鸡胫长和胫围的全基因组关联分析

畜牧兽医学报

鸡胫长和胫围的全基因组关联分析

孙艳发^1,2，刘冉冉²，郑麦青²，赵桂苹²，张磊²，吴丹²，胡耀东²，李鹏²，文杰^1，2*

（1. 扬州大学动物科学与技术学院，扬州 225009； 2. 中国农业科学院北京畜牧兽医研究所, 北京 100193）

收稿日期:2012-07-09 出版日期:2013-03-23 发布日期:2013-03-23
通讯作者: 文杰，研究员，主要从事家禽育种研究,E-mail：wenjie@caas.cn
作者简介:孙艳发（1981-），男，黑龙江哈尔滨人，博士，主要从事家禽营养与育种研究,E-mail：boysun2010@163.com
基金资助:
农业产业技术体系项目（nycytx-42）; 中央级公益性科研院所基本科研业务费专项（2012ZL068）；国家家养动物种质资源平台项目（2012）

Genome-wide Association Study on Shank Length and Shank Girth in Chicken

SUN Yan-fa^1,2, LIU Ran-ran², ZHENG Mai-qing², ZHAO Gui-ping², ZHANG Lei², WU Dan², HU Yao-dong², LI Peng², WEN Jie^1,2*

(1. College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; 2. Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China)

Received:2012-07-09 Online:2013-03-23 Published:2013-03-23

摘要/Abstract

摘要：

为了揭示影响鸡胫生长的遗传基础和分子机制，本试验以中国农业科学院北京畜牧兽医研究所昌平试验基地鸡场鸡F₂资源群体为基础，测定了F₂代个体93日龄的体重、胫长和胫围，并利用60 K SNP芯片对个体基因组DNA进行分型，进行胫长和胫围的全基因组关联分析（GWAS）。结果表明，与鸡胫长和胫围达到5%全基因组水平显著关联位点分别为1个和4个（P<2.98×10^-6），潜在关联位点分别为4个和25个（P<5.96×10^-5）。其中1个SNP位点位于13号染色体上的NKX2-5基因的下游138 834 bp，另一个SNPs位于8号染色体ELAVL4基因的下游52 248 bp处。4号染色体14.93 Mb（71.01～85.94 Mb）区域多个SNPs位点与胫围显著或潜在关联。该区域内含有的LDB2、BOD1L1和QDPR等基因。这些基因和区域可作为影响胫长和胫围的重要候选区域和基因，为揭示胫生长的遗传基础和分子机制以及后期的分子标记辅助选择奠定了基础。

Abstract:

To reveal genetic basis and molecular mechanism affecting shank growth in chicken, live weight, shank length and shank girth of F₂ generation individuals were measured at 93-day-old, these birds came from Chinese Academy of Agricultural Sciences (CAAS) chicken F₂ rescoure population. Genomic DNA was genotyped using chicken 60 K SNP Beadchip. The genome-wide association study (GWAS) on shank length and shank girth were performed. The results showed that 1 and 4 SNPs were significantly associated with shank length and girth (P<2.98×10^-6), respectively at 5% genome-wide level; 4 and 25 SNPs were suggestive associatied with the two traits (P<5.96×10^-5), respectively. SNPs located at downstream of NKX2-5 and ELAVL4 on chromosome 13 and 8 were signficantly associated with shank length and girth, respectively at 5% genome-wide level. Many SNPs associated with shank length were in 14.93 Mb region (71.01-85.94 Mb) on chromosome 4, and LDB2, BOD1L1 and QDPR were in this region. These genes and regions could be important candidate genes and regions for shank length and girth. The results lay a foundation for revealing the genetic basis and molecular mechanism for shank growth and marker assisted selection in the further.

中图分类号:

S831.2

孙艳发，刘冉冉，郑麦青，赵桂苹，张磊，吴丹，胡耀东，李鹏，文杰. 鸡胫长和胫围的全基因组关联分析[J]. 畜牧兽医学报, doi: .

SUN Yan-fa, LIU Ran-ran, ZHENG Mai-qing, ZHAO Gui-ping, ZHANG Lei, WU Dan, HU Yao-dong, LI Peng, WEN Jie. Genome-wide Association Study on Shank Length and Shank Girth in Chicken[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, doi: .

0
/ / 推荐

导出引用管理器 EndNote|Reference Manager|ProCite|BibTeX|RefWorks

链接本文: https://www.xmsyxb.com/CN/

https://www.xmsyxb.com/CN/Y2013/V44/I3/358

参考文献

［1］魏国辉，张德祥，张细权.优质黄羽肉鸡Lmbr1基因外显子16上TC突变与胫发育等相关性状的关联分析［C］//中国家禽科学研究进展：第十四次全国家禽科学学术讨论会论文集. 哈尔滨: 中国农业科学技术出版社, 2009.

