基于80K SNP芯片的梅花星猪群体遗传结构解析及全基因组连续纯合片段特征研究

doi:10.11843/j.issn.0366-6964.2025.08.017

畜牧兽医学报 ›› 2025, Vol. 56 ›› Issue (8): 3749-3760.doi: 10.11843/j.issn.0366-6964.2025.08.017

基于80K SNP芯片的梅花星猪群体遗传结构解析及全基因组连续纯合片段特征研究

刘莎¹(), 杨彩春²(), 张晓雨¹, 陈琼², 刘雄², 陈洪波¹^,³, 周焕焕¹^,³^,*(), 史良玉¹^,³^,*()

1. 武汉轻工大学动物科学与营养工程学院，动物遗传繁育与精准养殖实验室，武汉 430023
2. 黄梅县强立畜牧有限公司，黄冈 435500
3. 湖北省家畜种业技术创新中心，武汉 430023

收稿日期:2025-02-07 出版日期:2025-08-23 发布日期:2025-08-28
通讯作者: 周焕焕,史良玉 E-mail:liusha@163.com;842093731@qq.com;hhzhou@whpu.edu.cn;liangyu_shi@whpu.edu.cn
作者简介:刘莎(2001-)，女，湖北武汉人，硕士生，主要从事动物遗传育种研究，E-mail：liusha@163.com
杨彩春(1989-)，女，湖北黄冈人，硕士，主要从事地方猪育种及产业化推广，E-mail：842093731@qq.com
第一联系人：
刘莎和杨彩春为同等贡献作者
基金资助:
湖北省自然科学基金(面上)项目(2023AFB946)；国家自然科学基金(青年)项目(32202651)；湖北省科技计划项目(2023BEB036)

Population Genetic Structure and Genome-wide Runs of Homozygosity Analysis in Meihuaxing Pigs Based on 80K SNP Chip

LIU Sha¹(), YANG Caichun²(), ZHANG Xiaoyu¹, CHEN Qiong², LIU Xiong², CHEN Hongbo¹^,³, ZHOU Huanhuan¹^,³^,*(), SHI Liangyu¹^,³^,*()

1. Laboratory of Animal Genetic Breeding and Precision Breeding, School of Animal Science and Nutritional Engineering, Wuhan Polytechnic University, Wuhan 430023, China
2. Huangmei County Qiangli Livestock Co., Ltd., Huanggang 435500, China
3. Hubei Livestock Breeding Technological Innovation Centre, Wuhan 430023, China

Received:2025-02-07 Online:2025-08-23 Published:2025-08-28
Contact: ZHOU Huanhuan, SHI Liangyu E-mail:liusha@163.com;842093731@qq.com;hhzhou@whpu.edu.cn;liangyu_shi@whpu.edu.cn

摘要/Abstract

摘要：

旨在解析梅花星猪群体结构及其遗传多样性，促进该品种遗传资源的有效保护与利用。本研究利用“猪80K功能位点基因芯片”对307头梅花星猪进行SNP分型，基于SNP芯片数据进行群体遗传结构分析和连续纯合片段(runs of homozygosity，ROH)分析。主成分分析(principal component analysis，PCA)和群体祖先成分分析显示，梅花星猪资源群体存在明显的遗传分层，基于 G矩阵的亲缘关系和聚类分析进一步揭示，研究群体可划分为4个家系。其中部分个体亲缘关系较近，家系2的近交程度相对较高，需采取合理的选配措施来防止近交衰退。ROH分析共检测到18 442个ROHs，平均长度为4.65 Mb。此外共鉴定到13个ROH岛，注释到基因164个。进一步对不同家系的ROH岛区域进行比较，并结合文献与组织表达谱进行功能注释，鉴定出了一批与繁殖(RAB23、PRKD1、G2E3等)、生长(RUNX1T1、TMEM8B、NPR2等)、肉质(DECR1、NFKBIA)、胴体(PPP1R9A、PEG10)、适应性(DST、SLC26A7、IRF9)、免疫(SIT1)、饲料效率(SLC2A2、PHKB、GPT2)、疾病(AKAP6)等性状相关的候选基因。本研究在全基因组水平上系统分析了梅花星猪群体的遗传结构及其ROH分布，为深入解析该优良地方猪种群体特征、重要性状演化形成遗传基础以及核心种群的科学保护利用奠定了基础。

关键词: 梅花星猪, 群体遗传结构, 连续纯合片段, 遗传多样性, SNP芯片

Abstract:

