Developing SNPs and STR DNA markers for snub-nosed monkeys (Rhinopithecus roxellana) using next-generation sequencing technology

Caie Yan, Milena R. Shattuck, Jyothi Thimmapuram, Deepika Vullaganti, Ripan Malhi

Research output: Contribution to journalArticle

Abstract

In this study, we describe a protocol of generating a large number of candidate SNPs and STR loci quickly and cost-efficiently for an endangered species, snub-nosed monkeys (Rhinopithecus roxellana), using next-generation sequencing technology. First, we built a reduced representation library of snub-nosed monkeys through digesting the DNA of four individuals using HaeIII and pooling the 350-500 bp fragments together. Second, we sequenced the DNA pool using pyrosequencing technology. Third, we analyzed sequencing reads using bioinformatic software. We detected 23 putative SNPs, 10 polymorphic STR loci, and 347 candidate STR loci (number of repeats greater than 9). The markers generated by this study can be used to address questions regarding genetic diversity, population structure, phylogeography, and conservation of this endangered primate.

Original languageEnglish (US)
Pages (from-to)451-453
Number of pages3
JournalConservation Genetics Resources
Volume4
Issue number2
DOIs
StatePublished - Dec 1 2012

Keywords

  • Pyrosequencing
  • Rhinopithecus roxellana
  • SNP
  • STR

ASJC Scopus subject areas

  • Ecology, Evolution, Behavior and Systematics
  • Genetics

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