［2］GAO Y, DU Z Q, FENG C G, et al. Identification of quantitative trait loci for shank length and growth at different development stages in chicken ［J］. Anim Genet, 2010, 41(1): 101-104.

［3］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］. Anim Genet, 2010, 41(1): 400-405.

［4］FAN B, DU Z Q, DANIELLE M, et al. Development and application of high-density SNP arrays in genomic studies of domestic animals ［J］. AsianAust J Anim Sci, 2010, 23(7): 833-847.

［5］GROENEN M A M, MEGENS H, ZARE Y, et al. The development and characterization of a 60K SNP chip for chicken ［J］. BMC Genomics, 2011, 12:274.

［6］PURCELL S, NEALE B, TODD-BROWN K, et al. PLINK: a toolset for whole-genome association and population-based linkage analysis ［J］. Am J Hum Genet, 2007, 81(3):559-575.

［7］BRADBURY P J, ZHANG Z W, KROON D E, et al. TASSEL: software for association mapping of complex traits in diverse samples ［J］. Bioinformatics, 2007, 23(19):2633-2635.

［8］ZHANG Z, ERSOZ E, LAI C Q, et al. Mixed linear model approach adapted for genome-wide association studies ［J］.Nat Genet, 2010, 42:355-360.

［9］BARRETT J C, FRY B, MALLER J. Haploview: analysis and visualization of LD and haplotype maps ［J］. Bioinformatics, 2005, 21(2): 263-265.

［10］PRICE A L, PATTERSON N J, PLENGE R M, et al. Principal components analysis corrects for stratification in genomewide association studies ［J］. Nat Genet, 2006, 38: 904-909.

［11］顾晓荣. 影响鸡体重性状QTL的全基因组连锁和关联研究［D］. 北京:中国农业大学, 2011.

［12］PEARSON T A, MANOLIO T A. How to interpret a genome-wide association study ［J］. JAMA, 2008, 299(11): 1335-1344.

［13］VISSCHER P M, BROWN M A, McCARTHY M I, et al. Five years of GWAS discovery ［J］. Am J Hum Genet, 2012, 90: 7-24.

［14］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.

［15］LIU W, LI D, LIU J, et al. A genome-wide SNP scan reveals novel loci for egg production and quality traits in white leghorn and brown-egg dwarf layers ［J］. PLoS ONE, 2011, 6(12):e28600.

［16］XIE L, LUO C, ZHANG C, et al. Genome-wide association study identified a narrow chromosome 1 region associated with chicken growth traits ［J］. PLoS ONE, 2012, 7(2): e30910.

［17］FAN B, ONTERU S K, DU Z Q, et al. Genome-wide association study identifies Loci for body composition and structural soundness traits in pigs ［J］. PLoS ONE, 2011, 6(2): e14726.

［18］UIMARI P, SIRONEN A, SEVON-AIMONEN M L. Whole-genome SNP association analysis of reproduction traits in the Finnish Landrace pig breed ［J］. Genet Sel Evol, 2011, 43:42.

［19］BOUWMAN A C, BOVENHUIS H, VISKER M H P W, et al. Genome-wide association of milk fatty acids in Dutch dairy cattle ［J］. BMC Genet, 2011, 12: 43.

［20］SAHANA G, GULDBRANDTSEN B, LUND M S. Genome-wide association study for calving traits in Danish and Swedish Holstein cattle ［J］. J Dairy Sci, 2011, 11(1): 479-486.

［21］SHIOJIMA I, KOMURO I, INAZAWA J, et al. Assignment of cardiac homeobox gene CSX to human chromosome 5q34 ［J］.Genomics, 1995, 27(1): 204-206.

［22］KANANURA C, HAUG K, SANDER T, et al. A splice-site mutation in GABRG2 associated with childhood absence epilepsy and febrile convulsions ［J］. Arch Neurol, 2002, 59(7):1137-1141.

［23］SAUVAGEAU G, THORSTEINSDOTTIR U, HOUGH M R, et al. Overexpression of HOXB3 in hematopoietic cells causes defective lymphoid development and progressive myeloproliferation ［J］. Immunity, 1997, 6(1):13-22.

［24］SDILLE-MOSTAFAIE N, SEBESTA C, HUBER K R, et al. The role of memory-related gene polymorphisms, KIBRA and CLSTN2, on replicate memory assessment in the elderly ［J］. J Neural Transm, 2012, 119(1):77-80.

