The 81st Annual Meeting of the American Association of Physical Anthropologists (2012)

Developing STR loci for snub-nosed monkeys (Rhinopithecus roxellana) using next-generation sequencing technology


1Department of Anthropology, University of Illinois at Urbana-Champaign, 2W. M. Keck Center, University of Illinois at Urbana-Champaign

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Simple tandem repeats (STRs) are widely used to estimate genetic variation, population structure, and relatedness in wild species. However, developing STR systems are time consuming, especially for species where little is known about its genome. In this study, we describe a protocol of generating a large number of candidate STR loci quickly and cost-efficiently for a non-model species, snub-nosed monkeys using next-generation sequencing technology. First, we built a reduced representation library for snub-nosed monkeys. We digested the DNA of four individuals using HaeIII and pooled the 350-500bp fragments together. Second, we sequenced the DNA pool using pyrosequencing technology. We obtained 275,618 reads (330bp per read) from a single run of ΒΌ region of a titanium plate. Third, we used the program Msatcommander to detect STRs in the sequence dataset. This program reports the name of the sequence read, repeat type, repeat number, as well as the start and end positions of the repeat region. Using a script written for this study, we examined the output file reported by Msatcommander and detected 10 polymorphic STR loci. Furthermore, based on the assumption that STR loci with long repeats (> 9) are likely to be polymorphic, we detected 347 candidate STR loci, which are distributed across all autosomes and X chromosome. We validated two candidate loci by genotyping these two loci in 20 individuals. The confirmed polymorphic STRs can be put to use immediately and the large number of candidate loci can be easily screened for polymorphism and linkage for future use.

This project was supported by a National Science Foundation Dissertation Improvement Grant (BCS-0824466).

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