Identification and Analysis of MHC Ⅱ Genes in Wuzhishan Pig

doi:10.12300/j.issn.1674-5817.2024.135

Abstract

Abstract:

Objective To obtain the sequences of major histocompatibility complex (MHC) Ⅱgenes of Wuzhishan pig and analyze their genetic information, the biological function of MHC complex of Wuzhishan pig was investigated. Methods Spleen samples were collected from 3 adult male Wuzhishan pigs, Primers were designed according to MHCⅡ genes sequence, the coding sequences of Wuzhishan pig MHC Ⅱ genes was amplified by RT-PCR and sequenced by Sanger sequencing. The physical and chemical properties, phylogenetic relationships, conserved domains, motifs and chromosome locations of MHC Ⅱ genes in Wuzhishan pigs were analyzed with bioinformatics tools. Results A total of 8 MHC Ⅱ genes were identified in Wuzhishan pigs and GenBank entry numbers were obtained, namely SLA-DRA, SLA-DQA, SLA-DQB, SLA-DRB, SLA-DOB, SLA-DMB, SLA-DMA and SLA-DOA. The gene sequences were determined by Sanger sequencing and uploaded to GenBank to obtain accession numbers, namely PQ182796, PQ182797, PQ182798, PQ182799, PQ182800, PQ182801, PQ182802, and PQ164779. Phylogenetic analysis showed that the 6 MHC Ⅱ genes of Wuzhishan pig were not in the same branch as the MHC Ⅱ genes of Duroc pig, Meishan pig, Large White pig, Bama pig and other different breeds, so the MHC Ⅱ genes of Wuzhishan pig may have a certain diversity. Bioinformatics analysis shows that most of the MHC Ⅱ proteins are hydrophobic proteins, with a relative molecular weight range of 27 700 to 30 000. The four MHC class Ⅱ molecules encoded by the genes SLA-DQB, SLA-DRB, SLA-DOB, and SLA-DMB contain the MHC Ⅱβ conserved domain of MHC class Ⅱ, while the four MHC class Ⅱ molecules encoded by the genes SLA-DRA, SLA-DQA, SLA-DMA, and SLA-DOA contain the MHC Ⅱα conserved domain of MHC class Ⅱ. The 8 MHC class Ⅱ molecule genes are scattered along the long arm of chromosome 7 in the Wuzhishan pig, exhibiting a collinear relationship with three genes in humans and a collinear relationship with five genes in Duroc pigs. Conclusion The MHC Ⅱ genes of Wuzhishan pigs may have a special genetic origin.

Key words: Wuzhishan pig, Major histocompatibility complex, Bioinformatics

CLC Number:

Q95-33

LIU Yuanyuan,XIN Wenshui,CHAO Zhe,et al. Identification and Analysis of MHC Ⅱ Genes in Wuzhishan Pig[J]. Laboratory Animal and Comparative Medicine. 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 Amplified fragment /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 bp	55
SLA-DQB-R	GAAGAAGCTTCACAGCCAGAG
SLA-DRB-F	CACACTGTCCTCTCCTGTTC	886 bp	58
SLA-DRB-R	CTCATGCTGTGAAGACGCTG
SLA-DOB-F	CCTCATTTTCTTTTTCCCCCTCC	926 bp	55
SLA-DOB-R	GGAATCATCCAGAACATCGACC
SLA-DMB-F	CCGCTCAGTGTTTGGAGAT	967 bp	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 Amplified fragment /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 bp	55
SLA-DQB-R	GAAGAAGCTTCACAGCCAGAG
SLA-DRB-F	CACACTGTCCTCTCCTGTTC	886 bp	58
SLA-DRB-R	CTCATGCTGTGAAGACGCTG
SLA-DOB-F	CCTCATTTTCTTTTTCCCCCTCC	926 bp	55
SLA-DOB-R	GGAATCATCCAGAACATCGACC
SLA-DMB-F	CCGCTCAGTGTTTGGAGAT	967 bp	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 Chromosome mapping	氨基酸长度/aa Amino acid length/aa	相对分子质量，×10³ Molecular weight, ×10³	等电点 Isoelectric point	亲水性平均系数 Grand 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 Chromosome mapping	氨基酸长度/aa Amino acid length/aa	相对分子质量，×10³ Molecular weight, ×10³	等电点 Isoelectric point	亲水性平均系数 Grand 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

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