Mating strategies with genomic information reduce rates of inbreeding in animal breeding schemes without compromising genetic gain

Liu, H.; Henryon, Mark; Sørensen, A.C.

doi:10.1017/s1751731116001786

Cited by 20 publications

(20 citation statements)

References 25 publications

(34 reference statements)

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“…In practice, the introduction of genomic selection has led to increased inbreeding rates and loss of genetic variance in cattle populations [ 99 , 100 ]. However, it has been proven that genomic breeding can outperform traditional methods in respect to maintenance of genetic variance and effective population size when applied correctly [ 101 , 102 , 103 ].…”

Section: Discussionmentioning

confidence: 99%

Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies

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Bernstein

Hoppe

et al. 2020

Insects

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Modern breeding structures are emerging for European honeybee populations. However, while genetic evaluations of honeybees are becoming increasingly well understood, little is known about how selection decisions shape the populations’ genetic structures. We performed simulations evaluating 100 different selection schemes, defined by selection rates for dams and sires, in populations of 200, 500, or 1000 colonies per year and considering four different quantitative traits, reflecting different genetic parameters and numbers of influential loci. Focusing on sustainability, we evaluated genetic progress over 100 years and related it to inbreeding developments. While all populations allowed for sustainable breeding with generational inbreeding rates below 1% per generation, optimal selection rates differed and sustainable selection was harder to achieve in smaller populations and for stronger negative correlations of maternal and direct effects in the selection trait. In small populations, a third or a fourth of all candidate queens should be selected as dams, whereas this number declined to a sixth for larger population sizes. Furthermore, our simulations indicated that, particularly in small populations, as many sires as possible should be provided. We conclude that carefully applied breeding provides good prospects for currently endangered honeybee subspecies, since sustainable genetic progress improves their attractiveness to beekeepers.

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Section: Discussionmentioning

confidence: 99%

Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies

Plate

Bernstein

Hoppe

et al. 2020

Insects

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“…Therefore, in the calculation of the inbreeding coefficient, time step was translated to its corresponding generation. The rate of inbreeding per generation [ 28 ] for a replicate was computed as , where is the slope of the linear regression of on generation corresponding to time steps 31 to 40.…”

Section: Methodsmentioning

confidence: 99%

Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken

et al. 2018

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BackgroundA breeding program for commercial broiler chicken that is carried out under strict biosecure conditions can show reduced genetic gain due to genotype by environment interactions (G × E) between bio-secure (B) and commercial production (C) environments. Accuracy of phenotype-based best linear unbiased prediction of breeding values of selection candidates using sib-testing in C is low. Genomic prediction based on dense genetic markers may improve accuracy of selection. Stochastic simulation was used to explore the benefits of genomic selection in breeding schemes for broiler chicken that include birds in both B and C for assessment of phenotype.ResultsWhen genetic correlations () between traits measured in B and C were equal to 0.5 and 0.7, breeding schemes with 15, 30 and 45% of birds assessed in C resulted in higher genetic gain for performance in C compared to those without birds in C. The optimal proportion of birds phenotyped in C for genetic gain was 30%. When the proportion of birds in C was optimal and genotyping effort was limited, allocating 30% of the genotyping effort to birds in C was also the optimal genotyping strategy for genetic gain. When was equal to 0.9, genetic gain for performance in C was not improved with birds in C compared to schemes without birds in C. Increasing the heritability of traits assessed in C increased genetic gain significantly. Rates of inbreeding decreased when the proportion of birds in C increased because of a lower selection intensity among birds retained in B and a reduction in the probability of co-selecting close relatives.ConclusionsIf G × E interactions ( of 0.5 and 0.7) are strong, a genomic selection scheme in which 30% of the birds hatched are phenotyped in C has larger genetic gain for performance in C compared to phenotyping all birds in B. Rates of inbreeding decreased as the proportion of birds moved to C increased from 15 to 45%.

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“…These IBD markers are assigned unique alleles to each base plant, but not involved in selection. Within each locus of a descendant, each IBD marker allele could be traced directly back to the base plants from which it was derived (Liu et al, 2017). True inbreeding of each individual, which measures the level of inbreeding of the whole genome, is calculated using these IBD markers as the proportion of IBD markers that are identical by descent within an individual.…”

Section: Methodsmentioning

confidence: 99%

ADAM-Plant: A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs

et al. 2019

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Making decisions on plant breeding programs require plant breeders to be able to test different breeding strategies by taking into account all the crucial factors affecting crop genetic improvement. Due to the complexity of the decisions, computer simulation serves as an important tool for researchers and plant breeders. This paper describes ADAM-plant, which is a computer software that models breeding schemes for self-pollinated and cross-pollinated crop plants using stochastic simulation. The program simulates a population of plants and traces the genetic changes in the population under different breeding scenarios. It takes into account different population structures, genomic models, selection (strategies and units) and crossing strategies. It also covers important features e.g., allowing users to perform genomic selection (GS) and speed breeding, simulate genotype-by-environment interactions using multiple trait approach, simulate parallel breeding cycles and consider plot sizes. In addition, the software can be used to simulate datasets produced from very complex breeding program in order to test new statistical methodology to analyze such data. As an example, three wheat-breeding strategies were simulated in the current study: (1) phenotypic selection, (2) GS, and (3) speed breeding with genomic information. The results indicate that the genetic gain can be doubled by GS compared to phenotypic selection and genetic gain can be further increased considerably by speed breeding. In conclusion, ADAM-plant is an important tool for comparing strategies for plant breeding and for estimating the effects of allocation of different resources to the breeding program. In the current study, it was used to compare different methodologies for utilizing genomic information in cereal breeding programs for selection of best-fit breeding strategy as per available resources.

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Mating strategies with genomic information reduce rates of inbreeding in animal breeding schemes without compromising genetic gain

Cited by 20 publications

References 25 publications

Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies

Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies

Benefits of testing in both bio-secure and production environments in genomic selection breeding programs for commercial broiler chicken

ADAM-Plant: A Software for Stochastic Simulations of Plant Breeding From Molecular to Phenotypic Level and From Simple Selection to Complex Speed Breeding Programs

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