Variation block-based genomics method for crop plants.

ABSTRACT:

Background

In contrast with wild species, cultivated crop genomes consist of reshuffled recombination blocks, which occurred by crossing and selection processes. Accordingly, recombination block-based genomics analysis can be an effective approach for the screening of target loci for agricultural traits.

Results

We propose the variation block method, which is a three-step process for recombination block detection and comparison. The first step is to detect variations by comparing the short-read DNA sequences of the cultivar to the reference genome of the target crop. Next, sequence blocks with variation patterns are examined and defined. The boundaries between the variation-containing sequence blocks are regarded as recombination sites. All the assumed recombination sites in

SUBMITTER: Kim YH 

PROVIDER: S-EPMC4229737 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature