Long-term impact of conventional and optimal contribution conservation methods on genetic diversity and genetic gain in local pig breeds

Abstract Background China has rich and vast genetic resources of indigenous pig breeds. Currently, great attention is paid to either crossbreeding or conservation of these indigenous pig breeds, and insufficient attention is paid to the combination of conservation and breeding along with their long-term effects on genetic diversity. The genetic diversity of livestock is essential to increase productivity and respond to future challenges such as climate change. The genetic stability and product consistency of these indigenous pig breeds should be focused on and further improved. Therefore, the objective of this study is to compare the long-term effects of using conventional conservation and optimal contribution selection methods on genetic gain and genetic diversity. Results A total of 11 different methods including conventional conservation and optimal contribution selection methods were investigated using stochastic simulations with a population size of 600 animals in each generation. Each scenario was run for 20 generations and 100 replicates. The long-term effects of using these methods were evaluated in terms of rate of genetic gain, rate of true inbreeding based on genome-wide identity-by-descient (IBD) markers and various genetic diversity metrices such as expected heterozygosity (He). The results indicated that the rates of true inbreeding in these conventional conservation methods were maintained at around 0.01. The optimal contribution selection methods based either on the pedigree (POCS) or genome (GOCS) information showed more genetic gain than conventional methods, and POCS achieved the largest gentic gain. Furthermore, the effect of using GOCS methods on most of the genetic diversity metrics was slightly better than the conventional conservation methods when the the rate of true inbreeding was the same, but this also required more sires used in OCS methods. According to the rate of true inbreeding, there was no significant difference among these conventional methods. Conclusion In conclusion, there is no significant difference in different ways of selecting sows on inbreeding when we use different conventional conservation methods. Compared with conventional methods, POCS method could achieve the most genetic gain. However, GOCS methods can not only achieve higher genetic gain, but also maintain a relatively high level of genetic diversity. Therefore, GOCS is a better choice if we want to combine conservation and breeding in actual production in the Chinese national-level conservation farms.

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Improving short and long term genetic gain by accounting for within family variance in optimal cross selection

10.1101/634303 ◽

2019 ◽

Author(s):

Antoine Allier ◽

Christina Lehermeier ◽

Alain Charcosset ◽

Laurence Moreau ◽

Simon Teyssèdre

Keyword(s):

Genetic Diversity ◽

Genomic Selection ◽

Genetic Gain ◽

Family Selection ◽

Breeding Programs ◽

Short And Long Term ◽

Inbreeding Rate ◽

Genetic Value ◽

Optimal Set

AbstractThe implementation of genomic selection in recurrent breeding programs raised several concerns, especially that a higher inbreeding rate could compromise the long term genetic gain. An optimized mating strategy that maximizes the performance in progeny and maintains diversity for long term genetic gain on current and yet unknown future targets is essential. The optimal cross selection approach aims at identifying the optimal set of crosses maximizing the expected genetic value in the progeny under a constraint on diversity in the progeny. Usually, optimal cross selection does not account for within family selection, i.e. the fact that only a selected fraction of each family serves as candidate parents of the next generation. In this study, we consider within family variance accounting for linkage disequilibrium between quantitative trait loci to predict the expected mean performance and the expected genetic diversity in the selected progeny of a set of crosses. These predictions rely on the method called usefulness criterion parental contribution (UCPC). We compared UCPC based optimal cross selection and optimal cross selection in a long term simulated recurrent genomic selection breeding program considering overlapping generations. UCPC based optimal cross selection proved to be more efficient to convert the genetic diversity into short and long term genetic gains than optimal cross selection. We also showed that using the UCPC based optimal cross selection, the long term genetic gain can be increased with only limited reduction of the short term commercial genetic gain.

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Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection

10.1101/227215 ◽

2017 ◽

Cited By ~ 6

Author(s):

Gregor Gorjanc ◽

R. Chris Gaynor ◽

John M. Hickey

Keyword(s):

Genetic Diversity ◽

Genomic Selection ◽

Genetic Gain ◽

Balancing Selection ◽

Breeding Program ◽

Truncation Selection ◽

Part Program ◽

Population Improvement ◽

Selection For

AbstractThis study evaluates optimal cross selection for balancing selection and maintenance of genetic diversity in two-part plant breeding programs with rapid recurrent genomic selection. The two-part program reorganizes a conventional breeding program into population improvement component with recurrent genomic selection to increase the mean of germplasm and product development component with standard methods to develop new lines. Rapid recurrent genomic selection has a large potential, but is challenging due to genotyping costs or genetic drift. Here we simulate a wheat breeding program for 20 years and compare optimal cross selection against truncation selection in the population improvement with one to six cycles per year. With truncation selection we crossed a small or a large number of parents. With optimal cross selection we jointly optimised selection, maintenance of genetic diversity, and cross allocation with AlphaMate program. The results show that the two-part program with optimal cross selection delivered the largest genetic gain that increased with the increasing number of cycles. With four cycles per year optimal cross selection had 78% (15%) higher long-term genetic gain than truncation selection with a small (large) number of parents. Higher genetic gain was achieved through higher efficiency of converting genetic diversity into genetic gain; optimal cross selection quadrupled (doubled) efficiency of truncation selection with a small (large) number of parents. Optimal cross selection also reduced the drop of genomic selection accuracy due to the drift between training and prediction populations. In conclusion, optimal cross-selection enables optimal management and exploitation of population improvement germplasm in two-part programs.Key messageOptimal cross selection increases long-term genetic gain of two-part programs with rapid recurrent genomic selection. It achieves this by optimising efficiency of converting genetic diversity into genetic gain through reducing the loss of genetic diversity and reducing the drop of genomic prediction accuracy with rapid cycling.

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Crisis Phones - Suicide Prevention Versus Suggestion/Contagion Effects

Crisis ◽

10.1027/0227-5910/a000313 ◽

2015 ◽

Vol 36 (3) ◽

pp. 220-224 ◽

Cited By ~ 3

Author(s):

Steven Stack

Keyword(s):

Suicide Prevention ◽

Contagion Effects ◽

Long Term Impact

Abstract. Background: There has been no systematic work on the short- or long-term impact of the installation of crisis phones on suicides from bridges. The present study addresses this issue. Method: Data refer to 219 suicides from 1954 through 2013 on the Skyway Bridge in St. Petersburg, Florida. Six crisis phones with signs were installed in July 1999. Results: In the first decade after installation, the phones were used by 27 suicidal persons and credited with preventing 26 or 2.6 suicides a year. However, the net suicide count increased from 48 in the 13 years before installation of phones to 106 the following 13 years or by 4.5 additional suicides/year (t =3.512, p < .001). Conclusion: Although the phones prevented some suicides, there was a net increase after installation. The findings are interpreted with reference to suggestion/contagion effects including the emergence of a controversial bridge suicide blog.

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