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Identification and characterization of polymorphic Alu insertions in the Tibetan macaque (Macaca thibetana)

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Abstract

Young Alu elements that have been inserted recently in macaque genomes are still polymorphic for insertion presence/absence at the individual and population levels. They have been considered as a powerful tool in population genetics of primates. Combining a computational approach and a PCR display method based on primers of OWM-specific Alu subfamilies, in the present study, we identified and characterized 26 novel Alu insertions that are polymorphic in the Tibetan macaque (Macaca thibetana). Along with 20 previously reported loci, a total of 96 Alu insertions were found to be present in the Tibetan macaque but absent in rhesus macaques (Macaca mulatta) as validated by computational methods. After PCR verification, 27.1 % (26/96) of the analyzed insertions were confirmed to be heterozygous among Tibetan macaque individuals. These 26 newly identified loci were further genotyped in 41 individuals from two Tibetan macaque populations. The average allele frequencies across the 26 loci varied from 2.4 to 48.8 % in the two populations. The average expected heterozygosity per locus ranged from 25.3 to 50.6 %. The results indicate that the combination of a computational approach and a PCR display method is an efficient way to identify young polymorphic Alu insertions in macaques, and the newly identified polymorphic loci represent valuable genetic markers for the study of Tibetan macaque population genetics in the future.

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Acknowledgments

We are grateful to Prof. Xu Huailiang in Sichuan Agricultural University for providing samples, Prof. Timothy Moermond in Sichuan University for English revision. This research was funded by the National Natural Science Foundation of China (No. 31270431), this Project Sponsored by the Scientific Research Foundation for the Returned Overseas Scholars, State Education Ministry (20111568-8-3).

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Authors and Affiliations

  1. Key Laboratory of Bioresources and Ecoenvironment (Ministry of Education), College of Life Sciences, Sichuan University, Chengdu, 610064, Sichuan, China

    Huawei Guo, Juan Jiang, Yaoyao Cui, Bisong Yue & Jing Li

  2. Experimental Animal Institute of Sichuan Academy of Medical Sciences and Sichuan Provincial People’s Hospital, Chengdu, 610212, Sichuan, China

    Yong Yi & Hongxing Wang

  3. College of Resource and Environmental Engineering, Mianyang Normal University, Mianyang, 621000, Sichuan, China

    Xiaodong Jia

Authors
  1. Huawei Guo
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  2. Juan Jiang
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  3. Yaoyao Cui
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  4. Yong Yi
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  5. Xiaodong Jia
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  6. Hongxing Wang
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  7. Bisong Yue
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  8. Jing Li
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Corresponding author

Correspondence to Jing Li.

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Communicated by M. Scandura

Huawei Guo and Juan Jiang contributed equally to the work.

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Guo, H., Jiang, J., Cui, Y. et al. Identification and characterization of polymorphic Alu insertions in the Tibetan macaque (Macaca thibetana). Eur J Wildl Res 61, 143–149 (2015). https://doi.org/10.1007/s10344-014-0887-z

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  • DOI: https://doi.org/10.1007/s10344-014-0887-z

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