Xingquan Zeng, Hai Long, Zhuo Wang, Shancen Zhao, Yawei Tang, Zhiyong Huang, Yulin Wang, Qijun Xu, Likai Mao, Guangbing Deng, Xiaoming Yao, Xiangfeng Li, Lijun Bai, Hongjun Yuan, Zhifen Pan, Renjian Liu^b, Xin Chen, QiMei WangMu, Ming Chen, Lili Yu, Junjun Liang, DaWa DunZhu, Yuan Zheng, Shuiyang Yu, ZhaXi LuoBu, Xuanmin Guang, Jiang Li, Cao Deng, Wushu Hu^d, Chunhai Chen, XiongNu TaBa, Liyun Gao, Xiaodan Lv, Yuval Ben Abu, Xiaodong Fang, Eviatar Nevo, Maoqun Yu, Jun Wang, and Nyima Tashi

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.

See: http://www.pnas.org/content/112/4/1095.abstract.html?etoc

PNAS January 27 2015, Vo.112; no.4: 1095-1100  

Fig. 1.

Overview of Tibetan hulless barley genome. (Track a) Gene regions of cultivated barley cv. Morex (%) per 10 Mb—min., 0; max., 10. (Track b) Gene regions of Tibetan hulless barley (%) per 10 Mb—min., 0; max., 10. (Track c) LTR retro-transposon (%) per 10 Mb—min., 0; max., 100. (Track d) Synteny with the B. distachyon genome. (Track e) Tibetan hulless barley chromosomes with centromeres marked as black bands. (Track f) Syntenic blocks within and between chromosomes.

Fig. 2.

Phylogeny, WGD, and gene families of Tibetan hulless barley compared with other plant genomes. (A) The divergence time tree estimated on fourfold degenerate sites of single-copy orthologous genes. (B) WGD and divergence of Tibetan hulless barley indicated by 4DTv (deviation at the fourfold degenerate third codon position) distribution. (C) Chromosomal syntenic relationship between Tibetan hulless barley and wheat A- and D-genome progenitors. (D) Gene families of H. vulgare, T. urartu, T. aestivum, Ae.tauschii, and B. distachyon. (E) Gene families of Ehrhardtoideae, Bambusoideae, Pooideae, and Panicoideae