies

Abstract Background Mate allocation strategies that account for non-additive genetic effects can be used to maximize the overall genetic merit of future offspring. Accounting for dominance effects in genetic evaluations is easier in a genomic context, than in a classical pedigree-based context because the combinations of alleles at loci are known. The objective of our study was two-fold. First, dominance variance components were estimated for age at 100 kg (AGE), backfat depth (BD) at 140 days, and for average piglet weight at birth within litter (APWL). Second, the efficiency of mate allocation strategies that account for dominance and inbreeding depression to maximize the overall genetic merit of future offspring was explored. Results Genetic variance components were estimated using genomic models that included inbreeding depression with and without non-additive genetic effects (dominance). Models that included dominance effects did not fit the data better than the genomic additive model. Estimates of dominance variances, expressed as a percentage of additive genetic variance, were 20, 11, and 12% for AGE, BD, and APWL, respectively. Estimates of additive and dominance single nucleotide polymorphism effects were retrieved from the genetic variance component estimates and used to predict the outcome of matings in terms of total genetic and breeding values. Maximizing total genetic values instead of breeding values in matings gave the progeny an average advantage of − 0.79 days, − 0.04 mm, and 11.3 g for AGE, BD and APWL, respectively, but slightly reduced the expected additive genetic gain, e.g. by 1.8% for AGE. Conclusions Genomic mate allocation accounting for non-additive genetic effects is a feasible and potential strategy to improve the performance of the offspring without dramatically compromising additive genetic gain.

scholarly journals Additive genetic prediction for F3 families of common black beans (Phaseolus vulgaris L.) using linear mixed models

2019 ◽  
pp. 1950-1958
Author(s):  
Ivan Ricardo Carvalho ◽  
Vinícius Jardel Szareski ◽  
Luiz Leonardo Ferreira ◽  
Gustavo Henrique Demari ◽  
Maurício Horbach Barbosa ◽  
...  
Keyword(s):  
Plant Height ◽  
Mixed Models ◽  
Variance Components ◽  
Seed Mass ◽  
Phaseolus Vulgaris L ◽  
Future Studies ◽  
Black Beans ◽  
Genetic Value ◽  
Additive Genetic Effects ◽  
Selection Of

The aim of study is to estimate the variance components and genetic parameters (REML), as well as to predict the genetic value (BLUP) of F3 families of common black beans for the components of seed production. The experimental design was augmented blocks, where the 83 F3 families were arranged only in each block, and the commercial controls were organized in three replicates. The additive genetic effects were determinant for plant height and first pod insertion height. The pronounced effects of the environment are expressed for the number of pods, seeds and seed mass per plant. Potentiality in the selection of higher F3 families are revealed through the 2CBRS population for plant height and first pod insertion height, for the components of seed yield the selections should be directed to the populations 2CARS and 1FVRS. The number of seeds and seed mass per plant were potentiated in more than 28% of the selected F3 families, and pronounceable genetic gains are obtained by the selection of families 66, 65 and 67. The inferences obtained in this study present theoretical and practical foundation, and can be applied in future studies of breeding and production of common black bean seeds.

scholarly journals Environmental Variance Components of Fruit Ripening Date as Used in Both Phenotypic and Marker-assisted Selection in Japanese Pear Breeding

HortScience ◽  
2011 ◽  
Vol 46 (11) ◽  
pp. 1540-1544 ◽  
Author(s):  
Sogo Nishio ◽  
Masahiko Yamada ◽  
Yutaka Sawamura ◽  
Norio Takada ◽  
Toshihiro Saito
Keyword(s):  
Fruit Ripening ◽  
Variance Components ◽  
Genetic Variance ◽  
Japanese Pear ◽  
Pyrus Pyrifolia ◽  
Phenotypic Variance ◽  
Environmental Variance ◽  
Single Tree ◽  
Sib Families ◽  
Qtl Effects

The effectiveness of detected quantitative trait loci (QTLs) and molecular markers associated with them in tree fruit breeding is measured by the percentages of the variance associated with detected QTL effects accounting for not phenotypic variance, but genetic variance of the trait. The genetic variance can be obtained by subtracting environmental variance from the phenotypic variance. Once accurate environmental variance components are obtained for a given selection field, environmental variances under any number of replications and measurement repetitions can be estimated. We estimated environmental variance components of fruit ripening date measured by days in a Japanese pear (Pyrus pyrifolia Nakai) breeding field in the National Institute of Fruit Tree Science, Tsukuba, Ibaraki, Japan. We estimated variance among fruits within a tree (σf2) as 25.6, among trees within a genotype (σt2) as 0.2, among years (σy2) as 9.4, associated with genotype × year interaction (σgy2) as 7.9, and associated with tree × year interaction (σty2) as 1.2. Because σf2 was the largest environmental variance component, increasing the number of fruit evaluated would most effectively reduce the environmental variance, and tree replication would not because of very small σt2 and σty2. The 95% confidence limit of a genotypic value was ± 10 days in the evaluation of five fruits on a single tree in a year and ± 7 days over 2 years. Broad-sense heritability in a family, each offspring in which was evaluated using five fruits on a single tree in a single year, was estimated at 0.83 for three full-sib families analyzed.

