H-FABP gene cloning, SNPs screening and bioinformatics analysis in Gansu black pig

doi:10.3969/j.issn.1004-1524.2018.03.04

›› 2018, Vol. 30 ›› Issue (3): 378-385.DOI: 10.3969/j.issn.1004-1524.2018.03.04

• Animal Science • Previous Articles Next Articles

H-FABP gene cloning, SNPs screening and bioinformatics analysis in Gansu black pig

NONG Weilun, BI Yingjie, LI Hongxu, ZHANG Li^*

College of Life Science and Engineering, Northwest Minzu University, Lanzhou 730124, China

Received:2017-07-14 Online:2018-03-20 Published:2018-03-21

Abstract

Abstract: This study uses bioinformatics method to analyze the function and property of H-FABP gene encoding protein of Gansu black pig. DNA pooling and direct sequencing techniques were used for SNPs rapid screening and the function prediction of H-FABP protein of Gansu black pig. The results showed that the CDS region of H-FABP gene in Gansu black pig was 402 bp, encoding 133 amino residues, 4 SNPs in CDS region including C⁷³⁴T-Intron1, T¹⁵²C-Exon2,G³⁰A-Intron2 and T¹²¹G-Intron2. Among them, T¹⁵²C-Exon2 was a missense mutation, and the amino acids were converted from threonine (Ile) to threonine (Thr). The bioinformatics prediction showed that H-FABP protein of Gansu black pig was a stable hydrophilic protein, and the secondary structure and tertiary structure were mixed protein mainly with β-fold.

Key words: Gansu black pig, H-FABP gene, SNPs, allele frequency, bioinformatics

CLC Number:

S828

NONG Weilun, BI Yingjie, LI Hongxu, ZHANG Li. H-FABP gene cloning, SNPs screening and bioinformatics analysis in Gansu black pig[J]. , 2018, 30(3): 378-385.

