Genome-wide CNV analysis reveals variants associated with growth traits in Bos indicus

文献类型： 外文期刊

第一作者： Zhou, Yang

作者： Zhou, Yang;Xu, Lingyang;Hay, El Hamidi Abdel;Bickhart, Derek M.;Rosen, Benjamin D.;Schroeder, Steven G.;Sonstegard, Tad S.;Van Tassell, Curtis P.;Liu, George E.;Zhou, Yang;Utsunomiya, Yuri T.;Garcia, Jose Fernando;Xu, Lingyang;Alexandre, Pamela Almeida;Sterman Ferraz, Jose Bento;Fukumasu, Heidge;de Rezende Neves, Haroldo Henrique;Garcia, Jose Fernando;Sonstegard, Tad S.;Garcia, Jose Fernando

作者机构：

关键词： Copy number variation (CNV);EBV;Association;Body size;Bos indicus

期刊名称：BMC GENOMICS （ 影响因子：3.969； 五年影响因子：4.478 ）

ISSN： 1471-2164

年卷期： 2016 年 17 卷

页码：

收录情况： SCI

摘要： Background: Apart from single nucleotide polymorphism (SNP), copy number variation (CNV) is another important type of genetic variation, which may affect growth traits and play key roles for the production of beef cattle. To date, no genome-wide association study (GWAS) for CNV and body traits in beef cattle has been reported, so the present study aimed to investigate this type of association in one of the most important cattle subspecies: Bos indicus (Nellore breed). Results: We have used intensity data from over 700,000 SNP probes across the bovine genome to detect common CNVs in a sample of 2230 Nellore cattle, and performed GWAS between the detected CNVs and nine growth traits. After filtering for frequency and length, a total of 231 CNVs ranging from 894 bp to 4,855,088 bp were kept and tested as predictors for each growth trait using linear regression analysis with principal components correction. There were 49 significant associations identified among 17 CNVs and seven body traits after false discovery rate correction (P < 0.05). Among the 17 CNVs, three were significant or marginally significant for all the traits. We have compared the locations of associated CNVs with quantitative trait locus and the RefGene database, and found two sets of 9 CNVs overlapping with either known QTLs or genes, respectively. The gene overlapping with CNV100, KCNJ12, is a functional candidate for muscle development and plays critical roles in muscling traits. Conclusion: This study presents the first CNV-based GWAS of growth traits using high density SNP microarray data in cattle. We detected 17 CNVs significantly associated with seven growth traits and one of them (CNV100) may be involved in growth traits through KCNJ12.

分类号：

  • 相关文献

[1]Detection of genome-wide copy number variations in two chicken lines divergently selected for abdominal fat content. Zhang, Hui,Du, Zhi-Qiang,Dong, Jia-Qiang,Wang, Hai-Xia,Shi, Hong-Yan,Wang, Ning,Wang, Shou-Zhi,Li, Hui,Zhang, Hui,Du, Zhi-Qiang,Dong, Jia-Qiang,Wang, Hai-Xia,Shi, Hong-Yan,Wang, Ning,Wang, Shou-Zhi,Li, Hui,Zhang, Hui,Du, Zhi-Qiang,Dong, Jia-Qiang,Wang, Hai-Xia,Shi, Hong-Yan,Wang, Ning,Wang, Shou-Zhi,Li, Hui. 2014

[2]Fitness of Encarsia sophia (Hymenoptera: Aphelinidae) parasitizing Trialeurodes vaporariorum and Bemisia tabaci (Hemiptera: Aleyrodidae). Luo, Chen,Liu, Tong-Xian,Luo, Chen. 2011

[3]Contrasting patterns of ovarian development and oogenesis in two sympatric host-feeding parasitoids, Diglyphus isaea and Neochrysocharis formosa (Hymenoptera: Eulophidae). Wang, Wei,Guo, Jian-Yang,Wan, Fang-Hao,Wang, Wei,Cheng, Li-Sheng.

[4]The interaction of temperature, salinity and body weight on growth rate and feed conversion rate in turbot (Scophthalmus maximus). Huang Zhi-Hui,Ma Ai-Jun,Wang Xin-An,Lei Ji-Lin,Huang Zhi-Hui.

[5]Sexual selection drives the evolution of limb regeneration in Harmonia axyridis (Coleoptera: Coccinellidae). Wang, S.,Tan, X. L.,Shi, Z. K.,Zhang, F.,Michaud, J. P..