scholarly journals Simultane Zuchtwertschätzung mit Reinzucht- und Kreuzungsleistungen unter Dominanz

2000 ◽  
Vol 43 (1) ◽  
pp. 87-98
Author(s):  
N. Mielenz ◽  
L. Schüler ◽  
E. Groeneveld
Keyword(s):  
Genetic Variance ◽  
Additive Genetic Variance ◽  
Selection Index ◽  
Index Theory ◽  
Genetic Evaluation ◽  
Sources Of Information ◽  
Dominance Variance ◽  
The Cross ◽  
Efficiency Of Selection ◽  
Additive Genetic Effects

Abstract. Title of the paper: Joint genetic evaluation of purebred and crossbred data under dominance Currently available Software packages are not able to handle the Joint genetic evaluation of pure and crossbred data correctly. Instead, the same traits originating in the two purebreds and the crossbred are treated as three separate traits and analysed in a three trait animal model. Using selection index theory it can be demonstrated that this procedure contains model violations even if only additive genetic effects are considered. The effectiveness of the correct model which allows different contributions of the parental lines to the genetic variance of the cross including animal specific dominance effects is assessed on the basis of different selection indices. The sources of information chosen reflect those available in typical chicken breeding programs. The genetic parameters required for index construction – in particular the dominance variance and the genetic correlation between the pure and cross breds – were derived using a two locus model. If the purebred contribute extremely differently to the crossbred variance large losses in efficiency can be observed. With contributions of the sire line of 11, 19, 37 and 40% to the additive genetic variance of the cross corresponding losses in efficiency of selection where 13.1, 6.5, 0.6 and 0.2% respectively. Not considering the dominance variance – depending on its proportion relative to the total genetic variance – lead to a moderate loss of efficiency from 0.1 to 2.6%.

scholarly journals Genomic prediction with non-additive effects in beef cattle: stability of variance component and genetic effect estimates against population size

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Akio Onogi ◽  
Toshio Watanabe ◽  
Atsushi Ogino ◽  
Kazuhito Kurogi ◽  
Kenji Togashi
Keyword(s):  
Population Size ◽  
Genomic Prediction ◽  
Variance Components ◽  
Variance Component ◽  
Predictive Accuracy ◽  
Genetic Effect ◽  
Genetic Effects ◽  
Additive Effects ◽  
Additive Variance ◽  
Additive Genetic Effects

Abstract Background Genomic prediction is now an essential technology for genetic improvement in animal and plant breeding. Whereas emphasis has been placed on predicting the breeding values, the prediction of non-additive genetic effects has also been of interest. In this study, we assessed the potential of genomic prediction using non-additive effects for phenotypic prediction in Japanese Black, a beef cattle breed. In addition, we examined the stability of variance component and genetic effect estimates against population size by subsampling with different sample sizes. Results Records of six carcass traits, namely, carcass weight, rib eye area, rib thickness, subcutaneous fat thickness, yield rate and beef marbling score, for 9850 animals were used for analyses. As the non-additive genetic effects, dominance, additive-by-additive, additive-by-dominance and dominance-by-dominance effects were considered. The covariance structures of these genetic effects were defined using genome-wide SNPs. Using single-trait animal models with different combinations of genetic effects, it was found that 12.6–19.5 % of phenotypic variance were occupied by the additive-by-additive variance, whereas little dominance variance was observed. In cross-validation, adding the additive-by-additive effects had little influence on predictive accuracy and bias. Subsampling analyses showed that estimation of the additive-by-additive effects was highly variable when phenotypes were not available. On the other hand, the estimates of the additive-by-additive variance components were less affected by reduction of the population size. Conclusions The six carcass traits of Japanese Black cattle showed moderate or relatively high levels of additive-by-additive variance components, although incorporating the additive-by-additive effects did not improve the predictive accuracy. Subsampling analysis suggested that estimation of the additive-by-additive effects was highly reliant on the phenotypic values of the animals to be estimated, as supported by low off-diagonal values of the relationship matrix. On the other hand, estimates of the additive-by-additive variance components were relatively stable against reduction of the population size compared with the estimates of the corresponding genetic effects.

Genetic variance components for female fertility in Iranian Holstein cows

2011 ◽  
Vol 139 (3) ◽  
pp. 277-280 ◽  
Author(s):  
Heydar Ghiasi ◽  
Abbas Pakdel ◽  
Ardeshir Nejati-Javaremi ◽  
Hassan Mehrabani-Yeganeh ◽  
Mahmood Honarvar ◽  
...  
Keyword(s):  
Variance Components ◽  
Genetic Variance ◽  
Female Fertility ◽  
Holstein Cows

scholarly journals Genetic analysis of spike traits in two- and multi-rowed barley crosses

