The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

Xingquan Zenga; 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; Xin Chen; Qi Mei WangMu; Ming Chen; Lili Yu; Junjun Liang; Da Wa DunZhu; Yuan Zheng; Shuiyang Yu; Zha Xi LuoBu; Xuanmin Guang; Jiang Li; Cao Deng; Wushu Hu; Chunhai Chen; Xiong Nu TaBa; Liyun Gao; Xiaodan Lv; Yuval Ben Abu; Xiaodong Fang; Eviatar Nevo; Maoqun Yu; Jun Wang; Nyima Tashi

doi:10.1073/pnas.1423628112

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

Xingquan Zenga, 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, Xin Chen, Qi Mei WangMu, Ming Chen, Lili YuJunjun Liang, Da Wa DunZhu, Yuan Zheng, Shuiyang Yu, Zha Xi LuoBu, Xuanmin Guang, Jiang Li, Cao Deng, Wushu Hu, Chunhai Chen, Xiong Nu TaBa, Liyun Gao, Xiaodan Lv, Yuval Ben Abu, Xiaodong Fang, Eviatar Nevo, Maoqun Yu, Jun Wang, Nyima Tashi

Department of Evolutionary and Environmental Biology

Research output: Contribution to journal › Article › peer-review

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.

Original language	English
Pages (from-to)	1095-1100
Number of pages	6
Journal	Proceedings of the National Academy of Sciences of the United States of America
Volume	112
Issue number	4
DOIs	https://doi.org/10.1073/pnas.1423628112
State	Published - 27 Jan 2015

Keywords

Adaptation
Genetic diversity
Selective sweep
Tibetan hulless barley
Triticeae evolution

ASJC Scopus subject areas

General

UN SDGs

This output contributes to the following UN Sustainable Development Goals (SDGs)

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10.1073/pnas.1423628112

Cite this

Zenga, X., Long, H., Wang, Z., Zhao, S., Tang, Y., Huang, Z., Wang, Y., Xu, Q., Mao, L., Deng, G., Yao, X., Li, X., Bai, L., Yuan, H., Pan, Z., Liu, R., Chen, X., WangMu, Q. M., Chen, M., ... Tashi, N. (2015). The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau. Proceedings of the National Academy of Sciences of the United States of America, 112(4), 1095-1100. https://doi.org/10.1073/pnas.1423628112

@article{68d07e8e66ac419bbff4dc1601da66a7,

title = "The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau",

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.",

keywords = "Adaptation, Genetic diversity, Selective sweep, Tibetan hulless barley, Triticeae evolution",

author = "Xingquan Zenga and Hai Long and Zhuo Wang and Shancen Zhao and Yawei Tang and Zhiyong Huang and Yulin Wang and Qijun Xu and Likai Mao and Guangbing Deng and Xiaoming Yao and Xiangfeng Li and Lijun Bai and Hongjun Yuan and Zhifen Pan and Renjian Liu and Xin Chen and WangMu, {Qi Mei} and Ming Chen and Lili Yu and Junjun Liang and DunZhu, {Da Wa} and Yuan Zheng and Shuiyang Yu and LuoBu, {Zha Xi} and Xuanmin Guang and Jiang Li and Cao Deng and Wushu Hu and Chunhai Chen and TaBa, {Xiong Nu} and Liyun Gao and Xiaodan Lv and Abu, {Yuval Ben} and Xiaodong Fang and Eviatar Nevo and Maoqun Yu and Jun Wang and Nyima Tashi",

year = "2015",

month = jan,

day = "27",

doi = "10.1073/pnas.1423628112",

language = "English",

volume = "112",

pages = "1095--1100",

journal = "Proceedings of the National Academy of Sciences of the United States of America",

issn = "0027-8424",

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Zenga, X, Long, H, Wang, Z, Zhao, S, Tang, Y, Huang, Z, Wang, Y, Xu, Q, Mao, L, Deng, G, Yao, X, Li, X, Bai, L, Yuan, H, Pan, Z, Liu, R, Chen, X, WangMu, QM, Chen, M, Yu, L, Liang, J, DunZhu, DW, Zheng, Y, Yu, S, LuoBu, ZX, Guang, X, Li, J, Deng, C, Hu, W, Chen, C, TaBa, XN, Gao, L, Lv, X, Abu, YB, Fang, X, Nevo, E, Yu, M, Wang, J & Tashi, N 2015, 'The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau', Proceedings of the National Academy of Sciences of the United States of America, vol. 112, no. 4, pp. 1095-1100. https://doi.org/10.1073/pnas.1423628112

TY - JOUR

T1 - The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

AU - Zenga, Xingquan

AU - Long, Hai

AU - Wang, Zhuo

AU - Zhao, Shancen

AU - Tang, Yawei

AU - Huang, Zhiyong

AU - Wang, Yulin

AU - Xu, Qijun

AU - Mao, Likai

AU - Deng, Guangbing

AU - Yao, Xiaoming

AU - Li, Xiangfeng

AU - Bai, Lijun

AU - Yuan, Hongjun

AU - Pan, Zhifen

AU - Liu, Renjian

AU - Chen, Xin

AU - WangMu, Qi Mei

AU - Chen, Ming

AU - Yu, Lili

AU - Liang, Junjun

AU - DunZhu, Da Wa

AU - Zheng, Yuan

AU - Yu, Shuiyang

AU - LuoBu, Zha Xi

AU - Guang, Xuanmin

AU - Li, Jiang

AU - Deng, Cao

AU - Hu, Wushu

AU - Chen, Chunhai

AU - TaBa, Xiong Nu

AU - Gao, Liyun

AU - Lv, Xiaodan

AU - Abu, Yuval Ben

AU - Fang, Xiaodong

AU - Nevo, Eviatar

AU - Yu, Maoqun

AU - Wang, Jun

AU - Tashi, Nyima

PY - 2015/1/27

Y1 - 2015/1/27

N2 - 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.

AB - 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.

KW - Adaptation

KW - Genetic diversity

KW - Selective sweep

KW - Tibetan hulless barley

KW - Triticeae evolution

UR - http://www.scopus.com/inward/record.url?scp=84921713652&partnerID=8YFLogxK

U2 - 10.1073/pnas.1423628112

DO - 10.1073/pnas.1423628112

M3 - Article

C2 - 25583503

AN - SCOPUS:84921713652

SN - 0027-8424

VL - 112

SP - 1095

EP - 1100

JO - Proceedings of the National Academy of Sciences of the United States of America

JF - Proceedings of the National Academy of Sciences of the United States of America

IS - 4

ER -

The draft genome of Tibetan hulless barley reveals adaptive patterns to the high stressful Tibetan Plateau

Abstract

Keywords

ASJC Scopus subject areas

UN SDGs

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