生物多样性 ›› 2013, Vol. 21 ›› Issue (1): 117-126.DOI: 10.3724/SP.J.1003.2013.10133

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微卫星标记中的无效等位基因

文亚峰1,2,*(), KentaroUchiyama2, 韩文军1, SaneyoshiUeno2, 谢伟东3, 徐刚标1, YoshihikoTsumura2   

  1. 1 中南林业科技大学林学院, 长沙 410004
    2 日本森林综合研究所, 日本筑波 305-8687
    3 广西大学林学院, 南宁 530004
  • 收稿日期:2012-06-20 接受日期:2012-09-04 出版日期:2013-01-20 发布日期:2013-02-04
  • 通讯作者: 文亚峰
  • 基金资助:
    国家林业公益性行业科研专项(201104033);湖南省自然科学基金重点项目(10JJ2018);湖南省教育厅重点项目(09A103);日本JSPS特别研究员资助项目(11F00787)

Null alleles in microsatellite markers

Yafeng Wen1,2,*(), Kentaro Uchiyama2, Wenjun Han1, Saneyoshi Ueno2, Weidong Xie3, Gangbiao Xu1, Yoshihiko Tsumura2   

  1. 1 College of Forestry, Central South University of Forestry and Technology, Changsha 410004, China
    2 Forestry and Forest Products Research Institute, Tsukuba 305-8687, Japan
    3 College of Forestry, Guangxi University, Nanning 530004, China
  • Received:2012-06-20 Accepted:2012-09-04 Online:2013-01-20 Published:2013-02-04
  • Contact: Wen Yafeng

摘要:

微卫星标记以其独有的优点广泛应用于遗传学研究, 但无效等位基因(null alleles)的存在与潜在影响是其最大缺陷之一, 在研究工作中并未得到足够重视。本文在综述国内外相关文献的基础上, 明确了微卫星无效等位基因的概念与特点, 对其可能的产生原因、频率估算方法、相关分析软件及其对群体遗传学、亲本分析等研究结果的影响进行述评, 以期对无效等位基因有较为全面、深入的了解。微卫星无效等位基因的产生与SSR侧翼序列的变异(点突变、插入或缺失)及引物结合位点有关, 其与同工酶标记中的无效等位基因有本质区别, 并非基因本身的自然属性。虽然微卫星无效等位基因具有普遍性、复杂性和隐匿性等特点, 但完全可以通过Hardy-Weinberg平衡检验、亲子代基因型分析和重新设计引物等方法认识、检测并估算其频率。无效等位基因会对遗传学相关研究结果造成显著影响, 如降低群体遗传多样性, 加大群体间遗传分化; 降低亲本分析排除率, 甚至可能造成亲本分析结果的错误与混乱。今后研究工作中, 我们应对无效等位基因予以足够重视并谨慎对待, 从标记位点选择、无效等位基因数据调整及重新设计引物分析等多个方面尽可能减少和避免其影响, 以获得最真实的分析结果。

关键词: 无效等位基因, 微卫星标记, 等位基因频率, Hardy-Weinberg平衡

Abstract

Microsatellite markers are widely used in genetic analysis, but the common occurrence of null alleles, is an unfortunate drawback, and one which has not been paid enough attention. In this review, we confirm the concept of null alleles and their characteristics, detail methods for estimating the frequency of null alleles and discuss potential causes. We also consider the effect of null alleles on genetic studies, such as measurement of population genetic diversity, parentage analysis and assignment tests. The review has a certain reference value for future studies. One main cause of microsatellite null alleles is poor primer annealing due to nucleotide sequence divergence (point mutations or indels) in one or both flanking primers. Microsatellite null alleles are not a natural characteristic of a specific gene, and are essentially different from isozyme null alleles. Although microsatellite null alleles have the characteristics of universality, complexity and invisibility, we can test and estimate their frequency through multiplex approaches, using Hardy-Weinberg equilibrium tests, parent-offspring genotype analysis, and new primer design. Null alleles have significant effects on the results of genetic analysis, potentially decreasing population genetic diversity and increasing genetic differentiation among populations. Moreover, null alleles may decrease the probability of parentage exclusion, even leading to errors or confusion in parentage analysis. Null alleles should be paid more attention and demand caution in future studies. Through a variety of methods, such as locus selection, null allele data adjustment, and the design of new primers, we can escape the adverse effects of null alleles and achieve greater accuracy in genetic analysis.

Key words: null alleles, microsatellite markers, allele frequency, Hardy-Weinberg equilibrium