High-throughput targeted SNP discovery using Next Generation Sequencing (NGS) in few selected candidate genes in Eucalyptus camaldulensis

Abstract

Background The present era of high throughput technologies offer immense promise and innovative applications for SNP discovery and high quality parallel genotyping [1,2]. Using advancements in the next generation sequencing (NGS) technologies, the en masse SNP discovery for targeted genomic regions is possible for eucalypts. The river red gum or Eucalyptus camaldulensis (Ec) is a fast growing, hardy and highly adaptable eucalypt species acclimatized to Indian climatic conditions and these new advancements would aid in developing new tools and techniques for its improvement. In our knowledge, limited efforts have been undertaken to identify SNP markers in eucalypts either by employing RNA sequencing [3] or by using few genes available in the literature [4]. Despite these miniscule efforts, useful SNP markers were discovered in Cinnamoyl CoA Reductase (CCR) gene with potential application [5]. Using the recently released whole genome sequence of E. grandis (Eg), herein we describe targeted SNP discovery in 41 candidate genes by employing Illumina’s 72-bases paired end sequencing technology.