Bias in the prediction of genetic gain due to mass and half-sib selection in random mating populations

The aim of the present paper was to simulate the scenarios for a maximum avoidance of inbreeding (MAI) mating strategy, and compare it with a random mating alternative, with the main focus on inbreeding and development of the genetic gain. The parameters of the simulation were based on the structure of the Slovak Pinzgau active population of 2868 animals (930 purebred cows). The selection under a total merit index (TMI) was simulated, covering the milk, survival, and live weight breeding value estimation results. The heritability of TMI (h<sup>2</sup> = 0.09) was estimated using a REML single trait animal model. Alternatives assumed a closed population structure, fixed number of mating per parent, and equal use of sires in insemination. Animals in generation 0 were set as founders without pedigree information. In separate simulation runs, the number of sires of sires was set at 2, 4, 5 or 10 mated with 40 dams of sires in all cases. The sex ratio of the offspring was assumed to be 50/50 male/female. Twenty consecutive generations were simulated for both random and maximum avoidance of inbreeding mating, which resulted in a total of 8 scenarios. Significant positive differences in genetic gain were observed in the MAI mating system with 2 (0.74**), 4 (0.24**), 5 (0.13**) or 10 (0.09**) sires in comparison to random mating design. When using MAI, significantly lower inbreeding was observed with 2 (5.44**), 4 (3.18**), 5 (2.43**) or 10 (1.16**) sires. Simulation results showed that the use of a maximum avoidance of inbreeding mating strategy would lead to significantly decreased rates of inbreeding while maintaining suitable levels of genetic gain in the

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COMPARAÇÕES DE MÉTODOS DE SELEÇÃO EM POPULAÇÕES SIMULADAS DE FRANGOS CAIPIRAS

Colloquium Agrariae ◽

10.5747/ca.2017.v13.nesp2.00021 ◽

2017 ◽

Vol 13 (Especial 2) ◽

pp. 129-134

Author(s):

Bruno Eduardo Damacena Silva ◽

Jeferson Corrêa Ribeiro ◽

Wallacy Barbacena Rosa dos Santos ◽

Andreia Santos Cezário ◽

Eliandra Maria Bianchini Oliveira ◽

...

Keyword(s):

Genetic Gain ◽

Overlapping Generations ◽

Mating Systems ◽

Random Mating ◽

Selection Method ◽

The Other ◽

Individual Selection ◽

Selection Methods ◽

Slaughter Weight ◽

Selection Systems

The purpose of this study was to compare the two types of selection methods known as BLUP and individual selection (IS) in populations of rustic chicken, evaluating the trait of slaughter weight and considering the averages of genetic gain and phenotypic value as response variables. A population of rustic chicken was simulated in the program Genesys, considering the basal population with 500 males and 500 females, from which was randomly chosen 120 males and 240 females. Then, the selected population was simulated considering the sexual ratios of 3, 4, 5 e 6 females per male in two selection types: Individual Selection (IS) and BLUP. In each selection method, the random mating system between breed chickens was used. Selection was performed during 15 consecutive and non-overlapping generations, with 10 simulation repetitions per generation, in order to decrease the genetic oscillation effects. The average genetic gain and the average phenotypic value in all methods and mating systems were evaluated. The results show that the ratio 6:1 was superior to the other sexual ratios in the two types of selection. When comparing the two selection systems, IS was superior to BLUP for the high phenotypic value of slaughter weight. Thus, the sexual ratio of six females for each male is recommended for individual 130 Colloquium Agrariae, vol. 13, n. Especial 2, Jan–Jun, 2017, p. 129-134. ISSN: 1809-8215. DOI: 10.5747/ca.2017.v13.nesp2.000218 selection, with which will allow high phenotypic values, with lower need of males

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How to reach a higher selection plateau with optimal contribution selection and compensatory mating?

10.1101/2021.02.15.431233 ◽

2021 ◽

Author(s):

Tiret Mathieu ◽

Pégard Marie ◽

Sánchez Leopoldo

Keyword(s):

Genetic Gain ◽

Random Mating ◽

Snp Array ◽

Breeding Strategy ◽

Genetic Response ◽

Short Term ◽

Breeding Programs ◽

Trade Off ◽

Study Case

AbstractIn breeding programs, balancing short-term genetic gain and loss of diversity per generation is essential to sustain a long-term genetic response. Depending on the dynamic of the species, the acceptable trade-off will be different. One of the most common and successful tools to achieve this management is the Optimal Contribution Selection (OCS), which readily mathematically formulate the trade-off between genetic gain and coancestry. However, OCS only accounts for the next generation gain and diversity, which can lead to suboptimality given the uncertainties of random mating and segregation. In this paper, we have extended the OCS by conveniently integrating a way to promote certain parental pairs, so that this method can account for the next t+2 generation. In the study case of Populus nigra, fully phenotyped and SNP array genotyped, we have shown that (i) a non negligible part of the long-term success of a breeding strategy depends on the implemented mating strategy, and (ii) favoring a compensatory mating can accelerate the selection without compromising the future diversity.

