苏山猪和巴克夏猪全基因组ROH检测和选择信号分析

doi:10.11843/j.issn.0366-6964.2024.12.012

畜牧兽医学报 ›› 2024, Vol. 55 ›› Issue (12): 5452-5463.doi: 10.11843/j.issn.0366-6964.2024.12.012

苏山猪和巴克夏猪全基因组ROH检测和选择信号分析

戴超辉¹(), 崔乐康², 李辉¹, 赵为民¹, 付言峰¹, 李碧侠¹, 王学敏¹, 廖超¹, 陈彦羽³, 包文斌²^,*(), 程金花¹^,*()

1. 江苏省农业科学院畜牧研究所/农业农村部种养结合重点实验室/江苏省农业种质资源保护与利用平台，南京 210014
2. 扬州大学动物科学与技术学院，扬州 225009
3. 南京瑞源生物技术有限公司，南京 210033

收稿日期:2024-06-18 出版日期:2024-12-23 发布日期:2024-12-27
通讯作者: 包文斌,程金花 E-mail:chdai@jaas.ac.cn;wbbao@yzu.edu.cn;jhcheng@jaas.ac.cn
作者简介:戴超辉(1993-)，女，湖南新化人，博士，助理研究员，主要从事猪遗传育种与繁殖研究，E-mail: chdai@jaas.ac.cn
基金资助:
江苏省种业振兴揭榜挂帅项目(JBGS[2021]099);江苏省青年基金项目(BK20230753);国家生猪产业技术体系(CARS-PIG-35)

Whole Genome ROH Detection and Selection Signal Analysis in Sushan Pigs and Berkshire Pigs

DAI Chaohui¹(), CUI Lekang², LI Hui¹, ZHAO Weimin¹, FU Yanfeng¹, LI Bixia¹, WANG Xuemin¹, LIAO Chao¹, CHEN Yanyu³, BAO Wenbin²^,*(), CHENG Jinhua¹^,*()

1. Institute of Animal Science, Jiangsu Academy of Agricultural Sciences, Key Laboratory of Crop and Livestock Integration of Ministry of Agriculture and Rural Affairs, Jiangsu Germplasm Resources Protection and Utilization Platform, Nanjing 210014, China
2. College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China
3. ProNet Biotech Co., Ltd., Nanjing 210033, China

Received:2024-06-18 Online:2024-12-23 Published:2024-12-27
Contact: BAO Wenbin, CHENG Jinhua E-mail:chdai@jaas.ac.cn;wbbao@yzu.edu.cn;jhcheng@jaas.ac.cn

摘要/Abstract

摘要：

旨在明确苏山猪群体和巴克夏猪群体的遗传变异位点和多态信息，本研究首先对43个苏山猪样本和21个巴克夏猪样本进行DNA提取，然后利用“中芯一号”50K SNP芯片对DNA的SNP位点进行检测；使用Plink软件对SNP位点进行主成分分析；使用DetectRUNS软件包对样本进行全基因组ROH检测；选用3种方法(ROH、CLR和iHS)对选择信号进行分析。本研究总共鉴定到苏山猪42 282个SNPs位点和巴克夏猪27 718个SNPs位点。其中，苏山猪和巴克夏猪均被划分为3个家系。本研究在苏山猪中共检测到2 071个ROH片段，F_ROH平均值为0.096。巴克夏猪中共检测到1 853个ROH片段，F_ROH平均值为0.199。在苏山猪和巴克夏猪群体中分别检测到4个和40个高频ROH区域，分别注释到8个和103个基因，通过富集分析鉴定了50个显著的候选基因。另外，通过ROH、CLR和iHS共3种选择信号分析方法，对苏山猪和巴克夏猪的选择信号区域进行了鉴定，发现有42个基因可能受到选择。本研究初步揭示了苏山猪和巴克夏猪的基因组SNP图谱，并通过高频ROH分析和选择信号检测鉴定到一些可能影响猪的生长发育、肉质、营养和一般抗病力的基因，为苏山猪和巴克夏猪的选育利用提供了理论基础。

关键词: 猪, ROH, CLR, iHS, 选择信号

Abstract:

In order to clarify the genetic variation sites and polymorphic information of the Sushan pig population and the Berkshire pig population, the DNA samples from 43 Sushan pigs and 21 Berkshire pigs were extracted and SNP sites were detected by 50K SNP beadchip in this study. Plink software was used for principal component analysis of the SNP sites; The DetectRUNS software package was used for whole-genome ROH detection of the samples; Three methods (ROH, CLR, and iHS) were used to analyze the selection signals. A total of 42 282 SNPs were identified in Sushan pigs and 27 718 SNPs in Berkshire pigs. Both breeds were divided into 3 families. There were 2 071 ROH segments were detected in Sushan pigs with an average F_ROH value of 0.096, and 1 853 ROH segments were detected in Berkshire pigs with an average F_ROH value of 0.199. Four and 40 high-frequency ROH regions were detected in the Sushan pig and Berkshire pig populations, respectively, which were annotated to 8 and 103 genes. There were 50 significant candidate genes were identified through enrichment analysis. Additionally, three selection signal analysis methods (ROH, CLR and iHS) were used to identify selection signal regions in Sushan pigs and Berkshire pigs, which illustrated that 42 genes could be under selection. This study preliminarily revealed the genomic SNP pattern of Sushan pigs and Berkshire pigs and excavated some genes that may affect pig growth and development, meat quality, nutrition, and general disease resistance by high-frequency ROH analysis and selection signal detection, which provided a theoretical basis for the breeding and utilization of Sushan pigs and Berkshire pigs.

