1. Cost-Effective Discovery of Nucleotide Polymorphisms in Populations of an Allopolyploid Species Using Pool-Seq
- Author
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Tanaka Kenta, Rie Shimizu-Inatsugi, Jun Sese, Akira S. Hirao, Kentaro Shimizu, Yoshihiko Onda, and University of Zurich
- Subjects
0106 biological sciences ,0301 basic medicine ,Population genetics ,Individual ,Based Genotyping ,Biology ,010603 evolutionary biology ,01 natural sciences ,UFSP13-7 Evolution in Action: From Genomes to Ecosystems ,10127 Institute of Evolutionary Biology and Environmental Studies ,03 medical and health sciences ,Nucleotide ,Allele ,Gene ,Allele frequency ,High potential ,Arabidopsis kamchatica ,Homeolog ,chemistry.chemical_classification ,Genetics ,Massive parallel sequencing ,Massive Parallel Sequencing ,Allele Frequency ,Psychiatry and Mental health ,030104 developmental biology ,chemistry ,570 Life sciences ,biology ,590 Animals (Zoology) ,Ploidy - Abstract
Population genetics studies of allopolyploid species lag behind those of diploid species because of practical difficulties in analysis of homeologs-duplicated gene copies originating from hybridized parental species. Pool-Seq, i.e. massive parallel sequencing of pooled individuals, has high potential for detecting nucleotide polymorphisms within and among multiple populations; however, its use has been limited to diploid species. We applied Pool-Seq to an allopolyploid species by developing a bioinformatic pipeline that assigns reads to each homeolog as well as to each polymorphic allele within each homeolog. We simultaneously sequenced eight genes from twenty individuals from each of 24 populations, and found over 100 polymorphic sites in each homeolog. For two sites, we estimated allele frequencies using the number of reads and then validated these estimations by making individual-based estimations. Pool-Seq using our bioinformatic pipeline allows efficient evaluation of nucleotide polymorphisms in a large number of individuals, even in allopolyploid species.
- Published
- 2017