Biodiv Sci ›› 2013, Vol. 21 ›› Issue (1): 117-126.  DOI: 10.3724/SP.J.1003.2013.10133

• Orginal Article • Previous Articles     Next Articles

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


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