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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.
Tibetan barley genome reveals highland adaption
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