猪全基因组低密度SNP芯片的设计与效果评价

doi:10.11843/j.issn.0366-6964.2025.06.018

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (6): 2733-2740.doi: 10.11843/j.issn.0366-6964.2025.06.018

猪全基因组低密度SNP芯片的设计与效果评价

武建亮¹(), 苏洋²(), 毛瑞涵², 周磊², 闫田田¹, 李智¹, 刘剑锋²^,*()

1. 北京中育种猪有限责任公司, 北京 100194
2. 中国农业大学动物科学技术学院, 北京 100193

收稿日期:2025-01-15 出版日期:2025-06-23 发布日期:2025-06-25
通讯作者: 刘剑锋 E-mail:wwwjl1617@163.com;s20233040750@cau.edu.cn;liujf@cau.edu.cn
作者简介:武建亮(1979-)，男，山西文水人，博士，主要从事种猪育种、生产与管理工作，E-mail: wwwjl1617@163.com
苏洋(2001-)，男，四川眉山人，硕士，主要从事数量遗传学研究，E-mail: s20233040750@cau.edu.cn
第一联系人：
武建亮和苏洋为同等贡献作者
基金资助:
北京三元种业科技有限公司自立课题(SYZYZ20230004)：特色分子育种小型芯片研发与应用；首农食品集团自立科技项目(SNSPKJ(2021)13)：应用全基因组选择技术选育中育猪配套系2.0

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 100194, China
2. College of Animal Science and Technology, China Agricultural University, Beijing 100193, China

Received:2025-01-15 Online:2025-06-23 Published:2025-06-25
Contact: LIU Jianfeng E-mail:wwwjl1617@163.com;s20233040750@cau.edu.cn;liujf@cau.edu.cn

摘要/Abstract

摘要：

旨在探究低密度SNP芯片在猪育种中的应用效果，尤其是在基因型填充和育种值估计准确性方面的表现。本研究在中高密度SNP芯片“中芯一号”的基础上设计了一款密度为5K的低密度SNP芯片，可用于检测种猪遗传标记分型，并填充至质控后的“中芯一号”的面板上，最终应用于基因组选择。随后本研究使用来自某种猪育种场的3 239头纯种大白猪数据，通过五折交叉验证方法探究该低密度芯片的基因型填充准确性和填充后数据的基因组育种值估计准确性。结果表明，基因型填充的等位基因正确率达到了99.46%，达100 kg校正日龄和达100 kg背膘厚的遗传评估准确性均值分别达到了0.374 2和0.402 1，与原始基因型数据相比，准确性损失仅为0.001 5和0.001 2。结果提示，低密度SNP芯片在降低检测成本的同时，保留了绝大部分原始信息。本研究为畜禽全基因组低密度芯片的设计提供了依据和参考，这种策略大幅降低了基因型检测的成本，促进了我国猪全基因选择的普及。

关键词: 猪, 基因组选择, 低密度SNP芯片, 芯片设计, 基因型填充

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 100 kg weight and back-fat thickness adjusted to 100 kg weight were 0.374 2 and 0.402 1, respectively. Compared with the original genotype data, the accuracy loss was only 0.001 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 low-density 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.

Key words: pigs, genomic selection, low density SNP chip, chip design, genotype imputation

中图分类号:

S828.2

武建亮, 苏洋, 毛瑞涵, 周磊, 闫田田, 李智, 刘剑锋. 猪全基因组低密度SNP芯片的设计与效果评价[J]. 畜牧兽医学报, 2025, 56(6): 2733-2740.

WU Jianliang, SU Yang, MAO Ruihan, ZHOU Lei, YAN Tiantian, LI Zhi, LIU Jianfeng. Design and Effect Evaluation of A Whole-Genome Low-Density SNP Chip in Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(6): 2733-2740.

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性别/性状 Gender/trait	日龄 Age	背膘厚 Back-fat thickness
公Male	50.775	－7.277
母Female	46.415	－9.440

染色体号 Chromosome number	位点数量 Number of loci		位点平均MAF Average MAF of loci		位点平均LD Average LD of loci
染色体号 Chromosome number	50K	5K	50K	5K	50K	5K
1	5 474	664	0.265 7	0.319 0	0.608 1	0.556 2
2	2 989	357	0.262 1	0.319 1	0.576 1	0.522 4
3	2 633	320	0.247 2	0.306 1	0.575 7	0.439 1
4	2 485	314	0.259 9	0.319 7	0.589 0	0.506 5
5	1 922	244	0.254 8	0.316 5	0.579 0	0.442 5
6	2 897	402	0.273 5	0.307 9	0.606 6	0.489 2
7	2 464	291	0.261 7	0.309 0	0.548 0	0.452 1
8	2 834	329	0.269 6	0.320 4	0.574 6	0.488 7
9	2 913	328	0.272 9	0.318 8	0.570 4	0.492 5
10	1 387	158	0.264 5	0.305 4	0.541 0	0.408 3
11	1 557	190	0.269 9	0.316 4	0.567 9	0.427 6
12	1 207	146	0.279 8	0.324 4	0.529 9	0.464 7
13	4 122	505	0.303 1	0.331 8	0.628 6	0.521 4
14	2 854	338	0.271 4	0.309 9	0.612 7	0.496 0
15	2 823	335	0.258 3	0.312 6	0.579 8	0.452 7
16	1 635	188	0.256 8	0.311 7	0.550 6	0.476 0
17	1 254	148	0.265 0	0.307 0	0.522 3	0.456 0
18	1 056	128	0.246 3	0.316 4	0.521 3	0.422 7
平均Mean	--	--	0.265 7	0.315 1	0.571 2	0.473 0

基因组信息来源 Genomic information source	准确性Accuracy		无偏性Unbiasedness
基因组信息来源 Genomic information source	达100 kg日龄 Age adjusted to 100 kg weight	达100 kg背膘厚 Back-fat thickness adjusted to 100 kg weight	达100 kg日龄 Age adjusted to 100 kg weight	达100 kg背膘厚 Back-fat thickness adjusted to 100 kg weight
原始基因型 Raw genotype	0.375 7±0.036 7	0.403 3±0.032 5	0.788 8±0.123 3	0.961 5±0.117 5
填充后基因型 Imputed genotype	0.374 2±0.036 7	0.402 1±0.033 5	0.786 3±0.124 7	0.961 5±0.120 9

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猪全基因组低密度SNP芯片的设计与效果评价

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

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