Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley

Fei Dai, Xiaolei Wang, Xiao Qi Zhang, Zhonghua Chen, Eviatar Nevo, Gulei Jin, Dezhi Wu, Chengdao Li, Guoping Zhang

Research output: Contribution to journalArticlepeer-review

Abstract

Qingke, the local name of hulless barley in the Tibetan Plateau, is a staple food for Tibetans. The availability of its reference genome sequences could be useful for studies on breeding and molecular evolution. Taking advantage of the third-generation sequencer (PacBio), we de novo assembled a 4.84-Gb genome sequence of qingke, cv. Zangqing320 and anchored a 4.59-Gb sequence to seven chromosomes. Of the 46,787 annotated ‘high-confidence’ genes, 31 564 were validated by RNA-sequencing data of 39 wild and cultivated barley genotypes with wide genetic diversity, and the results were also confirmed by nonredundant protein database from NCBI. As some gaps in the reference genome of Morex were covered in the reference genome of Zangqing320 by PacBio reads, we believe that the Zangqing320 genome provides the useful supplements for the Morex genome. Using the qingke genome as a reference, we conducted a genome comparison, revealing a close genetic relationship between a hulled barley (cv. Morex) and a hulless barley (cv. Zangqing320), which is strongly supported by the low-diversity regions in the two genomes. Considering the origin of Morex from its breeding pedigree, we then demonstrated a close genomic relationship between modern cultivated barley and qingke. Given this genomic relationship and the large genetic diversity between qingke and modern cultivated barley, we propose that qingke could provide elite genes for barley improvement.

Original languageEnglish
Pages (from-to)760-770
Number of pages11
JournalPlant Biotechnology Journal
Volume16
Issue number3
DOIs
StatePublished - Mar 2018

Bibliographical note

Publisher Copyright:
© 2017 The Authors. Plant Biotechnology Journal published by Society for Experimental Biology and The Association of Applied Biologists and John Wiley & Sons Ltd.

Keywords

  • RNA-sequencing
  • genomic contribution
  • hulless barley
  • reference genome
  • third-generation sequencing

ASJC Scopus subject areas

  • Agronomy and Crop Science
  • Biotechnology
  • Plant Science

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