［25］NOUREDDINE M A, QIN X J, OLIVEIRA S A, et al. Association between the neuron-specific RNA-binding protein ELAVL4 and Parkinson disease ［J］. Hum Genet, 2005, 117(1):27-33.

［26］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.

［27］吴丹，刘冉冉，赵桂苹，等. 鸡体质量性状基因的全基因组关联研究［J］.畜牧兽医学报, 2012, 43(12): 1887-1896.

[1]	唐鑫鑫, 郑炬梅, 骆娜, 营凡, 朱丹, 李森, 刘大伟, 安炳星, 文杰, 赵桂苹, 李和刚. 基于全基因组关联分析揭示肉鸡腿病发生的遗传机制[J]. 畜牧兽医学报, 2024, 55(1): 99-109.
[2]	徐小静, 董瑞玲, 魏立民, 赵少猛, 赵桂苹, 张敏红, 冯京海. 文昌鸡母鸡生长模型的研究[J]. 畜牧兽医学报, 2023, 54(12): 4952-4961.
[3]	齐丽娜, 陆雪林, 杨凯旋, 周瑾, 李先玉, 刘珂, 张文刚, 顾欣, 章伟建. 基于SNP芯片分析新浦东鸡的遗传多样性和遗传结构[J]. 畜牧兽医学报, 2023, 54(12): 4962-4971.
[4]	王燕星, 张雨时, 姬海港, 刘阳, 牛玉芳, 韩瑞丽, 刘小军, 田亚东, 康相涛, 李转见. 鸡骨骼肌卫星细胞系的建立及分析[J]. 畜牧兽医学报, 2023, 54(12): 4972-4981.
[5]	范晨宇, 单艳菊, 章明, 姬改革, 巨晓军, 屠云洁, 贺喜, 束婧婷, 刘一帆, 张海涵. 立华麻黄鸡体重和肉品质性状全基因组关联分析[J]. 畜牧兽医学报, 2023, 54(12): 4982-4992.
[6]	陈诚, 乔西波, 孙亿, 康丽, 姜运良. 琅琊鸡FSHR基因-868位点的多态性及对产蛋性能的遗传效应研究[J]. 畜牧兽医学报, 2023, 54(11): 4560-4568.
[7]	金四华, 贾富民, 何培莉, 贾羽晴, 税斐, 刘旭玲, 刘星, 王新, 徐嫚, 耿照玉. IHH过表达对鸡原代软骨细胞增殖和分化的影响[J]. 畜牧兽医学报, 2023, 54(11): 4569-4576.
[8]	陈雪娇, 刘会杰, 臧蕾, 冯静, 鹏达, 张浩. 鸡胚心脏组织转录组数据鉴定雪域白鸡高原低氧适应性关键基因[J]. 畜牧兽医学报, 2023, 54(10): 4154-4163.
[9]	张寅梁, 岳巧娴, 黄晨轩, 陈辉, 王德贺, 周荣艳. 产蛋初期和后期蛋鸡胫骨转录谱的构建及骨代谢相关基因分析[J]. 畜牧兽医学报, 2023, 54(10): 4164-4173.
[10]	郑钢, 连玲. 鸡性别决定及分化关键调控基因DMRT1研究进展[J]. 畜牧兽医学报, 2023, 54(8): 3152-3163.
[11]	白露, 王梦杰, 马小春, 何政肖, 谭晓冬, 刘杰, 赵桂苹, 文杰, 刘冉冉. 一种快速挖掘鸡品种特征性SNP标记集合的方法[J]. 畜牧兽医学报, 2023, 54(8): 3252-3261.
[12]	陈春, 康昭风, 魏岳, 黎观红, 武艳平, 谢金防. Wnt3a基因多态性与崇仁麻鸡皮肤毛囊性状相关性研究[J]. 畜牧兽医学报, 2023, 54(7): 2810-2823.
[13]	刘航, 王欢欢, 葛莹, 张雷, 张伟武, 魏莹晖, 李庆海, 范京辉, 章学东. 基于转录组和蛋白组筛选乌骨鸡肤色性状候选基因[J]. 畜牧兽医学报, 2023, 54(6): 2320-2329.
[14]	王辉, 许梦缘, 刘灵康, 郑喜邦, 李恭贺, 吴文德. PhiC31整合酶电穿孔鸡成纤维细胞诱发位点特异性基因盒交换[J]. 畜牧兽医学报, 2023, 54(6): 2330-2342.
[15]	王政, 郭文婕, 程瑾, 原一桐, 罗榕, 薛毅, 张利环, 朱芷葳, 李慧锋. 营养转运相关基因调控区多态性与黄羽肉鸡饲料转化率关联分析[J]. 畜牧兽医学报, 2023, 54(6): 2343-2352.