母猪死胎和木乃伊全基因组关联分析

doi:10.11843/j.issn.0366-6964.2025.03.023

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (3): 1231-1241.doi: 10.11843/j.issn.0366-6964.2025.03.023

母猪死胎和木乃伊全基因组关联分析

周泰增¹^,²^,³(), 杨祎挺¹^,²^,³, 朱悦华⁴, 钱洪喜⁴, 刘一辉⁵, 甘麦邻¹^,²^,³, 朱砺¹^,²^,³, 沈林園¹^,²^,³^,*()

1. 四川农业大学猪禽种业全国重点实验室，成都 611130
2. 四川农业大学畜禽遗传资源发掘与创新利用四川省重点实验室，成都 611130
3. 四川农业大学动物科技学院农业农村部畜禽生物组学重点实验室，成都 611130
4. 铁骑力士食品有限责任公司，成都 610000
5. 四川省畜牧总站，成都 610066

收稿日期:2024-08-09 出版日期:2025-03-23 发布日期:2025-04-02
通讯作者: 沈林園 E-mail:zhoutaizeng666666@163.com;shenlinyuan@sicau.edu.cn
作者简介:周泰增(2003-)，男，辽宁鞍山人，本科，主要从事动物遗传育种与繁殖研究，E-mail: zhoutaizeng666666@163.com
基金资助:
国家重点研发计划(2021YFD1200801)；四川省科技计划(2021YFYZ0030；2021ZDZX0008)；国家现代农业产业技术体系四川生猪创新团队(SCCXTD-2024-8)；国家生猪产业体系(CARS-35)；中央引导地方科技发展资金项目(2023ZYDF056)

Genome-wide Association Study of Stillbirths and Mummies in Sows

ZHOU Taizeng¹^,²^,³(), YANG Yiting¹^,²^,³, ZHU Yuehua⁴, QIAN Hongxi⁴, LIU Yihui⁵, GAN Mailin¹^,²^,³, ZHU Li¹^,²^,³, SHEN Linyuan¹^,²^,³^,*()

1. National Key Laboratory of Pig and Poultry Seed Industry, Sichuan Agricultural University, Chengdu 611130, China
2. Sichuan Provincial Key Laboratory of Exploration and Innovative Utilization of Livestock and Poultry Genetic Resources, Sichuan Agricultural University, Chengdu 611130, China
3. Key Laboratory of Livestock and Poultry Biomics of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, Sichuan Agricultural University, Chengdu 611130, China
4. Tieqi Lishi Food Co., Ltd., Chengdu 610000, China
5. Sichuan Provincial Animal Husbandry Station, Chengdu 610066, China

Received:2024-08-09 Online:2025-03-23 Published:2025-04-02
Contact: SHEN Linyuan E-mail:zhoutaizeng666666@163.com;shenlinyuan@sicau.edu.cn

摘要/Abstract

摘要：

旨在鉴定大白母猪初胎的死胎和木乃伊性状相关候选基因与遗传标记。本研究采用“中芯一号”50K SNP芯片对1 805头大白母猪进行全基因组基因分型，经过数据结果的过滤与筛选，结合初胎死胎数和木乃伊数的表型数据，开展全基因组关联分析(GWAS)。研究结果表明，有24个SNPs与初胎死胎数、18个SNPs与木乃伊性状显著相关，并注释得到34个候选基因。其中，25个基因与死胎性状相关(如SIL1、FSTL4、DHX38、PLK2、PDE4D等)，9个基因与木乃伊性状相关(如LRRTM4、ERC2、ARHGEF3、U6等)。通过猪QTL数据库(Pig QTLdb)进行比对分析发现，部分候选基因位于已有文献报道的与死胎和木乃伊性状相关的基因区域内，且显著SNPs存在连锁现象。GO和KEGG富集分析揭示了显著SNPs的上、下游注释基因与免疫反应、细胞信号传导、细胞凋亡与分裂以及疾病的产生等过程密切相关。此项研究筛选了大白猪群体的初胎死胎和木乃伊性状相关候选基因，并为分子育种提供重要参考。

关键词: 母猪, 初胎, 死胎数, 木乃伊, GWAS, SNP, QTL

Abstract:

The aim of this research was to identify candidate genes and genetic markers associated with stillbirth and mummified fetus traits in the first litter of Large White sows. A total of 1 805 Large White sows were genotyped using the "Zhongxin No. 1" 50K SNP chip. After filtering and selecting the data, a genome-wide association study (GWAS) was conducted, incorporating phenotypic data of stillbirths and mummified fetuses from the first litter. The results showed that 24 SNPs were significantly associated with the number of stillbirths, and 18 SNPs were significantly associated with mummified fetus traits, identifying a total of 34 candidate genes. Among these, 25 genes were related to stillbirths (such as SIL1, FSTL4, DHX38, PLK2, PDE4D, etc.), while 9 genes were associated with mummified fetus traits (including LRRTM4, ERC2, ARHGEF3, U6, etc.). A comparison with the Pig QTL database (Pig QTLdb) revealed that some of the candidate genes were located within previously reported genomic regions associated with stillbirth and mummified fetus traits, and significant SNPs exhibited linkage disequilibrium. Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) enrichment analyses indicated that the genes annotated upstream and downstream of the significant SNPs were closely associated with biological processes such as immune responses, cell signaling, apoptosis and cell division, as well as disease development. This study screened the candidate genes related to the traits of stillbirth and mummy in Large White pig population, and provided an important reference for molecular breeding.

