烟台黑猪<em>SLA-DQA</em>基因编码区多态性及生物信息学分析

doi:10.7668/hbnxb.2016.05.013

华北农学报 ›› 2016, Vol. 31 ›› Issue (5): 86-93. doi: 10.7668/hbnxb.2016.05.013

所属专题： 畜牧；生物技术；

烟台黑猪SLA-DQA基因编码区多态性及生物信息学分析

黄晓宇¹, 袁军虎², 杨巧丽¹, 马艳萍¹, 滚双宝^1,3

1. 甘肃农业大学动物科学技术学院, 甘肃兰州 730070;
2. 河南省漯河市畜牧局, 河南漯河 462000;
3. 甘肃省现代养猪工程技术研究中心, 甘肃兰州 730070

收稿日期:2016-06-18 出版日期:2016-10-28
通讯作者: 滚双宝(1967-),男,甘肃张掖人,教授,博士,主要从事动物遗传育种与繁殖研究。
作者简介:黄晓宇(1989-),女,河南兰考人,在读博士,主要从事动物遗传育种与繁殖研究。
基金资助:
DQA和DRA基因与仔猪腹泻死亡的分子标记技术项目（GNSW-2008-04）；高繁殖力猪新品系选育研究项目（092NKDA036）；甘肃省优质猪肉生产配套技术研究与示范项目（0804NKCA065）

Polymorphism and Bioinformatics Analysis of SLA-DQA Gene CDs in Yantai Black Pig

HUANG Xiaoyu¹, YUAN Junhu², YANG Qiaoli¹, MA Yanping¹, GUN Shuangbao^1,3

1. College of Animal Science and Technology, Gansu Agricultural University, Lanzhou 730070, China;
2. Henan Luohe Animal Husbandry Bureau, Luohe 462000, China;
3. Gansu Research Center for Swine Production Engineering and Technology, Lanzhou 730070, China

Received:2016-06-18 Published:2016-10-28

摘要/Abstract

摘要： 采用PCR-SSCP、克隆测序和生物信息学等方法对烟台黑猪SLA-DQA基因多态性进行研究，预测其蛋白质结构并分析其功能特征。结果显示：SLA-DQA基因exon 2、exon 3、exon 4分别检测出4种等位基因，5种基因型、6种等位基因，8种基因型、4种等位基因，7种基因型，包括3种新等位基因。SLA-DQA基因共编码255个氨基酸，编码区共发现32个核苷酸突变和13个氨基酸变异，exon 2多态性最为丰富。蛋白质结构预测结果显示二级结构中无规则卷曲和延伸链比例最高，α螺旋数量多且集中，β折叠最少。功能预测结果显示，SLA-DQA基因蛋白质在能量代谢、结构蛋白和生长因子等方面几率较高。本研究结果可为SLA-DQA基因在猪抗病分子育种中的应用提供理论依据。

关键词: 烟台黑猪, SLA-DQA基因, 编码区, 多态性, 蛋白质结构

Abstract: The PCR-SSCP,cloning sequencing and bioinformatics methods were used to explore the Yantai black pig SLA-DQA gene coding polymorphisms,structural prediction and functional characteristics of the protein.The results showed that SLA-DQA gene exon 2,exon 3 and 4 were detected 4,6,4 alleles and 5,8,7 genotypes,respectively,and three new alleles were found for the first time.The SLA-DQA coding region encoded 255 amino acids,32 nucleotide mutations and 13 amino acid mutations were found,and exon 2 showed the most polymorphism.Protein prediction results showed that random coil and extended chain accounted for the highest level,alpha helix distribution concentrated,beta sheet appeared the least.The putative result of SLA-DQA gene protein function showed that the odds of energy metabolism,structural protein and growth factor were higher.These results could provide the theory foundation for the application of SLA-DQA gene to pig disease resistance molecular breeding.

Key words: Yantai black pig, SLA-DQA gene, Coding region, Polymorphism, Protein structure

中图分类号:

S828
Q78

黄晓宇, 袁军虎, 杨巧丽, 马艳萍, 滚双宝. 烟台黑猪SLA-DQA基因编码区多态性及生物信息学分析[J]. 华北农学报, 2016, 31(5): 86-93. doi: 10.7668/hbnxb.2016.05.013.

HUANG Xiaoyu, YUAN Junhu, YANG Qiaoli, MA Yanping, GUN Shuangbao. Polymorphism and Bioinformatics Analysis of SLA-DQA Gene CDs in Yantai Black Pig[J]. ACTA AGRICULTURAE BOREALI-SINICA, 2016, 31(5): 86-93. doi: 10.7668/hbnxb.2016.05.013.

