Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley

Kotaro Takahagi, Yukiko Uehara-Yamaguchi, Takuhiro Yoshida, Tetsuya Sakurai, Kazuo Shinozaki, Keiichi Mochida, Daisuke Saisho

Research output: Contribution to journalArticle

6 Citations (Scopus)

Abstract

Barley is one of the founder crops of Old world agriculture and has become the fourth most important cereal worldwide. Information on genome-scale DNA polymorphisms allows elucidating the evolutionary history behind domestication, as well as discovering and isolating useful genes for molecular breeding. Deep transcriptome sequencing enables the exploration of sequence variations in transcribed sequences; such analysis is particularly useful for species with large and complex genomes, such as barley. In this study, we performed RNA sequencing of 20 barley accessions, comprising representatives of several biogeographic regions and a wild ancestor. We identified 38,729 to 79,949 SNPs in the 19 domesticated accessions and 55,403 SNPs in the wild barley and revealed their genome-wide distribution using a reference genome. Genome-scale comparisons among accessions showed a clear differentiation between oriental and occidental barley populations. The results based on population structure analyses provide genome-scale properties of sub-populations grouped to oriental, occidental and marginal groups in barley. Our findings suggest that the oriental population of domesticated barley has genomic variations distinct from those in occidental groups, which might have contributed to barley's domestication.

Original languageEnglish
Article number33199
JournalScientific Reports
Volume6
DOIs
Publication statusPublished - Sep 12 2016

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single nucleotide polymorphism
sequence analysis
barley
genome
domestication
transcriptomics
population structure
ancestry
genetic polymorphism
agriculture
genomics
history
breeding
DNA
crops
genes

ASJC Scopus subject areas

  • General

Cite this

Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. / Takahagi, Kotaro; Uehara-Yamaguchi, Yukiko; Yoshida, Takuhiro; Sakurai, Tetsuya; Shinozaki, Kazuo; Mochida, Keiichi; Saisho, Daisuke.

In: Scientific Reports, Vol. 6, 33199, 12.09.2016.

Research output: Contribution to journalArticle

Takahagi, Kotaro ; Uehara-Yamaguchi, Yukiko ; Yoshida, Takuhiro ; Sakurai, Tetsuya ; Shinozaki, Kazuo ; Mochida, Keiichi ; Saisho, Daisuke. / Analysis of single nucleotide polymorphisms based on RNA sequencing data of diverse bio-geographical accessions in barley. In: Scientific Reports. 2016 ; Vol. 6.
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