Identification and Analysis of MHCⅡ Genes in Wuzhishan Pigs

doi:10.12300/j.issn.1674-5817.2024.135

Abstract

Abstract:

Objective To obtain the gene sequences of major histocompatibility complex (MHC ) Ⅱgenes of Wuzhishan pigs, analyze their genetic information, and explore the biological functions of their MHC system. Methods Spleen samples were collected from 3 adult male Wuzhishan pigs. Primers were designed according to MHCⅡ gene sequences, and the coding sequences of Wuzhishan pig MHCⅡ genes were amplified by RT-PCR. Sanger sequencing was performed to determine the full-length sequences. Bioinformatics tools were employed to analyze the physicochemical properties, phylogenetic relationships, conserved motifs, structural domains, chromosomal localization, and syntenic relationships of these genes. Results Eight MHCⅡ genes were identified in Wuzhishan pigs, designated as SLA-DRA, SLA-DQA, SLA-DQB, SLA-DRB, SLA-DOB, SLA-DMB, SLA-DMA and SLA-DOA. The full-length sequences of these genes were determined by Sanger sequencing and subsequently deposited in GenBank under accession numbers PQ182796, PQ182797, PQ182798, PQ182799, PQ182800, PQ182801, PQ182802, and PQ164779. Phylogenetic analysis showed that the six MHCⅡ genes of Wuzhishan pigs clustered separately from their counterparts in Duroc, Meishan, Large White, and Bama pigs, indicating distinct evolutionary trajectories. Bioinformatics analysis demonstrated that most MHC Ⅱ proteins were hydrophobic, with molecular weights ranging from 27 700 to 30 000 Da. Genes within the same subregion shared conserved motifs. Specifically, four MHCⅡ proteins encoded by SLA-DQB, SLA-DRB, SLA-DOB, and SLA-DMB contained the MHCⅡβ conserved domain, while those encoded by the genes SLA-DRA, SLA-DQA, SLA-DMA, and SLA-DOA contained the MHCⅡα conserved domain. The eight MHCⅡ genes were scattered along the long arm of chromosome 7 in the Wuzhishan pigs, exhibiting syntenic relationships with three human genes and five Duroc pig genes. Conclusion The MHCⅡ genes of Wuzhishan pigs may possess a unique evolutionary origin.

Key words: Wuzhishan pigs, Major histocompatibility complex, Bioinformatics, Gene sequence

CLC Number:

Q95-33

LIU Yuanyuan,XIN Wenshui,CHAO Zhe,et al. Identification and Analysis of MHCⅡ Genes in Wuzhishan Pigs[J]. Laboratory Animal and Comparative Medicine, 2025, 45(3): 340-348. DOI: 10.12300/j.issn.1674-5817.2024.135.

Figures/Tables 6

References 23

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引物名称 Primer name	引物序列（5' to 3'） Primer sequence（5' to 3'）	扩增片段长度/bp Amplicon size /bp	退火温度/℃ Annealing temperature/℃
SLA-DRA-F	GCTTGTATTGCTGTCCATCC	851	55
SLA-DRA-R	CAAAGTCCATTCCCTGCAAG
SLA-DQA-F	ATGGTCCCAGGCCGAGTT	768	55
SLA-DQA-R	TCACAAGGACCCTTGGTGTC
SLA-DQB-F	CCATTACTTCTTCGTTTGCCC	995	55
SLA-DQB-R	GAAGAAGCTTCACAGCCAGAG
SLA-DRB-F	CACACTGTCCTCTCCTGTTC	886	58
SLA-DRB-R	CTCATGCTGTGAAGACGCTG
SLA-DOB-F	CCTCATTTTCTTTTTCCCCCTCC	926	55
SLA-DOB-R	GGAATCATCCAGAACATCGACC
SLA-DMB-F	CCGCTCAGTGTTTGGAGAT	967	55
SLA-DMB-R	CCATACGAGACCAAATTGCC
SLA-DMA-F	GGACCTGGGTTAGCTAGTTAG	1 028	55
SLA-DMA-R	ACATGGCAGTGATGTCGTAGG
SLA-DOA-F	GGTTAAAACACCAGAGGGCC	807	55
SLA-DOA-R	GTCTCTCTCACATCCCAGCC

引物名称 Primer name	引物序列（5' to 3'） Primer sequence（5' to 3'）	扩增片段长度/bp Amplicon size /bp	退火温度/℃ Annealing temperature/℃
SLA-DRA-F	GCTTGTATTGCTGTCCATCC	851	55
SLA-DRA-R	CAAAGTCCATTCCCTGCAAG
SLA-DQA-F	ATGGTCCCAGGCCGAGTT	768	55
SLA-DQA-R	TCACAAGGACCCTTGGTGTC
SLA-DQB-F	CCATTACTTCTTCGTTTGCCC	995	55
SLA-DQB-R	GAAGAAGCTTCACAGCCAGAG
SLA-DRB-F	CACACTGTCCTCTCCTGTTC	886	58
SLA-DRB-R	CTCATGCTGTGAAGACGCTG
SLA-DOB-F	CCTCATTTTCTTTTTCCCCCTCC	926	55
SLA-DOB-R	GGAATCATCCAGAACATCGACC
SLA-DMB-F	CCGCTCAGTGTTTGGAGAT	967	55
SLA-DMB-R	CCATACGAGACCAAATTGCC
SLA-DMA-F	GGACCTGGGTTAGCTAGTTAG	1 028	55
SLA-DMA-R	ACATGGCAGTGATGTCGTAGG
SLA-DOA-F	GGTTAAAACACCAGAGGGCC	807	55
SLA-DOA-R	GTCTCTCTCACATCCCAGCC

基因ID Gene ID	染色体定位 Chromosomal localization	氨基酸长度/aa Amino acid length/aa	相对分子质量，×10³ Relative molecular mass, ×10³	等电点 Isoelectric point	亲水性平均系数 Grade average of hydropathicity
SLA-DRA	Chr07	252	28.4	5.03	0.029
SLA-DQA	Chr07	255	28.2	5.53	0.007
SLA-DQB	Chr07	261	29.5	6.97	-0.222
SLA-DRB	Chr07	266	30.0	8.59	-0.135
SLA-DOB	Chr07	264	29.8	5.32	0.024
SLA-DMB	Chr07	272	29.8	5.69	0.027
SLA-DMA	Chr07	260	28.9	4.69	0.152
SLA-DOA	Chr07	250	27.7	6.18	0.016

基因ID Gene ID	染色体定位 Chromosomal localization	氨基酸长度/aa Amino acid length/aa	相对分子质量，×10³ Relative molecular mass, ×10³	等电点 Isoelectric point	亲水性平均系数 Grade average of hydropathicity
SLA-DRA	Chr07	252	28.4	5.03	0.029
SLA-DQA	Chr07	255	28.2	5.53	0.007
SLA-DQB	Chr07	261	29.5	6.97	-0.222
SLA-DRB	Chr07	266	30.0	8.59	-0.135
SLA-DOB	Chr07	264	29.8	5.32	0.024
SLA-DMB	Chr07	272	29.8	5.69	0.027
SLA-DMA	Chr07	260	28.9	4.69	0.152
SLA-DOA	Chr07	250	27.7	6.18	0.016