References

[1] 刘顺德, 李娜, 高小艳,等. 动物FABP家族基因与脂肪沉积关联研究进展[J]. 农业科学研究, 2010, 31(3):44-48.
LIU S D, LI N, GAO X Y, et al.Progress of animal FABP family genes and their association with fat deposition[J]. Journal of Agricultural Sciences,2010, 31(3):44-48. (in Chinese with English abstract)
[2] 徐海霞,房兴宏,陈宏,等. 脂肪酸结合蛋白及其家族主要基因研究进展[J].畜牧与兽医,2008,40(1):94-97.
XU H X, FANG X H, CHEN H, et al.Progress on fatty acid-binding proteins and related genes[J]. Animal Husbandry & Veterinary Medicine, 2008,40(1): 94-97. (in Chinese with English abstract)
[3] 陈璐. 脂肪酸结合蛋白(FABPs)基因多态性对畜产品品质的影响[J]. 畜牧与饲料科学,2013,34(10):82-84.
CHEN L.Effect of fatty acid-binding proteins (FABPs) gene polymorphism on animal products quality[J]. Animal Husbandry and Feed Science, 2013,34(10):82-84. (in Chinese with English abstract)
[4] 陈志辉, 徐良梅, 单安山.脂肪酸结合蛋白及其基因[J]. 东北农业大学学报, 2006, 37(5):689-692.
CHEN Z H, XU L M, SHAN A S.Fatty acid-binding proteins (FABPs) and their genes of FABPs[J].Journal of Northeast Agricultural University, 2006,37(5):689-692. (in Chinese with English abstract)
[5] 曹红鹤,李宏滨,王立贤,等.FABPs基因作为猪肌内脂肪含量沉积候选基因的研究进展[J].国外畜牧科技,1999,26(6):31-33.
CAO H H, LI H B, WANG L X, et al.Review on FABPs gene as candidate gene for intramuscular fat content in pig[J]. Animal Science Aboard, 1999,26(6):31-33. (in Chinese with English abstract)
[6] GERBENS F, VERBURG F J, VAN MOERKERK H T, et al. Associations of heart and adipocyte fatty acid-binding protein gene expression with intramuscular fat content in pigs[J]. Journal of Animal Science, 2001,79(2):347-354.
[7] CHEN Q M, WANG H, ZENG Y Q.Developmental changes and effect on intramuscular fat content of H-FABP and A-FABP mRNA expression in pigs[J]. Journal of Applied Genetics, 2013, 5(1):119-123.
[8] 李长龙,萨晓婴,孟和,等. H-FABP基因的多态性和营养因素对猪肉质的影响[J].遗传,2009,31(7):713-718.
LI C L, SA X Y, MENG H, et al.Effects of H-FABP gene polymorphisms and nutritional factors on pork quality[J]. Hereditas, 2009, 31(7): 713-718.(in Chinese with English abstract)
[9] 李文娟,李宏宾,陈继兰,等. 鸡H-FABPs基因和A-FABPs基因表达与肌内脂肪含量相关研究[J].畜牧兽医学报,2006,37(5):417-423.
LI W J, LI H B, CHEN J L, et al.Association of the H-FABP and A-FABP gene expression with intramuscular fat content in chickens[J]. Acta Veterinaria et Zootechnica Sinica, 2006, 37(5):417-423. (in Chinese with English abstract)
[10] 李芳芳,魏杰,王洪,等.三种血液基因组 DNA 提取方法的比较研究[J].实验动物学,2014,31(5):28-32.
LI F F, WEI J, WANG H, et al.Comparison of three methods for blood genomic DNA extraction[J]. Acta Laboratorium Animalis Scientia Sinica, 2014,31(5): 28-32. (in Chinese with English abstract)
[11] 刘志成,强巴央宗,杨涛,等.藏猪FABPs基因PCR-RFLP多样性研究[J].中国农业大学学报,2009, 14(6):6-10.
LIU Z C, QIANGBA Y Z, YANG T, et al.Research on PCR-RFLP polymorphisms of FABPs genes in Tibet pigs[J].Journal of China Agricultural University,2009,14(6): 6-10. (in Chinese with English abstract)
[12] 林万华,任军,丁能水,等. H-FABP基因型对二花脸猪相关性状影响的初步分析[J].畜牧兽医学报,2003,34(4):318-324.
LIN W H, REN J, DING N S, et al.Influences of H-FABP genotype on the related traits in Erhualian pig[J]. Journal of Animal Husbandry and Veterinary Medicine, 2003,34(4): 318-324. (in Chinese with English abstract)
[13] 张陈华,王阳,丁月云,等.圩猪H-FABP基因多态性分析及其与IMF含量的相关性[J].中国农业科学,2011,44(4):1063-1070.
ZHANG C H, WANG Y, DING Y Y, et al.Polymorphism analysis of H-FABP gene and correlation with IMF content in Wei pig[J]. Scientia Agricultura Sinica, 2011,44(4):1063-1070. (in Chinese with English abstract)
[14] 祝仁铸,尹逊河,王元虎,等.猪肌肉组织MDH和LPL基因表达与肌内脂肪含量和脂肪酸组成关系的研究[J].畜牧兽医学报,2013,44(8):1182-1188.
