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张栋, 高风英, 卢迈新, 曹建萌, 刘志刚, 可小丽, 王淼. 尼罗罗非鱼β2m基因SNP位点和单倍型与无乳链球菌抗性的关联分析[J]. 水生生物学报, 2018, 42(5): 903-912. DOI: 10.7541/2018.111
引用本文: 张栋, 高风英, 卢迈新, 曹建萌, 刘志刚, 可小丽, 王淼. 尼罗罗非鱼β2m基因SNP位点和单倍型与无乳链球菌抗性的关联分析[J]. 水生生物学报, 2018, 42(5): 903-912. DOI: 10.7541/2018.111
ZHANG Dong, GAO Feng-Ying, LU Mai-Xin, CAO Jian-Meng, LIU Zhi-Gang, KE Xiao-Li, WANG Miao. ASSOCIATION OF SNPs AND HAPLOTYPES OF β2mGENE IN NILE TILAPIA (OREOCHROMIS NILOTICUS) WITH ITS RESISTANCE TO STREPTOCOCCUS AGALACTIAE[J]. ACTA HYDROBIOLOGICA SINICA, 2018, 42(5): 903-912. DOI: 10.7541/2018.111
Citation: ZHANG Dong, GAO Feng-Ying, LU Mai-Xin, CAO Jian-Meng, LIU Zhi-Gang, KE Xiao-Li, WANG Miao. ASSOCIATION OF SNPs AND HAPLOTYPES OF β2mGENE IN NILE TILAPIA (OREOCHROMIS NILOTICUS) WITH ITS RESISTANCE TO STREPTOCOCCUS AGALACTIAE[J]. ACTA HYDROBIOLOGICA SINICA, 2018, 42(5): 903-912. DOI: 10.7541/2018.111

尼罗罗非鱼β2m基因SNP位点和单倍型与无乳链球菌抗性的关联分析

ASSOCIATION OF SNPs AND HAPLOTYPES OF β2mGENE IN NILE TILAPIA (OREOCHROMIS NILOTICUS) WITH ITS RESISTANCE TO STREPTOCOCCUS AGALACTIAE

  • 摘要: β2-微球蛋白(β2-microglobulin, β2m)作为MHCⅠ类分子的亚基, 在鱼类的免疫系统中发挥重要作用。实验采用直接测序法从P0代尼罗罗非鱼(Oreochromis niloticus)的β2m基因组序列中筛选到30个SNPs, 其中1个SNP位于5ʹUTR, 16个SNPs位于外显子区域(15个非同义突变位点, 1个同义突变位点), 9个SNPs位于内含子区域, 4个SNPs位于3ʹUTR。利用snapshot分型法对F1代的102尾易感群体和102尾抗病群体进行基因分型, 并通过Popgen32和PIC-CALC软件统计分析尼罗罗非鱼β2m基因序列的SNPs的HeHoNePIC等遗传参数, 表明易感群体中7个SNPs属于中度多态水平(0.25<PIC<0.5), 抗病群体中25个SNPs属于中度多态水平(0.25<PIC<0.5)。采用SPSS 23.0软件分析了30个SNPs在F1代2个群体中的基因型频率和等位基因频率, 分析其与链球菌抗性或易感性状之间的相关性。结果表明: 24个SNPs的基因型和等位基因频率与无乳链球菌(Streptococcus agalactiae)抗性/易感性状显著相关(P<0.05)。通过连锁不平衡分析发现30个SNPs构成4个单倍块和14种单倍型。其中, 4个单倍型与无乳链球菌抗性性状显著相关(P<0.05), 4个单倍型与易感性状显著相关(P<0.05)。标签SNP分析发现, 单倍块2中的4个SNPs和单倍块3中的13个SNPs彼此之间高度连锁(r2>0.9), 这意味着我们在β2m基因中发现2个htSNPs。研究筛选到的与链球菌抗性/易感性状相关的SNP位点及单倍型具有辅助尼罗罗非鱼抗链球菌病品种选育的潜力。

     

    Abstract: β2-microglobulin plays an important role in the immune system of fish as an essential subunit of MHC class I molecules. We identified 30 SNPs in the β2m gene by directly sequencing method from the parents (P0) of Oreochromis niloticus. The results showed that 1 SNP located in 5′UTR, 17 SNPs located in the exon region (16 synonymous mutations, a synonymous mutation site), 9 SNPs located in the intron region, and 4 SNPs located in the 3′UTR. Snapshot method was used to genotype 102 resistant individuals and 102 susceptible individuals of F1 generation. The genetic parameters such as He, Ho, Ne and PIC of SNPs of β2m gene in Nile tilapia were analyzed with Popgen 32 and PIC-CALC software. The results indicated that 7 SNPs in the susceptible group were moderate polymorphism (0.25<PIC<0.5), and 25 SNPs in the resistant group were moderate polymorphism (0.25<PIC<0.5). In order to reveal its correlation with streptococcal resistant or susceptible traits, the genotype and allele frequencies of 30 SNPs in both resistant and susceptible groups of F1 generation were analyzed by SPSS 23.0 software. These results indicated that 24 SNPs were significantly associated with the streptococcal resistant or susceptible trait (P<0.05). The results of linkage disequilibrium analysis showed that 30 SNPs formed 4 haplotype blocks and 14 haplotypes. 4 haplotypes were significantly associated with streptococcal susceptible trait, and 4 haplotypes were significantly associated with streptococcal resistance trait (P<0.05). Haplotype block 2 and block 3 were two htSNPs inβ2m gene, which contain 4 SNPs and 13 SNPs, respectively, and highly link with each other (r2> 0.9). In this study, the SNPs and haplotypes associated with streptococcal resistant or susceptible traits can be applied to the breeding of streptococcicosis-resistant Nile tilapia as potential markers.

     

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