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Genomic selection in dairy cattle simulated populations

Journal of Dairy Research ◽

10.1017/s0022029918000304 ◽

2018 ◽

Vol 85 (2) ◽

pp. 125-132

Author(s):

Leonardo de Oliveira Seno ◽

Diego Gomes Freire Guidolin ◽

Rusbel Raul Aspilcueta-Borquis ◽

Guilherme Batista do Nascimento ◽

Thiago Bruno Ribeiro da Silva ◽

...

Keyword(s):

Dairy Cattle ◽

Genomic Selection ◽

Milk Yield ◽

Genetic Gain ◽

Random Mating ◽

Allelic Frequency ◽

Genetic Evaluation ◽

Phenotypic Data ◽

Generation Structure ◽

Frequency Changes

Genomic selection is arguably the most promising tool for improving genetic gain in domestic animals to emerge in the last few decades, but is an expensive process. The aim of this study was to evaluate the economic impact related to the implementation of genomic selection in a simulated dairy cattle population. The software QMSim was used to simulate genomic and phenotypic data. The simulated genome contained 30 chromosomes with 100 cm each, 1666 SNPs markers equally spread and 266 QTLs randomly designated for each chromosome. The numbers of markers and QTLs were designated according to information available from Animal QTL (http://www.animalgenome.org/QTLdb) and Bovine QTL (http://bovineqtl.tamu.edu/). The allelic frequency changes were assigned in a gamma distribution with alpha parameters equal to 0·4. Recurrent mutation rates of 1·0e−4 were assumed to apply to markers and QTLs. A historic population of 1000 individuals was generated and the total number of animals was reduced gradually along 850 generations until we obtained a number of 200 animals in the last generation, characterizing a bottleneck effect. Progenies were created along generations from random mating of the male and female gametes, assuming the same proportion of both genders. Than the population was extended for another 150 generations until we obtained 17 000 animals, with only 320 male individuals in the last generation. After this period a 25 year of selection was simulated taking into account a trait limited by sex with heritability of 0·30 (i.e. milk yield), one progeny/cow/year and variance equal to 1·0. Annually, 320 bulls were mated with 16 000 dams, assuming a replacement rate of 60 and 40% for males and females, respectively. Selection and discard criteria were based in four strategies to obtain the EBVs assuming as breeding objective to maximize milk yield. The progeny replaced the discarded animals creating an overlapping generation structure. The selection strategies were: RS is selection based on random values; PS is selection based on phenotypic values; Blup is selection based on EBVs estimated by BLUP; and GEBV is selection based on genomic estimated breeding values in one step, using high (GBlup) and low (GBlupi) density panels. Results indicated that the genetic evaluation using the aid of genomic information could provide better genetic gain rates in dairy cattle breeding programs as well as reduce the average inbreeding coefficient in the population. The economic viability indicators showed that only Blup and GBlup/GBlupi strategies, the ones that used milk control and genetic evaluation were economic viable, considering a discount rate of 6·32% per year.

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Numerical Analysis of the Age-Sex-Structured Population Dynamics Taking into Account Spatial Diffusion

Nonlinear Analysis Modelling and Control ◽

10.15388/na.2005.10.4.15116 ◽

2005 ◽

Vol 10 (4) ◽

pp. 365-381 ◽

Cited By ~ 1

Author(s):

Š. Repšys ◽

V. Skakauskas

Keyword(s):

Population Dynamics ◽

Numerical Analysis ◽

Population Model ◽

Local Stability ◽

Deterministic Model ◽

Random Mating ◽

Spatial Diffusion ◽

Neumann Problems ◽

Structured Population ◽

Structured Population Dynamics

We present results of the numerical investigation of the homogenous Dirichlet and Neumann problems to an age-sex-structured population dynamics deterministic model taking into account random mating, female’s pregnancy, and spatial diffusion. We prove the existence of separable solutions to the non-dispersing population model and, by using the numerical experiment, corroborate their local stability.

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