Genetika ◽  
2012 ◽  
Vol 44 (3) ◽  
pp. 475-482
Author(s):  
Milomirka Madic ◽  
Desimir Knezevic ◽  
Aleksandar Paunovic ◽  
Dragan Djurovic
Keyword(s):  
Variance Components ◽  
Genetic Variance ◽  
Grain Weight ◽  
Spike Length ◽  
Grain Number ◽  
Partial Dominance ◽  
Grain Number Per Spike ◽  
Diallel Crossing ◽  
Barley Genotypes ◽  
Mode Of Inheritance

Mode of inheritance and genetic variance components for spike length, grain number per spike and grain weight per spike were evaluated in four parental genotypes and their F1 and F2 hybrids obtained through incomplete diallel crossing. Multi-rowed barley genotypes HVW-247 and Partizan and two-rowed barley genotypes KG-15 and NS-293 were selected for the crossing based on the trait concept with the parents being divergent for spike length, grain number per spike and grain weight per spike. The average values for spike length in F1 and F2 generations were intermediate or close to those of the parent having longer spikes, with the mode of inheritance being partial dominance, dominance or overdominance, depending on the crossing combination. The six-rowed x six-rowed and two-rowed x two-rowed crossing combinations showed dominance of increased grain number per spike and increased grain weight per spike in the inheritance of grain number per spike and grain weight per spike, respectively, whereas the six-rowed x two-rowed cross was predominated by partial dominance.

scholarly journals Quantitative genetics and the evolution of ontogeny: I. Ontogenetic changes in quantitative genetic variance components in randombred mice

1983 ◽  
Vol 42 (1) ◽  
pp. 65-75 ◽  
Author(s):  
James M. Cheverud ◽  
Larry J. Leamy ◽  
William R. Atchley ◽  
J. J. Rutledge
Keyword(s):  
Maternal Effects ◽  
Environmental Effects ◽  
Variance Components ◽  
Genetic Variance ◽  
Tail Length ◽  
Head Length ◽  
Ontogenetic Changes ◽  
Trunk Length ◽  
Quantitative Genetic ◽  
Significant Difference

SUMMARYWe report the results of an ontogenetic analysis of quantitative genetic variance components with two replicates drawn from the randombred ICR strain of mice. A total of 432 mice from 108 full-sib families raised in a cross-fostering design were used to estimate direct effects heritability, maternal effects, and environmental effects for weight, head length, trunk length, trunk circumference, and tail length at 17, 24, 31, 38, 45, 52, 59, and 66 days of age. There was no significant difference in heritability between the replicates. Heritabilities either stayed more or less constant with age at about 0·30 (weight, trunk length, trunk circumference) or increased slightly with age (head length, tail length). Maternal effects decreased with age from a maximum of about 0·50 at weaning to about 0·15 at age 66 when growth was nearly complete. Environmental effects increased in relative importance during ontogeny.

scholarly journals Genetic parameters and phenotypic and genetic trends for weight at weaning and visual scores during this phase estimated for Angus-Nellore crossbred young bulls

2010 ◽  
Vol 39 (11) ◽  
pp. 2398-2408 ◽  
Author(s):  
Ronyere Olegário de Araújo ◽  
Paulo Roberto Nogara Rorato ◽  
Tomás Weber ◽  
Dionéia Magda Everling ◽  
Jader Silva Lopes ◽  
...  
Keyword(s):  
Animal Model ◽  
Genetic Gain ◽  
Genetic Parameters ◽  
Southern Brazil ◽  
Linear Effect ◽  
Quadratic Effects ◽  
Genetic Value ◽  
Additive Genetic Effects ◽  
Maternal Heritability ◽  
Genetic Trends

Genetic parameters and genetic and phenotypic trends were estimated for weight at weaning (WW) and visual scores (VS) of conformation (C), precocity (P), musculature (M) and navel (N) for Angus × Nellore crossbred calves. It was used 39,676 records from pre-weaning phase of animals born from 1992 to 2002 in mid-western, southeastern and southern Brazil. The components of covariance were estimated using REML, in animal model, considering as random the maternal and direct additive genetic effects, and as fixed, the effects of contemporaneous group, the genetic group of the animal and of the cow, and as covariates the age of the calf at weaning and the age of the cow at calving, both on days and with linear and quadratic effects, besides direct (DH) and maternal heterosis (MH), both with only the linear effect. Estimates of direct and maternal heritability were 0.30 and 0.19, respectively, for WW, whereas VSs ranged from 0.16 to 0.20 and from 0.09 to 0.16, which indicates the possibility to obtain genetic gain through selection. It is expected answer correlated to C, P and for M when selection is practiced for weight at weaning is expected, as well as for P and M when selection is practiced for C. The direct and maternal genetic trends for WW (g/year) and for C, P, M and N (points/year) were: 221.0 and -312.0; 0.0022 and 0.00003; 0.0010 and 0.0001; 0.0013 and -0.0008; 0.0010 and 0.00009, respectively, while the phenotypic were: -685.2; -0.0102; -0.0219; -0.0256 and -0.0453, which highlights the need to adopt criteria for identifying young bulls of higher genetic value for WW and VSs.

Sign in / Sign up

Export Citation Format

Share Document