[6]Estimates of Genetic Parameters for Body Weight and Carcass Composition in Pekin Ducks. Xu, T. S.,Huang, W.,Hou, S. S.,Xu, T. S.,Liu, X. L.,Xu, T. S.. 2011

[7]A push-pull strategy to control aphids combines intercropping with semiochemical releases. Hatt, Severin,Zhang, Yong,Chen, Julian,Xu, Qinxuan,Hatt, Severin,Lopes, Thomas,Zhang, Yong,Francis, Frederic,Hatt, Severin,Bodson, Bernard. 2018

[8]Determination of Residual Feed Intake and Its Associations with Single Nucleotide Polymorphism in Chickens. Xu Zhen-qiang,Chen Jie,Zhang De-xiang,Zhang Xi-quan,Zhang Yan,Ji Cong-liang. 2014

[9]Associations of GBP2 gene copy number variations with growth traits and transcriptional expression in Chinese cattle. Zhang, Gui-Min,He, Hua,Song, Cheng-Chuang,Cao, Xiu-Kai,Lei, Chu-Zhao,Lan, Xian-Yong,Chen, Hong,Huang, Yong-Zhen,Zheng, Li,He, Hua,Zhang, Zi-Jing,Qi, Xing-Lei. 2018

[10]Copy number variations at LEPR gene locus associated with gene expression and phenotypic traits in Chinese cattle. Shi, Tao,Xu, Yao,Yang, Mingjuan,Huang, Yongzhen,Lan, Xianyong,Lei, Chuzhao,Chen, Hong,Yang, Xiaoming,Qi, Xinglei.

[11]Identification and characterization of a novel adenine phosphoribosyltransferase gene (ZmAPT2) from maize (Zea mays L.). Wu, Suowei,Yu, Zhanwang,Li, Weihua,Yang, Qingkai,Ye, Chunjiang,Sun, Yan,Jin, Demin,Wang, Bin,Wu, Suowei,Li, Weihua,Yang, Qingkai,Wang, Fengge,Zhao, Jiuran.

[12]TaCKX6-D1, the ortholog of rice OsCKX2, is associated with grain weight in hexaploid wheat. Zhang, Lei,Zhao, Yong-Liang,Gao, Li-Feng,Zhao, Guang-Yao,Zhou, Rong-Hua,Jia, Ji-Zeng,Zhang, Lei,Zhang, Bao-Shi.

[13]DNA methylation pattern of Photoperiod-B1 is associated with photoperiod insensitivity in wheat (Triticum aestivum). Sun, Han,Guo, Zhiai,Gao, Lifeng,Zhao, Guangyao,Zhang, Wenping,Zhou, Ronghua,Wu, Yongzhen,Jia, Jizeng,Sun, Han,An, Hailong,Wang, Haiyang.

[14]Subcellular localization, expression patterns, SNPs and association analyses of the porcine HUMMLC2B gene. Wang, Huan L.,Wang, Heng,Zhu, Zheng M.,Wang, Chen F.,Zhu, Meng J.,Mo, De L.,Yang, Shu L.,Li, Kui.

[15]Population Variation Reveals Independent Selection toward Small Body Size in Chinese Debao Pony. Kader, Adiljan,Dong, Kunzhe,Zhao, Qianjun,He, Xiaohong,Pu, Yabin,Gorkhali, Neena Amatya,Liu, Xuexue,Jiang, Lin,Li, Xiangchen,Guan, Weijun,Ma, Yuehui,Li, Yan,Zhang, Yaping,Wu, Dong-Dong,Irwin, David M.,Liu, Jianfeng. 2016

[16]Polymorphisms in GJA1 and their association with growth traits in chicken. Shahjahan, M.,Liu, R. R.,Zhao, G. P.,Zhang, J. J.,Zheng, M. Q.,Li, Q. H.,Wen, J.,Liu, R. R.,Zhao, G. P.,Zhang, J. J.,Zheng, M. Q.,Li, Q. H.,Wen, J.. 2015

[17]Association of polygalacturonase-inhibiting protein gene 2 (MsPGIP2) to common leaf spot resistance in alfalfa. Gui, Zhi,Gao, Jianming,Xin, Nan,Pi, Yongshuo,Liu, Huiqin,Gui, Zhi,Gao, Jianming,Wang, Yu,Yuan, Qinghua,Li, Xianglin.

[18]Novel Nucleotide Variations, Haplotypes Structure and Associations with Growth Related Traits of Goat AT Motif-Binding Factor (ATBF1) Gene. Zhang, Xiaoyan,Wu, Xianfeng,Pan, Chuanying,Lei, Chuzhao,Chen, Hong,Lan, Xianyong,Jia, Wenchao,Li, Xiangcheng.

[19]Association of Calpain 1 (CAPN1) and HRSP12 allelic variants in beef cattle with carcass traits. Hou, Guanyu,Huang, Meng,Gao, Xue,Li, Junya,Gao, Huijiang,Ren, Hongyan,Xu, Shangzhong,Hou, Guanyu. 2011

[20]Characterization and identification of ISSR markers associated with oil content in sea buckthorn berries. Ding, J.,Bao, Y. H.,Ding, J.,Ruan, C. J.,Li, H.,Ding, J.,Guan, Y.,Shan, J. Y.. 2016

作者其他论文 更多>>

微信小程序