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

Abstract

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

CLC Number:

S828.2

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.

Figures/Tables 8

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

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