ZHU R Z, YIN X H, WANG Y H, et al.The gene expression of MDH and LPL in muscle and their association with content of intramuscular fat and composition of fatty acids in pigs[J]. Acta Veterinaria et Zootechnica Sinica, 2013,44(8):1182-1188. (in Chinese with English abstract)
[15] 李延恩, 周艳红. SNP功能分析的生物信息学方法及其资源[J]. 计算机仿真, 2007, 24(4):297-300.
LI Y E, ZHOU Y H.Bioinformatics methods and resources for SNP functional analysis[J]. Computer Simulation, 2007, 24(4):297-300. (in Chinese with English abstract)
[16] 柴志欣, 钟金城, 李键,等. 麦洼牦牛H-FABP和MC4R基因的克隆及生物信息学分析[J]. 西北农业学报, 2015, 24(5):6-12.
CHAI Z X, ZHONG J C, LI J, et al.Cloning and bioinformatics analysis of H-FABP and MC4R gene in Maiwa yak[J]. Acta Agriculturae Boreali-Occidentalis Sinica, 2015, 24(5):6-12. (in Chinese with English abstract)
[17] 高红, 彭静, 沈一飞,等. 不同物种FABP3基因编码区及蛋白生物信息学分析[J]. 扬州大学学报(农业与生命科学版), 2014, 35(1):31-36.
GAO H, PENG J, SHEN Y F, et al.Bioinformatic analysis of coding regions and proteins of FABP3 gene among different species[J]. Journal of Yangzhou University(Agriculture and Life Sciences Edition), 2014, 35(1): 31-36. (in Chinese with English abstract)
[18] 盘道兴, 王振, 杨茂林,等. 江口萝卜猪FABPs主要家族基因SNPs筛选及生物信息学分析[J]. 基因组学与应用生物学, 2015, 34(1):47-52.
PAN D X, WANG Z, YANG M L, et al.SNP screening and bioinformatics analysis of the main family genes of FABPs in Jiang kou Luobo pig[J]. Genomics and Applied Biology, 2015, 34(1): 47-52. (in Chinese with English abstract)
[19] 曹健, 罗玉柱, 胡江,等. 甘南牦牛H-FABP基因CDS区多态性及生物信息学分析[J]. 甘肃农业大学学报, 2012, 47(4):14-20.
CAO J, LUO Y Z, HU J, et al.Polymorphism and bioinformatics analysis of CDS in H-FABP gene in Gannan yak[J].Journal of Gansu Agricultural University, 2012, 47(4):14-20. (in Chinese with English abstract)
[20] 王悦冰, 郎志宏, 黄大昉. 内含子对真核基因表达调控的影响[J]. 生物技术通报, 2008(4):1-4.
WANG Y B, LANG Z H, HUANG D F.Effects of pre-mRNA introns on regulation of eukaryotic gene expression[J]. Biotechnology Bulletin, 2008(4): 1-4. (in Chinese with English abstract)
[21] 宋士芹. 不同剪接频率外显子的组成特征分析[D]. 合肥:中国科学技术大学, 2009.
SONG S Q.Comparative component analysis of exons with different splicing frequencies[D]. Hefei: University of Science and Technology of China, 2009. (in Chinese with English abstract)
[22] 王立刚, 张龙超, 赵克斌,等. 猪H-FABP基因第2内含子SNPs分布及连锁不平衡遗传模式研究[J]. 中国畜牧兽医, 2011, 38(1):122-125.
WANG L G, ZHANG L C, ZHAO K B, et al.Nucleotide variability and linkage disequilibrium patterns at the porcine H-FABP gene[J]. China Animal Husbandry & Veterinary Medicine, 2011, 38(1): 122-125. (in Chinese with English abstract)
[23] 贾浩,张小白,宋晓峰.人类胞内蛋白半衰期与其亚细胞定位的相关性研究[J].计算机与应用化学, 2011, 28(4):411-414.
JIA H, ZHANG X B, SONG X F.Relationship between intracellular protein half-life and subcellular localization in human cells[J].Computers and Applied Chemistry, 2011, 28(4):411-414. (in Chinese with English abstract)
[24] ROST B, SANDER C.Combining evolutionary information and neural networks to predict protein secondary structure[J]. Proteins Structure Function & Bioinformatics, 1994, 19(1):55-72.
[25] 郑海军,朱荣,葛春蕾,等.人白细胞介素-29的生物信息学分析[J].中国生物制品学杂志, 2013, 26(2):209-212.
ZHENG H J, ZHU R, GE C L, et al.Bioinformatics of human interleukin-29[J]. Chinese Journal of Biologicals, 2013, 26(2): 209-212. (in Chinese with English abstract)
[26] 钱成, 罗卫星, 孙岩岩,等. 贵州地方山羊品种H-FABP基因第3外显子SNP研究[J]. 生物技术, 2015(4):349-354.
QIAN C, LUO W X, SUN Y Y, et al.Study on SNP of H-FABP Exon3 of Guizhou local goat breeds[J]. Biotechnology, 2015 (4): 349-354. (in Chinese with English abstract)

