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


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
Issue number3
StatePublished - Mar 2018

Bibliographical note

Funding Information:
This work is supported by the National Natural Science Foundation of China (NSFC) grant 31471480 to F.D., NSFC grant 31620103912 to G.Z., the Natural Science Foundation of Zhejiang Province grant LR15C130001 to F.D., the Fundamental Research Funds for the Central Universities to F.D. and G.Z., and the Jiangsu Collaborative Innovation Center for Modern Crop Production. We thank Professor Timothy Close (University of California, Riverside, USA), Dr. Nils Stein and Dr. Martin Mascher (Leibniz Institute of Plant Genetics and Crop Plant Research, Germany), Dr. Robbie Waugh (The James Hutton Institute, UK), Dr. Ilka Braumann (Carlsberg Research Laboratory, Denmark), Professor Mats Hansson (Lund University, Sweden) and other members of the International Barley Genome Sequencing Consortium ( for providing prepublication access to the genome sequence data set of Morex. We thank Ms. Zheying Wang (Hangzhou Guhe Information and Technology Co., Ltd), Ms. Sanling Wu (Zhejiang University, China) and Dr. Andrea Braeutigam (Leibniz Institute of Plant Genetics and Crop Plant Research, Germany) for their assistance in sequencing and bioinformatics analysis. We thank Dr. Ganggang Guo (Institute of Crop Science, Chinese Academy of Agricultural Sciences) for providing seeds of qingke.

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.


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

ASJC Scopus subject areas

  • Biotechnology
  • Agronomy and Crop Science
  • Plant Science


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