Genome-wide SNP and STR discovery in the Japanese crested ibis and genetic diversity among founders of the Japanese population.

ABSTRACT: The Japanese crested ibis is an internationally conserved, critically threatened bird. Captive-breeding programs have been established to conserve this species in Japan. Since the current Japanese population of crested ibis originates only from 5 founders donated by the Chinese government, understanding the genetic diversity between them is critical for an effective population management. To discover genome-wide single nucleotide polymorphisms (SNPs) and short tandem repeats (STRs) while obtaining genotype data of these polymorphic markers in each founder, reduced representation libraries were independently prepared from each of the founder genomes and sequenced on an Illumina HiSeq2000. This yielded 316 million 101-bp reads. Consensus sequences were created by clustering sequence reads, a

SUBMITTER: Taniguchi Y 

PROVIDER: S-EPMC3749161 | biostudies-literature | 2013

REPOSITORIES: biostudies-literature