http://www.hbnxb.net/CN/Y2016/V31/I5/86

参考文献

[1] Lunney J K,Ho C S,Wysocki M,et al.Molecular genetics of the swine major histocompatibility complex,the SLA complex[J].Developmental and Comparative Immunology,2009,33(3,SI):362-374.
[2] Moutou K A,Koutsogiannouli E A,Stanmatis C,et al.Domestication does not narrow MHC diversity in Sus scrofa[J].Immunogenetics,2013,65(3):195-209.
[3] Luetkemeier E S,Malhi R S,Beever J E,et al.Diversification of porcine MHC class Ⅱ genes:evidence for selective advantage[J].Immunogenetics,2009,61(2):119-129.
[4] Bao W B,Ye L,Pan Z Y,et al.Microarray analysis of differential gene expression in sensitive and resistant pig to Escherichia coli F18[J].Animal Genetics,2012,43(5):525-534.
[5] Liu L X,Zhao S G,Lu H N,et al.Association between polymorphisms of the swine MHC-DQA gene and diarrhoea in three Chinese native piglets[J].International Journal of Immunogenetics,2015,42(3):208-216.
[6] Huang X Y,Yang Q L,Yuan J H,et al.Polymorphism and haplotype analyses of swine leukocyte antigen DQA exons 2,3,4,and their associations with Piglet diarrhea in Chinese native pig[J].Genetics and Molecular Research,2015,14(3):10461-10472.
[7] Yang Q L,Zhao S G,Wang D W,et al.Association between genetic polymorphism in the Swine Leukocyte antigen-DRA gene and piglet diarrhea in three Chinese pig breeds[J].Asian-Australasian Journal of Animal Sciences,2014,27(9):1228-1235.
[8] Yang Q L,Kong J J,Wang D W,et al.Swine leukocyte antigen-DQA gene variation and its association with piglet diarrhea in large white,landrace and duroc[J].Asian-Australasian Journal of Animal Sciences,2013,26(8):1065-1071.
[9] 杨巧丽,孔晶晶,赵生国,等.猪SLA-DRA基因外显子2多态性及其与仔猪腹泻的关联分析[J].畜牧兽医学报,2012,43(7):1020-1027.
[10] 刘子展,王在贵,李奎,等.广西巴马小型猪白细胞抗原经典Ⅱ类基因克隆及生物信息学分析[J].畜牧兽医学报,2012,43(9):1353-1359.
[11] Zheng X L,Wang F,Wei L M,et al.Cloning and cDNA sequence analysis of SLA-DQA gene from Hainan wuzhishan miniature pig[J].Animal Husbandry and Feed Science,2009,1(1):17-21.
[12] 刘丽霞,张丽,赵生国,等.八眉猪DQA基因编码区多态性及生物信息学分析[J].华北农学报,2015,30(1):103-108.
[13] 白小青,刘文,黄微,等.荣昌猪SLA-DQB基因β1结构域突变分析及蛋白质序列模式预测[J].畜牧兽医学报,2012,43(8):1306-1309.
[14] 唐医亚,邢晓为,薛立群,等.湖南沙子岭猪SLA-DR基因克隆及生物信息学分析[J].遗传,2007,29(12):1491-1496.
[15] 许刚璞,许瑜伟.烟台黑猪的调查报告[J].中国畜禽种业,2011,7(6):61-62.
[16] Sambrook J,Fritsch E F,Maniatis T.Molecular cloning:A laboratory manual[M].Beijing:Science Press,1996:464-467.
[17] Botstein D,White R L,Skolnick M,et al.Construction of a genetic linkage map in man using restriction fragment length polymorphisms[J].American Journal of Human Genetics,1980,32(3):314-331.
[18] Vaiman D,Mecier D,Moazmi-Goudarzi K,et al.A set of 99 cattle mircosatellites:characterization,synteny mapping and polymorphism[J].Mammalian Genome,1994,5(5):288-297.
[19] Sethi D K,Schubert D A,Anders A,et al.A highly tilted binding mode by a self-reactive T cell receptor results in altered engagement of peptide and MHC[J].Journal of Experimental Medicine,2011,208(1):91-102.
[20] Lee K H,Wucherpfennig K W,Wiley D C.Structure of a human insulin peptide HLA-DQ8 complex and susceptibility to type 1 diabetes[J].Nature Immunology,2001,2(6):501-507.
[21] Arnold K,Bordoli L,Kopp J,et al.The SWISS-MODEL workspace:a web-based environment for protein structure homology modelling[J].Bioinformatics,2006,22(2):195-201.
[22] Ho C S,Lunney J,Ando A,et al.Nomenclature for factors of the SLA system,update 2008[J].Tissue Antigens,2009,73(4):307-315.
[23] Garamszegi L Z,De Groot N G,Bontron R E.Correlated evolution of nucleotide substitution rates and allelic variation in MHC-DRB lineages of primates[J].BMC Evolutionary Biology,2009,9:73.
[24] 孔晶晶.三个猪品种SLA-DQA基因多态性与仔猪腹泻的相关性分析[D].兰州:甘肃农业大学,2012.
[25] Biasini M,Bienert S,Waterhouse A,et al.SWISS-MODEL:modelling protein tertiary and quaternary structure using evolutionary information[J].Nucleic Acids Research,2014,42(W1):W252-W258.
[26] Laatsch R L.Glycerol phosphate dehydrogenase activity of developing rat central nervous system[J].Journal of Neurochemistry,1962(9):487-492.
[27] Arnold J N,Wormald M R,Sim R B,et al.The impact of glycosylation on the biological function and structure of human immunoglobulins[J].Annual Review of Immunology,2007,25:21-50.
[28] Litynska A,Przybyuulo M,Pochec E,et al.Comparison of the lectin-binding pattern in different human melanoma cell lines[J].Melanoma Research,2001,11(3):205-212.
[29] Chardon P,Renard C,Vaiman M.The major histocompatibility complex in swine[J].Immunological Reviews,1999,167(1):179-192.

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烟台黑猪SLA-DQA基因编码区多态性及生物信息学分析

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