Key words: pig, ROH, CLR, iHS, selection signal

中图分类号:

S828.2

戴超辉, 崔乐康, 李辉, 赵为民, 付言峰, 李碧侠, 王学敏, 廖超, 陈彦羽, 包文斌, 程金花. 苏山猪和巴克夏猪全基因组ROH检测和选择信号分析[J]. 畜牧兽医学报, 2024, 55(12): 5452-5463.

DAI Chaohui, CUI Lekang, LI Hui, ZHAO Weimin, FU Yanfeng, LI Bixia, WANG Xuemin, LIAO Chao, CHEN Yanyu, BAO Wenbin, CHENG Jinhua. Whole Genome ROH Detection and Selection Signal Analysis in Sushan Pigs and Berkshire Pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2024, 55(12): 5452-5463.

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功能分类 Functional classification	功能注释号 Functional annotation	功能描述 Functional description	基因个数 Genes number	基因名称 Genes name
GO-BP	GO: 0051129	细胞成分组织的负调控	9	SEMA6D, TFIP11, KREMEN1, LIMK2, MAPRE1, RAD21, IGF1, NFATC4, RDX
GO-BP	GO: 0031345	细胞突起组织负调控	4	KREMEN1, LIMK2, NFATC4, SEMA6D
GO-BP	GO: 0043254	蛋白质复合物组装的调控	6	TFIP11, DRG1, MAPRE1, RASA1, STXBP6, RDX
GO-BP	GO: 0032091	蛋白质结合的负调控	3	TFIP11, PIN1, NFATC4
GO-BP	GO: 0097435	超分子纤维组织	8	CAPN3, LIMK2, DRG1, MAPRE1, RASA1, EXT1, RIPK3, RDX
GO-CC	GO: 0070603	SWI/SNF超家族型复合体	3	INO80, SMARCB1, BAZ1A
GO-CC	GO: 1904949	酶复合体	3	INO80, SMARCB1, BAZ1A
GO-CC	GO: 0000228	核染色体	4	INO80, SMARCB1, BRMS1L, BAZ1A
GO-CC	GO: 0043025	神经元细胞体	4	BRINP3, KCNK1, CPNE5, KREMEN1
GO-CC	GO: 0044297	细胞体	4	BRINP3, KCNK1, CPNE5, KREMEN1
GO-MF	GO: 0019957	C-C趋化因子结合	2	XCR1, CCR3
GO-MF	GO: 0045309	蛋白质磷酸化氨基酸结合	2	PIN1, RASA1
GO-MF	GO: 0042578	磷酸酯水解酶活性	5	NT5E, PFKFB4, MTMR3, PDE4A, NAPEPLD
GO-MF	GO: 0019956	趋化因子结合	2	XCR1, CCR3
GO-MF	GO: 0030234	酶调节活性	9	CAPN3, COL7A1, SGSM1, HPS4, ANGPT4, RASA1, CAST, MBIP, RIPK3
KEGG pathway	ssc04070	磷脂酰肌醇信号系统	6	PPIP5K1, SACM1L, MTMR3, PIP5K1C, ITPR3, IP6K3
KEGG pathway	ssc00760	烟酸和烟酰胺代谢	3	NT5E, NAMPT, NMNAT2
KEGG pathway	ssc03250	病毒生命周期-HIV-1	3	SMARCB1, PIN1, ELL2
KEGG pathway	ssc03082	ATP依赖性染色质重塑	4	INO80, SMARCB1, MBD3, BAZ1A
KEGG pathway	ssc04360	Axon引导	5	SEMA6D, LIMK2, EFNA2, RASA1, NFATC4

染色体 Chromosome	分析方法 Analysis method	基因名称 Genes name
1	CLR, iHS	PCMT1
1	ROH, iHS	COL9A1, SEMA6D, NT5E, INO80, CEP162, KCNQ5
4	CLR, iHS	SNTB1, CRTC2, ZFAT, LOC102166862
4	ROH, iHS	EXT1, DECR1, SDHC, RAD21
6	CLR, iHS	CA5A, PRELID3A, LOC110261323, LOC100514110
6	ROH, iHS	NDUFS5, SLC1A5, C5AR1
8	ROH, iHS	TDO2, DMP1, MEPE, PGRMC2
9	ROH, iHS	SLC36A4, RDX, ZC3H12C, FDX1, NAPEPLD, NAMPT
13	CLR, iHS	NEK4, LAMP3, SEC22A
13	ROH, iHS	FYCO1, XCR1, COL7A1, CCR3, PFKFB4
14	ROH, iHS	MYL2, P2RX7

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苏山猪和巴克夏猪全基因组ROH检测和选择信号分析

Whole Genome ROH Detection and Selection Signal Analysis in Sushan Pigs and Berkshire Pigs

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