鸡16号染色体SNP单倍型和拷贝数变异对血清IgG含量的影响

doi:10.11843/j.issn.0366-6964.2013.09.004

畜牧兽医学报 ›› 2013, Vol. 44 ›› Issue (9): 1355-1362.doi: 10.11843/j.issn.0366-6964.2013.09.004

鸡16号染色体SNP单倍型和拷贝数变异对血清IgG含量的影响

周伟^1,2，刘冉冉¹，郑麦青¹，文杰^{1, 2}，赵桂苹^1*，陈国宏^2*，常国斌²，张磊¹，孙艳发^1,2，李鹏¹，孙艳¹

(1.中国农业科学院北京畜牧兽医研究所，动物营养学国家重点实验室，北京 100193；2.扬州大学动物科学与技术学院，扬州 225009）

收稿日期:2013-03-15 出版日期:2013-09-23 发布日期:2013-09-23
通讯作者: 赵桂苹，研究员，主要从事家禽育种研究，E-mail：zhaoguiping@caas.cn；陈国宏，教授，主要从事家禽育种研究，E-mail：ghchen@yzu.edu.cn
作者简介:周伟（1987-），男，安徽濉溪人，硕士，主要从事家禽育种研究，E-mail：abcxiaowei2008@126.com
基金资助:
中央级公益性科研院所基本科研业务费增量项目（2012ZL068）；农业产业技术体系项目（nycytx-42）

Haplotypes and Copy Number Variation of Genome in Chromosome 16 and Their Association with IgG Level in Chickens

ZHOU Wei^1,2, LIU Ran-ran¹, ZHENG Mai-qing¹, WEN Jie^1,2, ZHAO Gui-ping^1*,CHEN Guo-hong^2*, CHANG Guo-bin², ZHANG Lei¹, SUN Yan-fa^1,2, LI Peng¹, SUN Yan¹

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

Received:2013-03-15 Online:2013-09-23 Published:2013-09-23

摘要/Abstract

摘要：

旨在探讨鸡16号染色体SNP单倍型和拷贝数变异（Copy number variation，CNV）对血清IgG含量的影响。采用鸡60 K SNP芯片对995只北京油鸡进行分型，同时测定80日龄IgG含量。分别采用PennCNV、Haploview 4.1和PHASE 2.0软件对拷贝数变异、连锁不平衡、单倍型分析及与IgG的关联分析。结果发现，该区域存在2个单倍型块和2个拷贝数变异区。Block1（59 984~73 717 bp）单倍型分析发现3种单倍型和6种双倍型，其中双倍型H1H2血清中IgG含量是H3H3的1.45倍（P<0.05）；Block2（102 256~138 076 bp）内发现9种单倍型和9种常见双倍型，不同型之间差异不显著（P>0.05）。CNV1（6 471~59 984 bp）是稀有型拷贝数变异区；CNV2（201 882~299 166 bp）缺失型IgG含量是增加型的1.25倍（P<0.05）。分析挑选出8个与IgG抗体含量相关的SNP位点，结果发现Gga_rs16057310、Gga_rs15788237及Gga_rs15788101不同基因型之间差异显著（P<0.05）。结果表明：Block1和拷贝数变异CNV2（201 882~299 166 bp）及SNP位点Gga_rs16057310、Gga_rs15788237、Gga_rs15788101对IgG含量有显著影响，位于这些区域附近含有CD1b、TRIM27、ZNF692及MHC与免疫机能相关的重要基因。

Abstract:

This study was performed to examine the haplotypes and copy number variation (CNV) of genome in chromosome 16 of Beijing-You chicken and their association with IgG level. A total of 995 chickens were genotyped using 60 K Beadchip and IgG level were measured at 80 d in serum. PennCNV, Haploview 4.1 and PHASE 2.0 were used to analyze CNV, linkage disequilibrium (LD) and haplotypes. The results represent two CNVs and two Blocks. In Block1, three haplotypes and six diplotypes were observed where IgG level of H1H2 was 1.45 times as H3H3 (P<0.05). In Block2, nine haplotypes and nine normal diplotypes were analyzed, but no significant difference were identified (P>0.05). Detection of copy number variations at GGA16（201 882-299 166 bp）was 1.25 times as that of the duplication of this region (P<0.05). Eight SNPs markers were chosen for analysis. The SNP markers Gga_rs16057310, Gga_rs15788237 and Gga_rs15788101 were significantly differed in IgG level among genotypes (P<0.05). In all, Block1, CNV2 (201 882-299 166 bp) and SNPs Gga_rs16057310, Gga_rs15788101, Gga_rs15788237 may be influenced on IgG level. The genes in these regions such as CD1b, TRIM27,ZNF692 and MHC could be related with chicken immunity function.

中图分类号:

S831.2

周伟，刘冉冉，郑麦青，文杰，赵桂苹，陈国宏，常国斌，张磊，孙艳发，李鹏，孙艳. 鸡16号染色体SNP单倍型和拷贝数变异对血清IgG含量的影响[J]. 畜牧兽医学报, 2013, 44(9): 1355-1362.

ZHOU Wei, LIU Ran-ran, ZHENG Mai-qing, WEN Jie, ZHAO Gui-ping,CHEN Guo-hong, CHANG Guo-bin, ZHANG Lei, SUN Yan-fa, LI Peng, SUN Yan. Haplotypes and Copy Number Variation of Genome in Chromosome 16 and Their Association with IgG Level in Chickens[J]. ACTA VETERINARIA ET ZOOTECHNICA SINICA, 2013, 44(9): 1355-1362.

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鸡16号染色体SNP单倍型和拷贝数变异对血清IgG含量的影响

Haplotypes and Copy Number Variation of Genome in Chromosome 16 and Their Association with IgG Level in Chickens

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