Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

Journal of Animal Science and Biotechnology

Research

Dorian Garrick¹  Deniz Akdemir²  Jun He³  Lixian Wang⁴  Pengfei Zhang⁴  Xiaoqing Wang⁴  Fuping Zhao⁴ 

[1] AL Rae Centre for Genetics and Breeding, Massey University, 3240, Hamilton, New Zealand;Center for Blood and Marrow Transplant Research, Minneapolis, MN, USA;College of Animal Science and Biotechnology, Hunnan Agricultural University, 410128, Changsha, China;Key Laboratory of Animal Genetics, Breeding and Reproduction (Poultry) of Ministry of Agriculture and Rural Affairs, Institute of Animal Science, Chinese Academy of Agricultural Sciences, 100193, Beijing, China;

关键词: Genetic gain;    Genomic mating;    Genomic selection;    Inbreeding;    Pig;   

DOI  :  10.1186/s40104-023-00872-x

 received in 2022-05-19, accepted in 2023-04-02,  发布年份 2023

来源: Springer

【 摘 要 】

BackgroundGenomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values (GEBV) to accelerate the speed of genetic improvement in domestic animals. But after multi-generation selection, the rate of inbreeding and the occurrence of homozygous harmful alleles might increase, which would reduce performance and genetic diversity. To mitigate the above problems, we can utilize genomic mating (GM) based upon optimal mate allocation to construct the best genotypic combinations in the next generation. In this study, we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population. These factors included: the algorithm used to derive inbreeding coefficients; the trait heritability (0.1, 0.3 or 0.5); the kind of GM scheme (focused average GEBV or inbreeding); the approach for computing the genomic relationship matrix (by SNP or runs of homozygosity (ROH)). The outcomes were compared to three traditional mating schemes (random, positive assortative or negative assortative matings). In addition, the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.ResultsGenomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain. The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs. The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%–2.6% higher rates of genetic gain ΔG, and 13%–83.3% lower ΔF than positive assortative mating regardless of heritability. The rates of inbreeding were always the fastest with positive assortative mating. Results from a purebred Large White pig population, confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.ConclusionCompared with traditional mating schemes, genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population. Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.

【 授权许可】

CC BY   
© The Author(s) 2023

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