H-FABP gene cloning, SNPs screening and bioinformatics analysis in Gansu black pig

RichHTML

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	ZHAO Xiuping, WANG Shuang, YAN Xingyi, DUAN Qiang, ZHANG Shuai, CHEN Yongsheng, LI Guorui. Expression, purification and bioinformatics analysis of Magnaporthe oryzae MGG-01005 [J]. Acta Agriculturae Zhejiangensis, 2021, 33(3): 470-478.
[2]	LIANG Liqin, YANG Rui, GAO Gang. Bioinformatics analysis of StUOXs gene family in potato [J]. , 2020, 32(9): 1523-1532.
[3]	WU Jia, CHEN Lang, JIANG Tao, HUANG Guoming, LI Zhuo, LI Yaodong, ZHANG Li, LIU Lixia. Genetic polymorphism screening of CSF3 gene in dairy cow and its bioinformatics analysis [J]. , 2020, 32(6): 986-993.
[4]	WANG Yuanhong, XING Xue, LI Chuanfeng, ZHU Jie, WANG Yong, LIU Guangqing. Bioinformatics analysis and prokaryotic expression of FIPV AH1905 strain N gene [J]. , 2020, 32(3): 406-414.
[5]	WANG Xiaopeng, ZHAO Liang, LIU Zimin, BAI Caixia, YANG Kankan, ZHANG Da, SUN Pei, JIANG Shudong, LI Yongdong, WANG Yong. Prokaryotic expression and bioinformatics analysis of PPV7 Cap gene [J]. , 2020, 32(2): 200-209.
[6]	TAN Guanghui, QIN Yuanyu, LI Jiezhang, WU Lei, YUE Yong, ZHANG Yiyu. Single nucleotide polymorphism screening and bioinformatics analysis of ATF4 gene in Cherry Valley ducks [J]. , 2020, 32(2): 218-225.
[7]	QIN Ling, ZHANG Xin, RONG Chunxiao, MO Chuanyuan, FAN Lu, YAN Jie, MENG Ying, ZHANG Manrang. Identification and expression analysis of polyamine oxidase (PAO) gene family in apple [J]. , 2020, 32(2): 262-273.
[8]	LIU Jialin, LIU Shili, JIANG Wenping, CHENG Shun, CHI Meili, ZHENG Jianbo, JIA Yongyi, ZHAO Jinliang, YIN Shaowu, GU Zhimin. Cloning and bioinformatics analysis of GH gene and its flanking region in Odontobutis potamophila [J]. , 2019, 31(9): 1461-1470.
[9]	YUAN Xiaolong, LI Yunqin, WANG Yi. Cloning and expression of three chalcone synthase-like genes from Paeonia delavayi [J]. , 2019, 31(9): 1478-1484.
[10]	PENG Shuai, CHEN Lang, ZHENG Tianyu, LU Huining, ZHANG Li, LIU Lixia. SNP site screening and bioinformatics analysis of TLR2 gene in Datong yak [J]. , 2019, 31(8): 1280-1285.
[11]	LIU Zhengkui, WU Yuan, CHEN Lin, WANG Lei, MU Hongye, ZHU Xuhang, WANG Xiaodu. Prokaryotic expression and bioinformatics analysis of Nsp5 gene of porcine epidemic diarrhea virus [J]. , 2019, 31(4): 532-538.
[12]	DONG Xinxing, LI Mingli, CUI Yijia, LAN Guoxiang, WANG Xiaoyi, YAN Dawei. Cloning, bioinformatics analysis and tissue expression detection of MCUR1 gene in Saba pig [J]. , 2019, 31(11): 1825-1833.
[13]	ZHANG Gaofeng, YANG Kankan, ZHANG Qian, WANG Yuanhong, YU Zhaorong, ZHANG Xueqi, LU Zhimin, LIU Zimin, LI Yongdong, WANG Yong. Prokaryotic expression and bioinformatics analysis of orf virus Anhui strain 023 gene [J]. , 2019, 31(1): 30-38.
[14]	RUAN Xianle, WANG Junsheng, LIU Hongzhan, CHEN Liangbing, ZHAO Jinhui. Bioinformatics analysis of miR169 gene family in Brassica napus L. and prediction of their target genes [J]. , 2018, 30(8): 1273-1280.
[15]	YANG Yongjiang, WU Enyun, REN Wenwen, MA Boyan, GAO Chenghong, LI Hongxu, LIU Lixia, CAO Xin, ZANG Rongxin, YANG Jutian, ZHANG Li. SNP screening and protein function prediction of TLR2 gene in Chinese Holstein cattle [J]. , 2018, 30(8): 1321-1327.