The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau
- aTibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet 850002, China;
- bBarley Improvement and Yak Breeding Key Laboratory of Tibet Autonomous Region, Lhasa 850002, China;
- cChengdu Institute of Biology, Chinese Academy of Sciences, Chengdu 610041, P. R. China;
- dBGI-Tech, BGI-Shenzhen, Shenzhen 518083, China;
- eCollege of Life Science, University of Chinese Academy of Sciences, Beijing 100049, China;
- fProjects and Physics Section, Sapir Academic College, D.N. Hof Ashkelon 79165, Israel;
- gInstitute of Evolution, University of Haifa, Mount Carmel, Haifa 31905, Israel;
- hBGI-Shenzhen, Shenzhen 518083, China;
- iDepartment of Biology, University of Copenhagen, Copenhagen 2200, Denmark; and
- jPrincess Al Jawhara Center of Excellence in the Research of Hereditary Disorders, King Abdulaziz University, Jeddah 21441, Saudi Arabia
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Contributed by Eviatar Nevo, December 11, 2014 (sent for review September 15, 2014)

Significance
The draft genome of Tibetan hulless barley provides a robust framework to better understand Poaceae evolution and a substantial basis for functional genomics of crop species with a large genome. The expansion of stress-related gene families in Tibetan hulless barley implies that it could be considered as an invaluable gene resource aiding stress tolerance improvement in Triticeae crops. Genome resequencing revealed extensive genetic diversity in Tibetan barley germplasm and divergence to sequenced barley genomes from other geographical regions. Investigation of genome-wide selection footprints demonstrated an adaptive correlation of genes under selection with extensive stressful environmental variables. These results reveal insights into the adaptation of Tibetan hulless barley to harsh environments on the highland and will facilitate future genetic improvement of crops.
Abstract
The Tibetan hulless barley (Hordeum vulgare L. var. nudum), also called “Qingke” in Chinese and “Ne” in Tibetan, is the staple food for Tibetans and an important livestock feed in the Tibetan Plateau. The diploid nature and adaptation to diverse environments of the highland give it unique resources for genetic research and crop improvement. Here we produced a 3.89-Gb draft assembly of Tibetan hulless barley with 36,151 predicted protein-coding genes. Comparative analyses revealed the divergence times and synteny between barley and other representative Poaceae genomes. The expansion of the gene family related to stress responses was found in Tibetan hulless barley. Resequencing of 10 barley accessions uncovered high levels of genetic variation in Tibetan wild barley and genetic divergence between Tibetan and non-Tibetan barley genomes. Selective sweep analyses demonstrate adaptive correlations of genes under selection with extensive environmental variables. Our results not only construct a genomic framework for crop improvement but also provide evolutionary insights of highland adaptation of Tibetan hulless barley.
Footnotes
↵1X.Z., H.L., Z.W., S.Z., Y.T., Z.H., and Y.W. contributed equally to this work.
- ↵2To whom correspondence may be addressed. Email: nima_zhaxi{at}sina.com, nevo{at}research.haifa.ac.il, yumaoqun{at}cib.ac.cn, or wangj{at}genomics.org.cn.
Author contributions: M.Y., J.W., and N.T. designed research; X.Z., H.L., Y.T., Y.W., Q.X., H.Y., R.L., Q.W., D.D., Z.L., X.T., and L.G. performed research; L.B. and X. Lv coordinated the project; H.L., Z.W., S.Z., Z.H., L.M., G.D., X.Y., X. Li, L.B., Z.P., X.C., M.C., L.Y., J. Liang, Y.Z., S.Y., X.G., J. Li, C.D., W.H., C.C., X. Lv, Y.B.A., X.F., and E.N. analyzed data; and H.L., S.Z., Z.H., E.N., and N.T. wrote the paper.
The authors declare no conflict of interest.
Data deposition: The sequences reported in this paper have been deposited in the Sequence Read Archive, www.ncbi.nlm.nih.gov/sra (accession no. SRA201388).
This article contains supporting information online at www.pnas.org/lookup/suppl/doi:10.1073/pnas.1423628112/-/DCSupplemental.
Freely available online through the PNAS open access option.