Key words: sow, first parity, the number of stillborn, mummy, GWAS, SNP, QTL

中图分类号:

S828.3

周泰增, 杨祎挺, 朱悦华, 钱洪喜, 刘一辉, 甘麦邻, 朱砺, 沈林園. 母猪死胎和木乃伊全基因组关联分析[J]. 畜牧兽医学报, 2025, 56(3): 1231-1241.

ZHOU Taizeng, YANG Yiting, ZHU Yuehua, QIAN Hongxi, LIU Yihui, GAN Mailin, ZHU Li, SHEN Linyuan. Genome-wide Association Study of Stillbirths and Mummies in Sows[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(3): 1231-1241.

图/表 8

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性状 Trait	窝数 The number of nests	均值 Mean	变异系数 Coefficient of variation	标准差 Standard deviation	最小值 Minimum	最大值 Maximum
死胎Stillborn	1 805	1.089	1.398	1.522	0	14
木乃伊Mummy	1 805	0.463	2.658	1.229	0	18

SNP	染色体 Chromosome	位置 Position	频率 Frequency	效应 Effect	P-value	等位基因 Allele gene	候选基因 Candidate gene
CNC10015399	1	266284487	0.365	0.218	1.690×10^-4	T/C	MAPKAP1
CNC10022904	2	136056964	0.238	0.228	4.817×10^-4	A/G	FSTL4
CNC10022911	2	136443463	0.270	0.237	1.188×10^-4	A/G	TCF7、SKP1
CNCB10002244	2	140800714	0.077	0.462	1.288××10^-5	G/A	CTNNA1、LRRTM2
CNCB10002245	2	140818901	0.077	0.462	1.250×10^-5	C/T	CTNNA1、LRRTM2
CNC10023000	2	140880523	0.077	0.462	1.288×10^-5	A/G	CTNNA1、SIL1
CNCB10002246	2	140914537	0.077	0.462	1.288×10^-5	G/T	SIL1
CNC10042275	4	111347753	0.244	0.230	3.443×10^-4	C/T	FNDC7、HENMT1
CNCB10004339	6	14980246	0.380	0.217	2.687×10^-4	C/T	DHODH、TXNL4B、DHX38、PMFBP1
CNC10071783	7	80726302	0.240	-0.260	3.804×10^-4	A/G	RYR3
CNC10092856	9	130414550	0.358	-0.204	4.193×10^-4	A/G	RPS6KC1、ANGEL2
CNC10092857	9	130527089	0.358	-0.204	4.193×10^-4	A/G	VASH2、LVCR1
CNC10100524	10	20759440	0.094	0.321	4.534×10^-4	G/A	LHX9、C1orf53
CNC10160815	16	37286024	0.185	-0.318	6.683×10^-5	T/C	PLK2
CNCB10011377	16	38483053	0.211	-0.287	1.049×10^-4	G/T	PDE4D
CNC10161206	16	56466146	0.072	0.399	1.833×10^-4	T/C	TENM2
CNC10180344	18	16144023	0.057	0.444	3.188×10^-4	C/T	CHCHD3
CNCB10012226	18	48373518	0.288	0.206	4.401×10^-4	T/A	FAM221A

SNP	染色体 Chromosome	位置 Position	频率 Frequency	效应 Effect	P-value	等位基因 Allele gene	候选基因 Candidate gene
CNC10021238	2	60582816	0.371	0.154	3.458×10^-4	G/A	MYO9B、HAUS8
CNC10013054	3	65253390	0.237	0.208	3.825×10^-5	T/C	U1
CNC10031386	3	66636195	0.194	0.205	1.437×10^-4	T/C	LRRTM4
CNCB10007328	10	8008894	0.275	-0.171	3.907×10^-4	A/G	SPATA17
CNC10130837	13	38240463	0.071	0.322	2.214×10^-4	A/G	ERC2
CNC10130848	13	38604017	0.071	0.322	2.214×10^-4	G/C	ARHGEF3、U6
CNCB10008586	13	40637583	0.243	0.172	4.920×10^-4	T/C	CFAP20DC

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母猪死胎和木乃伊全基因组关联分析

Genome-wide Association Study of Stillbirths and Mummies in Sows

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