3个贵州地方鸡种NKX2-5基因多态性及生物信息学分析

Abstract

Abstract: In this study, Gaojiao chickens, Weining chickens, Wumeng black-bone chickens (including blue-shell chickens and white-shell chickens) from three local breeds of Guizhou were selected for research subjects. By constructing DNA pools to amplify the all sequences of extron 1 and the segmental sequences of intron 2 on NKX2-5 gene. Taking direct sequencing method to detect the single nucleotide polymorphisms on NKX2-5 gene of three varieties (four groups). By bioinformatics software to predict the effects of different polymorphism loci on mRNA, protein secondary structure of NKX2-5 gene. The results showed that 5 SNPs including G108A, T288C, C400T, T420G and G429A were discovered. And among these SNPs, G108A was located in non-coding regions, T288C and C400T were located in extron 1, T420G and G429A were located in intron region. T288C and C400T were missense mutations, T288C mutation leaded to serine (Ser) into proline (Pro), C400T mutation leaded to alanine (Ala) into valine (Val), and SNPs sites had some effects on mRNA secondary structure, protein secondary structure of NKX2-5 gene.

Key words: local chicken breeds in Guizhou; NKX2-5 gene; SNPs; bioinformatics

CLC Number:

S813.3

YANG Hong, SUN Juan, QIU Gui-hua, SONG Ru-mou, YANG Kai-ming, ZHU Ming-gui, LI Jun, ZHANG Yong. Polymerphism Detection and Bioinformatics Analysis of NKX2-5 Gene of Three Local Chicken Breeds in Guizhou[J]. , 2014, 41(12): 209-214.

References

1 冉莉, 文格渡. GATA-4、NKx2-5转录因子的研究进展[J]. 现代医药卫生, 2008, 24(15):2287～2288.
2 孙艳发, 刘冉冉, 郑麦青,等. 鸡胫长和胫围的全基因组关联分析[J]. 畜牧兽医学报, 2013, 44(3):358～365.
3 李敬瑞, 丁远华, 向程举,等. 猪DAZ基因的DNA池测序分析[J]. 中国畜牧兽医, 2011, 38(8):60～62.
4 陈丹盈. Nkx2.5/TBX5/GATA4等基因在鸡、鹌鹑及其属间杂交种胚胎心脏发育过程中的表达研究[D]. 石河子:石河子大学, 2012.
5 汪剑, 卓莉莉, 姜之文,等. CSX/Nkx2.5基因在大鼠胚胎心脏发育过程中的表达[J]. 南京医科大学学报(自然科学版), 2008, 28(5):605～608.
6 胡易池. NKX2.5和TBX5与先天性心脏病的研究进展[J]. 医学综述,2012,18(13):1986～1989.
7 高爱琴, 李金泉, 李宁, 等. 绵羊FGF5基因SNP的生物信息学分析[J]. 中国畜牧杂志,2008,44(5):5～7.
8 崔建勋, 杜红丽, 张细权, 等. 利用DNA池和测序技术快速筛查SNPs及估算基因频率[J]. 遗传学报, 2005,32(4):372～377.
9 Ankra-Badu G A, Le Bihan-Duval E, Mignon-Grasteau S, et al. Mapping QTL for growth and shank traits in chickens divergently selected for high or low body weight [J]. Animal Genet,2010, 41(1):400～405.
10 Clark C D, Zhang B, Lee B, et al. Evolutionary conservation of Nkx2.5 autoregulation in the second heart field[J]. Developmental Biology, 2013, 374(1):198～209.
11 Gao Y, Du Z Q, Feng C G, et al. Identification of quantitative trait loci for shank length and growth an different development stages in chicken[J]. Animal Genet, 2010, 41(1):101～104.
12 Kabir M, Oni O O, Akpa G N,et al. Heritability estimates and the interrelationships of body weight and shank length in Rhode island red and white chickens[J]. Pakistan Journal of Biological Sciences,2010,9(15):2892～2896.
13 Pashmforoush M, Lu J T, Chen H,et al. Nkx2-5 pathways and congenital heart disease; Ioss of ventricular myocyte lineage specification leads to progressive cardiomyopathy and complete heart block[J]. Cell, 2004, 117(3):373～386.
14 Qian B, Liu X J, Hui W Q, et al. Comparative analysis of Nkx2-5/GATA4/TBX5 expression in chicken, quail and chicken-quail hybrids during the early stage of cardiac development in embryos[J]. Asian-Australasian Journal of Animal Sciences,2013,26(4):476～482.
15 Shiojima I, Komuro I, Inazawa J, et al. Assignment of cardiac homebox gene CSX to human chromosome 5q34 [J]. Genomics, 1995, 27(1):204～206.
16 Sun G R, Zhang Y F, Li G X ,et al. Mapping quantitative trait loci associated with growth quality traits in a chicken population on chromosome 8, 9, 10, 11, 13[J]. Journal of Animal and Veterinary Advances, 2012,11(11):1939～1945.

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Polymerphism Detection and Bioinformatics Analysis of NKX2-5 Gene of Three Local Chicken Breeds in Guizhou

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