猪全基因组低密度SNP芯片的设计与效果评价

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中图分类号：S828.2 文献标志码：A 文章编号：0366-6964（2025）06-2733-08

Design and Effect Evaluation of A Whole-Genome Low-Density SNP Chip in Pigs

WU Jianliang1，SU Yang²，MAO Ruihan²，ZHOU Lei²，YAN Tiantian1，LI Zhi1 ，LIU Jianfeng² * （1. Beijing Zhongyu Pig Breeding Co.， Ltd.， Beijing l00194， China ; 2.College of Animal Science and Technology，China Agricultural University，Beijing 1Ool93，China）

Abstract：This study aimed to explore the application effect of low-density SNP chips in pig breeding， especially in terms of genotype imputation and breeding value estimation accuracy. This study designed a low-density SNP chip with a density of 5K based on the medium to high density SNP chip "KPS Porcine breeding chip v2"，which can be used for detecting genetic marker typing in breeding pigs and imputed into the quality control panel of "KPS Porcine breeding chip v2）"，ultimately applied to genome selection. Subsequently， this study used data from 3 239 purebred Large White pigs from a certain pig breeding farm to investigate the genotype imputation accuracy and genome breeding value estimation accuracy of the low-density chip through five fold cross validation method. The results showed that the allele accuracy of genotype imputation reached 99.46% ，and the average accuracy of genetic evaluation for age adjusted to 100kg weight and back-fat thickness adjusted to 100kg weight were 0.374 2 and 0.402 1， respectively. Compared with the original genotype data，the accuracy loss was only O.Ool 5 and

0.001 2. The results indicate that low-density SNP chips retain the vast majority of original information while reducing detection costs. This study provides a basis and reference for the design of lowdensity chips for the whole genome of livestock and poultry. This strategy significantly reduces the cost of genotype testing and promotes the popularization of genomic selection of pigs in China.

Keywords： pigs; genomic selection; low density SNP chip;chip design; genotype imputation ∗ Corresponding author：LIU Jianfeng，E-mail： liujf@cau. edu. cn

基因组选择（genomicselection，GS）是利用覆盖全基因组的高密度分子遗传标记进行的标记辅助选择，由Meuwissen等[在20O1年提出。（剩余12839字）