Genotyping-by-Sequencing SNP Identification for Crops without a Reference Genome: Using Transcriptome Based Mapping as an Alternative Strategy.

ABSTRACT: Next-generation sequencing opens the way for genomic studies of diversity even for non-model crops and animals. Genome reduction techniques are becoming progressively more popular as they allow a fraction of the genome to be sequenced for multiple individuals and/or populations. These techniques are an efficient way to explore genome diversity in non-model crops and animals for which no reference genome is available. Genome reduction techniques emerged with the development of specific pipelines such as UNEAK (Universal Network Enabled Analysis Kit) and Stacks. However, even for non-model crops and animals, transcriptomes are easier to obtain, thereby making it possible to directly map reads. We investigate the direct use of transcriptome as an alternative strategy. Our specific objective w

SUBMITTER: Berthouly-Salazar C 

PROVIDER: S-EPMC4908121 | biostudies-literature | 2016

REPOSITORIES: biostudies-literature