Single-nucleotide polymorphism discovery by high-throughput sequencing in sorghum.

ABSTRACT:

Background

Eight diverse sorghum (Sorghum bicolor L. Moench) accessions were subjected to short-read genome sequencing to characterize the distribution of single-nucleotide polymorphisms (SNPs). Two strategies were used for DNA library preparation. Missing SNP genotype data were imputed by local haplotype comparison. The effect of library type and genomic diversity on SNP discovery and imputation are evaluated.

Results

Alignment of eight genome equivalents (6 Gb) to the public reference genome revealed 283,000 SNPs at ≥82% confirmation probability. Sequencing from libraries constructed to limit sequencing to start at defined restriction sites led to genotyping 10-fold more SNPs in all 8 accessions, and correctly imputing 11% more missing data, than from semirandom libraries.

SUBMITTER: Nelson JC 

PROVIDER: S-EPMC3146956 | biostudies-literature | 2011 Jul

REPOSITORIES: biostudies-literature