Microsatellite null alleles affected population genetic analyses: a case study of Maire yew (Taxus chinensis var. mairei)

ABSTRACT

Microsatellite markers are widely used in population genetic analyses. However, the common occurrence of null alleles and their effect on population parameters such as observed heterozygosity, genetic differentiation coefficient, etc., needs to be addressed. Two microsatellite data sets based on original and redesigned primers were used to assess the effect of null alleles on population genetic analyses of Maire yew (Taxus chinensis var. mairei). When amplified with the original primer set, both loci exhibited the presence of null alleles. Four populations significantly deviated from Hardy-Weinberg equilibrium due to heterozygote deficiencies. Once the null alleles were eliminated using new primers, almost all populations were in Hardy-Weinberg equilibrium. Average observed heterozygosity values (He) increased from He = 0.197 to He = 0.497 while the fixation index (F_IS) decreased from F_IS = 0.566 to F_IS = −0.060.Genetic differentiation (F_ST) between populations was more pronounced using the new set of primers (F_ST = 0.221) compared to the original one (F_ST = 0.150). When the original data were corrected for the presence of null alleles using the ENA method, global F_ST was still biased compared to the actual results estimated by the new primer set. Our empirical study on Maire yew populations suggests that null alleles can alter the results of population genetic analyses significantly. This suggests that re-designing new primers or increasing the number of markers may eliminate the effect of the null alleles.

KEYWORDS:

• Null alleles
• microsatellite marker
• population genetic
• Hardy-Weinberg deviation
• Maire yew

Acknowledgments

This work was supported by the National Natural Science Foundation of China under Grant (31470666); JSPS Fellows under Grant (11F00787).Supported by Hunan Provincial Innovation Foundation for Postgraduate. Supported by Scientific Innovation Fund for Graduate of Central South University of Forestry and Technology. Part of the experiment was finished in the forest genetics laboratory of Forestry and Forest Products Research Institute of Japan. We are grateful to Dr. Saneyoshi Ueno for his help with the design of new primers and to Dr. Markus Ruhsam for checking the English.

Disclosure statement

No potential conflict of interest was reported by the authors.

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Additional information

Funding

This work was supported by the National Natural Science Foundation of China (NSFC) [31470666].