Genome-wide SNP discovery in walnut with an AGSNP pipeline updated for SNP discovery in allogamous organisms.

ABSTRACT:

Background

A genome-wide set of single nucleotide polymorphisms (SNPs) is a valuable resource in genetic research and breeding and is usually developed by re-sequencing a genome. If a genome sequence is not available, an alternative strategy must be used. We previously reported the development of a pipeline (AGSNP) for genome-wide SNP discovery in coding sequences and other single-copy DNA without a complete genome sequence in self-pollinating (autogamous) plants. Here we updated this pipeline for SNP discovery in outcrossing (allogamous) species and demonstrated its efficacy in SNP discovery in walnut (Juglans regia L.).

Results

The first step in the original implementation of the AGSNP pipeline was the construction of a reference sequence and the identification of single-c

SUBMITTER: You FM 

PROVIDER: S-EPMC3527177 | biostudies-literature | 2012 Jul

REPOSITORIES: biostudies-literature