京海黄鸡腹脂重性状的全基因组关联分析

doi:10.16431/j.cnki.1671-7236.2016.05.003

Abstract

Abstract: The study was conducted to reveal the genetic basis of abdominal fat weight trait and scan molecular markers which could be used to improve the abdominal fat weight.The abdominal fat weight of female Jinghai Yellow chicken in core group were measured after being slaughtered.Genome-wide association study was carried out using specific-locus amplified fragment sequencing technology to detect SNPs associated with abdominal fat weight.Finally, five SNPs that associated with abdominal fat weight and reached suggestive genome-wide significance (P<1.1×10^-5) were found, and four of them (rs18144674, rs18144680, rs12246236 and rs12257795) reached chromosome significance level.Three SNPs (rs18144674, rs18144680 and rs19745739) located in a 1.6 Mb area of chromosome 2, and two SNPs (rs12246236 and rs12257795) located in a 12 kb area of chromosome 14.Genes in the candidate regions with 0.1 Mb windows were screened.Finally, eleven candidate genes of VIM, TRDMT1, AXIN1, PDIA2, ARHGDIG, gga-mir-1763, gga-mir-1564, CLCN7, ECL1, DNASE1 and SDOS were obtained.The molecular function and biological processes were analyzed using GO database.The results showed that those genes might be candidate genes affecting abdominal fat weight in Jinghai Yellow chicken.

Key words: SLAF-seq; Jinghai Yellow chicken; abdominal fat weight; genome-wide association study

CLC Number:

DUAN Lian, WANG Wen-hao, LI Ting-ting, WANG Jin-yu, HAN Kun-peng, WANG Yong-juan. Genome-wide Association Study on Abdominal Fat Weight in Jinghai Yellow Chicken[J]. , 2016, 43(5): 1140-1147.

References

[1] 冯春刚,胡晓湘,赵要风,等.全基因组选择及其在动物育种中的应用[J].中国家禽,2008,30(22):5-8.
[2] Klein R J,Zeiss C,Chew E Y,et al.Complement factor H polymorphism in age-related macular degeneration[J].Science,2005,308(5720):385-389.
[3] Sun X,Liu D,Zhang X,et al.SLAF-seq:An efficient method of large-scale de novo SNP discovery and genotyping using high-throughput sequencing[J].PLoS One,2013,8(3):e58700.
[4] Nicodemus K K,Liu W,Chase G A,et al Comparison of type Ⅰ error for multiple test corrections in large single- nucleotide polymorphism studies using principal components versus haplotype blocking algorithms[J].BMC Genet,2005,6(Suppl 1):S78.
[5] Deng Y Y,Li J Q,Wu S F,et al.Integrated nr database in protein annotation system and its localization[J].Computer Engineering,2006,32(5):71-74.
[6] Liu R,Sun Y,Zhao G,et al.Genome-wide association study identifies loci and candidate genes for body composition and meat quality traits in Beijing-You chickens[J].PLoS One,2013,8(4):e61172.
[7] Gu X,Feng C,Ma L,et al.Genome-wide association study of body weight in chicken F2 resource population[J].PLoS One,2011,6(7):e21872.
[8] 王文浩,张涛,张跟喜,等.京海黄鸡γ-干扰素水平的全基因组关联分析[J].中国畜牧兽医,2015,42(2):245-250.
[9] 吴丹.北京油鸡体重和屠体性状的全基因组关联研究[D].北京:中国农业科学院,2012.
[10] Luo C,Qu H,Ma J,et al.Genome-wide association study of antibody response to Newcastle disease virus in chicken[J].BMC genetics,2013,14:42.
[11] Luo C,Qu H,Ma J,et al.A genome-wide association study identifies major loci affecting the immune response against infectious bronchitis virus in chicken[J].Infection,Genetics and Evolution,2014,21:351-358.
[12] Li D F,Lian L,Qu L J,et al.A genome-wide SNP scan reveals two loci associated with the chicken resistance to Marek's disease[J].Animal Genetics,2013,44(2):217-222.
[13] Abasht B,Lamont S J.Genome-wide association analysis reveals cryptic alleles as an important factor in heterosis for fatness in chicken F2 population[J].Animal Genetics,2007,38:491-498.
[14] 俆浩翔,王宝玺.波形蛋白与疾病关系的研究进展[J].基础医学与临床,2009,29(10):1117-1119.
[15] 金利华,李勤喜,叶志云.Axin在肿瘤发生中的作用机制[J].细胞生物学杂志,2007,29:207-212.
[16] Frattini A,Pangrazio A,Susani L,et al.Chloride channel ClCN7 mutations are responsible for severe recessive,dominant,and intermediate osteopetrosis[J].J Bone Miner Res,2003,18(10):1740-1747.