This study aimed to analyze the population structure and genetic diversity of the Meihuaxing pig to promote the effective conservation and utilization of its genetic resources. SNP typing was performed on 307 Meihuaxing pigs by using the 'Porcine 80K Functional Variants Genotyping Array', and the population genetic structure and runs of homozygosity (ROH) analyses were performed based on the SNP chip data. Principal component analysis (PCA) and population ancestry component analysis showed that there was obvious genetic stratification in the Meihuaxing pig resource population, and kinship based G matrix and clustering analysis further revealed that the studied population could be divided into 4 lineages. Some of these individuals were closely related, and the degree of inbreeding in family line 2 was relatively high, which requires reasonable selection measures to prevent inbreeding decline. A total of 18 442 ROHs were detected by ROH analysis, with an average length of 4.65 Mb. In addition, a total of 13 ROH islands were identified, and 164 genes were annotated. Further comparison of the ROH island regions of different family lines and functional annotation with literature and tissue expression profiles identified a number of genes associated with reproduction (RAB23, PRKD1, G2E3, etc.), growth (RUNX1T1, TMEM8B, NPR2, etc.), meat quality (DECR1, NFKBIA), carcass (PPP1R9A, PEG10), adaptability (DST, SLC26A7, IRF9), immunity (SIT1), feed efficiency (SLC2A2, PHKB, GPT2), disease (AKAP6) and other trait-related candidate genes.This study systematically analyzes the genetic structure of the Meihuaxing pig population and its ROH distribution at the genome-wide level, which lays the foundation for the in-depth analysis of the population characteristics of this excellent local pig breed, the genetic basis for the development of important traits, and the scientific conservation and utilization of the core population.

Key words: Meihuaxing pig, population genetic structure, runs of homozygosity, genetic diversity, SNP chips

中图分类号:

S828.2

刘莎, 杨彩春, 张晓雨, 陈琼, 刘雄, 陈洪波, 周焕焕, 史良玉. 基于80K SNP芯片的梅花星猪群体遗传结构解析及全基因组连续纯合片段特征研究[J]. 畜牧兽医学报, 2025, 56(8): 3749-3760.

LIU Sha, YANG Caichun, ZHANG Xiaoyu, CHEN Qiong, LIU Xiong, CHEN Hongbo, ZHOU Huanhuan, SHI Liangyu. Population Genetic Structure and Genome-wide Runs of Homozygosity Analysis in Meihuaxing Pigs Based on 80K SNP Chip[J]. Acta Veterinaria et Zootechnica Sinica, 2025, 56(8): 3749-3760.

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ROH分类 ROH classification	数量 Number	数量百分比/% Percent	均值±标准差/Mb Mean±SD	总长度/Mb Total length	长度百分比/% Length percentage
0~5 Mb	13 908	75.41	2.42±1.04	33 628.31	39.22
5~10 Mb	2 797	15.17	6.92±1.38	19 349.33	22.56
>10 Mb	1 737	9.42	18.87±10.02	32 782.82	38.22

ROH长度 ROH length	样本数 Sample size	均值 Mean	标准差 Standard deviation	最小值 Minimum	最大值 Maximum
总长度Total	307	0.123	0.041	0.043	0.274
0~5 Mb	307	0.048	0.012	0.023	0.099
5~10 Mb	306	0.028	0.012	0.004	0.068
>10 Mb	303	0.048	0.035	0.004	0.184

染色体 Chromosome	起始位点/bp Start site	终止位点/bp End site	长度/bp Length	SNPs数目 Number of SNPs	基因数目 Number of genes
1	236 150 856	236 554 494	403 638	15	20
2	29 416 962	32 427 185	3 010 223	68	7
4	44 943 952	49 689 676	4 745 724	105	16
4	50 087 861	53 278 776	3 190 915	87	16
7	27 892 821	29 166 944	1 274 123	77	8
7	68 593 944	75 591 285	6 997 341	140	51
9	32 385 323	32 922 009	536 686	13	6
9	72 730 719	75 643 707	2 912 988	57	25
11	10 283 011	11 674 505	1 391 494	67	3
13	84 810 974	88 123 512	3 312 538	58	9
14	84 657 706	85 208 724	551 018	23	1
15	107 456 185	107 639 796	183 611	6	0
17	44 058 583	44 806 701	748 118	11	2

重要经济性状 Economically important trait	基因Gene
繁殖Reproduction	RAB23⁴、PRKD1⁵、G2E3⁵、ASTN1⁴、NFATC4⁵、PLSCR4⁵、KIF18A¹、DYNC1I1⁵、BAG2⁴、YAP1⁵、WWTR1⁵、SLC26A7⁵、FXR1³、MORC2¹、TDRD5⁴、SGCE⁵
生长Growth	RUNX1T1¹、TMEM8B¹、NPR2⁵、SPAG8⁵、NOVA1⁵
免疫Immune	SIT1¹
胴体Carcass	PPP1R9A⁵、PEG10⁵
环境适应性 Environmental adaptation	DST⁴、SLC26A7⁵、IRF9⁵
肉质Meat quality	DECR1⁵、NFKBIA⁵
饲料效率Feed efficiency	SLC2A2³、PHKB⁴、GPT2⁴
疾病Diseases	AKAP6²

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基于80K SNP芯片的梅花星猪群体遗传结构解析及全基因组连续纯合片段特征研究

Population Genetic Structure and Genome-wide Runs of Homozygosity Analysis in Meihuaxing Pigs Based on 80K SNP Chip

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