Journal article
Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley
Plant Biotechnology Journal, Vol.16(3), pp.760-770
2017
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.
Details
- Title
- Assembly and analysis of a qingke reference genome demonstrate its close genetic relation to modern cultivated barley
- Authors/Creators
- F. Dai (Author/Creator) - Zhejiang UniversityX. Wang (Author/Creator) - Zhejiang UniversityX-Q Zhang (Author/Creator) - Murdoch UniversityZ. Chen (Author/Creator) - Western Sydney UniversityE. Nevo (Author/Creator) - University of HaifaG. Jin (Author/Creator) - Zhejiang UniversityD. Wu (Author/Creator) - Zhejiang UniversityC. Li (Author/Creator) - Murdoch UniversityG. Zhang (Author/Creator) - Zhejiang University
- Publication Details
- Plant Biotechnology Journal, Vol.16(3), pp.760-770
- Publisher
- Blackwell Publishing Inc.
- Identifiers
- 991005542614107891
- Copyright
- © 2017 The Authors
- Murdoch Affiliation
- School of Veterinary and Life Sciences; State Agricultural Biotechnology Centre; Western Barley Genetics Alliance
- Language
- English
- Resource Type
- Journal article
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- Collaboration types
- Domestic collaboration
- International collaboration
- Citation topics
- 3 Agriculture, Environment & Ecology
- 3.4 Crop Science
- 3.4.96 QTL
- Web Of Science research areas
- Biotechnology & Applied Microbiology
- Plant Sciences
- ESI research areas
- Plant & Animal Science