Genome-wide Association Study on Abdominal Fat Weight in Jinghai Yellow Chicken

PDF (PC)

Knowledge

Abstract

Cite this article

share this article

References

Related Articles 15

Recommended Articles

Metrics

Comments

[1]	MO Jiayuan, GAO Jiuyu, FENG Lingli, LI Yueyue, TIAN Weilong, LIU Xiaoxiao, CHENG Feng, LIANG Liang, LEI Shuqiao, WEN Wei, LIANG Jing, LAN Ganqiu. Genome-wide Association Study on Alive Litter Size Trait in Bama Xiang Pigs [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(12): 3965-3975.
[2]	LYU Shijie, CHEN Fuying, ZHANG Zijing, SHI Qiaoting, XIN Xiaoling, CHU Qiuxia, LI Wenjun, BAI Zhonglin, WANG Eryao, XU Zhaoxue. Genomic Regions Associated with Growth Traits in Nanyang Cattle Using Genome-wide Association Analysis [J]. China Animal Husbandry and Veterinary Medicine, 2020, 47(1): 74-82.
[3]	ZHAO Desheng, ZHANG Chongzhi. Research Progress on Genome-wide Association in Livestock [J]. , 2018, 45(2): 463-470.
[4]	YUAN Man-man, ZHANG Tao, ZHANG Xiang-qian, LI Ting-ting, LING Jiao-jiao, WU Peng-fei, WANG Jin-yu, SHI Hui-qiang. Bioinformatics and Tissue Expression Analysis of G Protein-coupled Receptor 1 Gene in Jinghai Yellow Chicken [J]. , 2017, 44(8): 2215-2225.
[5]	ZHANG Xiang-qian, DONG Xin-long, LING Jiao-jiao, HAN Kun-peng, ZHANG Tao, WANG Jin-yu, WANG Yong-juan. Tissue Expression and Bioinformatics Analysis of HOXC10 Gene in Jinghai Yellow Chicken [J]. , 2016, 43(7): 1702-1708.
[6]	HAN Kun-peng, DUAN Lian, LI Ting-ting, WANG Jing-yu, ZHANG Tao, LI Guo-hui, ZHANG Gen-xi, XUE Qian. Study on RNA-Seq of Jinghai Yellow Chicken Ovary:Analysis of Gene Structure and Mining New Genes [J]. , 2016, 43(4): 854-861.
[7]	XIE Jian, YU Chang-yan, XU Yao, NIU Xi, RAN Xue-qin, WANG Jia-fu. Genome-wide Association Study of Teats Number Traits in Kele Pigs [J]. , 2016, 43(11): 2866-2872.
[8]	WANG Wen-hao, LI Guo-hui, WANG Jin-yu, ZHANG Gen-xi, ZHANG Tao, HAN Kun-peng, WANG Yong-juan. Genome-wide Association Studies for Jinghai Yellow Chicken's AIV Disease Resistance Trait [J]. , 2015, 42(3): 509-515.
[9]	WANG Wen-hao, ZHANG Tao, ZHANG Gen-xi, WANG Jin-yu, LI Guo-hui, WANG Yong-juan. Genome-wide Association Study on INF-γ in Jinghai Yellow Chicken [J]. , 2015, 42(2): 245-250.
[10]	ZHANG Tao, ZHANG Gen-xi,WANG Jin-yu, FAN Qing-can, WANG Wen-hao, WEI Yue, CHEN Xue-sen, TANG Ying，WANG Yong-juan. Cloning and Bioinformatics Analysis of MyoG Gene in Jinghai Yellow Chicken [J]. , 2014, 41(8): 1-8.
[11]	XUE Qian,WANG Jin-yu,ZHANG Gen-xi, WANG Ya-nan,TANG Ying，WEI Yue,SHI Hui-qiang. Relationship between Polymorphisms of Exon 1 of THRSPα Gene and the Carcass and Abdominal Fat Traits in Jinghai Yellow Chicken [J]. , 2014, 41(7): 169-174.
[12]	ZHAO Xiu-hua, LI Man-yu, WANG Jin-yu, LIU Guo-jun. Genetic Effects of IGF-Ⅰ Gene on the Growth and Reproductive Traits in Jinghai Yellow Chicken [J]. , 2014, 41(7): 178-181.
[13]	ZHANG Tao, WANG Jin-yu ZHANG Gen-xi WANG Wen-hao, WEI Yue, CHEN Xue-sen, TANG Ying, WANG Yong-juan3. Cloning and Prokaryotic Expression of Gonadotropin Releasing Hormone 1 Gene in Jinghai Yellow Chicken [J]. , 2014, 41(5): 94-98.
[14]	TANG Ying, WANG Jin-yu, ZHANG Gen-xi, GE Ying, XUE Qian, WANG Ya-nan, WANG Yong-juan. Research on Genetic Effects of Myogenin Gene SNPs on the Reproductive Traits in Jinghai Yellow Chicken [J]. , 2014, 41(4): 170-174.
[15]	CHEN Xue-sen, WANG Jin-yu, ZHANG Gen-xi, ZHANG Tao, TANG Ying, SHI Hui-qiang. Establishment of Standard Curves for Detection of Na⁺/H⁺ Exchanger 1 Gene in Jinghai Yellow Chicken Using Real-time PCR [J]. , 2014, 41(2): 39-42.