畜牧兽医学报 ›› 2016, Vol. 47 ›› Issue (2): 268-275.doi: 10.11843/j.issn.0366-6964.2016.02.008

• 遗传繁育 • 上一篇    下一篇

利用SNP标记估计西门塔尔牛亲缘关系系数的准确性

张静静1,2,高会江2,吴洋2,朱波2,齐欣2,高雪2,张路培2,陈燕2*   

  1. (1.吉林农业大学动物科技学院,长春 130118; 2.中国农业科学院北京畜牧兽医研究所,北京 100193)
  • 收稿日期:2015-03-30 出版日期:2016-02-23 发布日期:2016-02-23
  • 通讯作者: 陈燕,E-mail:chenyan@caas.cn
  • 作者简介:张静静(1989-),女,山东莘县人,硕士,主要从事动物遗传育种与繁殖研究,E-mail:zhang_jingjing89@163.com
  • 基金资助:

    国家自然科学基金(31402039);北京市自然科学基金(6154032);中国农业科学院基本科研业务费(2014ywf-yb-4);农业部物种资源保护(畜禽)项目(F557);中国农业科学院科技创新工程经费(cxgc-ias-03);科技支撑计划(2011BAD28B04);863项目(2013AA102505-4);中国农业科学院院本级增量业务费(2013ZL031)

Estimation of the Kinship Coefficient in Simmental Cattle Based on SNP Markers

ZHANG Jing-jing1,2,GAO Hui-jiang2,WU Yang2,ZHU Bo2,QI Xin2,GAO Xue2,ZHANG Lu-pei2,CHEN Yan2*   

  1. (1.College of Animal Science and Technology,Jilin Agricultural University,Changchun 130118,China;2.Institute of Animal Science,Chinese Academy of Agricultural Sciences,Beijing 100193,China)
  • Received:2015-03-30 Online:2016-02-23 Published:2016-02-23

摘要:

本研究旨在利用SNP标记估计西门塔尔牛亲缘关系系数,以期准确确定估计个体间亲缘关系系数所需的SNPs数量。研究以1 059头出生于2008-2012年的西门塔尔牛为试验群体,利用Illumina bovineHD(770 k)芯片,根据最小等位基因频率(MAF)区间,分别选择100、500、1 000、1 500、2 000、2 500和3 000 个SNPs用于个体间亲缘关系系数的估计。结果显示,随着标记数目的增多,估计的亲缘关系系数准确性逐渐增加。且当SNP标记数目达到2 500时,所估计的亲缘关系系数与利用所有标记估计的个体间亲缘关系系数差异不显著,二者相关系数达到0.89 以上。同时,利用不同等位基因频率区间内标记估计的个体间亲缘关系系数差异不显著。由此可以看出,当所选标记数目达到2 500以上时,可以得到较高的亲缘关系系数估计准确性。本研究为基于SNP标记信息估计亲缘关系系数的进一步研究提供了理论基础,同时为西门塔尔牛群体个体间亲缘关系的研究提供依据。

Abstract:

The objective of the study was to determine the number of SNPs which could efficiently estimate the kinship coefficient in Simmental cattle.1 059 Simmental cattle born between 2008 and 2012 year were used as the reference population.Based on the interval of the minor allele frequency (MAF),100,500,1 000,1 500,2 000,2 500 and 3 000 SNPs located in Illumina bovineHD(770 k)chip were selected to estimate individual kinship coefficient.The results showed that with the increase of the SNPs’ number,the estimation accuracy showed an increasing trend as well.Especially,when the SNPs’ number reached to 2 500,there was no significant difference between relationship coefficients estimated using 2 500 SNPs and all SNPs,and the relationship coefficients were above 0.89 between them.Furthermore,the SNPs in the same interval with different allele frequency had no significant impact on the results.It was concluded that when the number of selected SNPs reached more than 2 500,a relatively higher estimation accuracy could be obtained.Our work has built a theoretical basis for further study of the kinship coefficient with high density SNP and provides a new clue for analyzing individual kinship relationship in Simmental cattle.

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