Wei Xia, Zhang Tian, Wang Ligang, Zhang Longchao, Hou Xinhua, Yan Hua, Wang Lixian
Key Laboratory of Farm Animal Genetic Resources and Germplasm Innovation of Ministry of Agriculture, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.
State Key Laboratory Breeding Base of Dao-di Herbs, National Resource Center for Chinese Materia Medica, China Academy of Chinese Medical Sciences, Beijing, China.
Front Genet. 2022 Jun 8;13:938947. doi: 10.3389/fgene.2022.938947. eCollection 2022.
Optimizing the construction and update strategies for reference and candidate populations is the basis of the application of genomic selection (GS). In this study, we first simulated1200-purebred-pigs population that have been popular in China for 20 generations to study the effects of different population sizes and the relationship between individuals of the reference and candidate populations. The results showed that the accuracy was positively correlated with the size of the reference population within the same generation ( = 0.9366, < 0.05), while was negatively correlated with the number of generation intervals between the reference and candidate populations ( = -0.9267, < 0.01). When the reference population accumulated more than seven generations, the accuracy began to decline. We then simulated the population structure of 1200 purebred pigs for five generations and studied the effects of different heritabilities (0.1, 0.3, and 0.5), genotyping proportions (20, 30, and 50%), and sex ratios on the accuracy of the genomic estimate breeding value (GEBV) and genetic progress. The results showed that if the proportion of genotyping individuals accounts for 20% of the candidate population, the traits with different heritabilities can be genotyped according to the sex ratio of 1:1male to female. If the proportion is 30% and the traits are of low heritability (0.1), the sex ratio of 1:1 male to female is the best. If the traits are of medium or high heritability, the male-to-female ratio is 1:1, 1:2, or 2:1, which may achieve higher genetic progress. If the genotyping proportion is up to 50%, for low heritability traits (0.1), the proportion of sows from all genotyping individuals should not be less than 25%, and for the medium and high heritability traits, the optimal choice for the male-to-female ratio is 1:1, which may obtain the greatest genetic progress. This study provides a reference for determining a construction and update plan for the reference population of breeding pigs.
优化参考群体和候选群体的构建及更新策略是基因组选择（GS）应用的基础。在本研究中，我们首先模拟了在中国已繁衍20代的1200头纯种猪群体，以研究不同群体规模以及参考群体与候选群体个体间关系的影响。结果表明，在同一代中，准确性与参考群体规模呈正相关（ = 0.9366， < 0.05），而与参考群体和候选群体之间的世代间隔数呈负相关（ = -0.9267， < 0.01）。当参考群体积累超过七代时，准确性开始下降。然后，我们模拟了五代1200头纯种猪的群体结构，并研究了不同遗传力（0.1、0.3和0.5）、基因分型比例（20%、30%和50%）以及性别比例对基因组估计育种值（GEBV）准确性和遗传进展的影响。结果表明，如果基因分型个体比例占候选群体的20%，对于不同遗传力的性状，可按照1:1的公母性别比例进行基因分型。如果比例为30%且性状遗传力较低（0.1），1:1的公母性别比例最佳。如果性状具有中等或高遗传力，公母比例为1:1、1:2或2:1可能会实现更高的遗传进展。如果基因分型比例高达50%，对于低遗传力性状（0.1），所有基因分型个体中母猪的比例不应低于25%，对于中等和高遗传力性状，公母比例的最佳选择是1:1，这可能会获得最大的遗传进展。本研究为确定种猪参考群体的构建和更新计划提供了参考。
