The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

Liuhui Kuang; Qiufang Shen; Liyang Chen; Lingzhen Ye; Tao Yan; Zhong-Hua Chen; Robbie Waugh; Qi Li; Lu Huang; Shengguan Cai; Liangbo Fu; Pengwei Xing; Kai Wang; Jiari Shao; Feibo Wu; Lixi Jiang; Dezhi Wu; Guoping Zhang

doi:10.1016/j.xplc.2022.100333

The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

Liuhui Kuang
, Qiufang Shen
, Liyang Chen
, Lingzhen Ye
, Tao Yan
, Zhong-Hua Chen
, Robbie Waugh
, Qi Li
, Lu Huang
, Shengguan Cai
, Liangbo Fu
, Pengwei Xing
, Kai Wang
, Jiari Shao
, Feibo Wu
, Lixi Jiang
, Dezhi Wu (Lead / Corresponding author)
, Guoping Zhang (Lead / Corresponding author)

Plant Sciences

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

36 Citations (Scopus)

248 Downloads (Pure)

Abstract

The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.

Original language	English
Article number	100333
Number of pages	16
Journal	Plant Communications
Volume	3
Issue number	5
Early online date	5 May 2022
DOIs	https://doi.org/10.1016/j.xplc.2022.100333
Publication status	Published - 12 Sept 2022

Keywords

divergence
genome
salt tolerance
sea barleygrass
transcriptome

ASJC Scopus subject areas

Plant Science
Biochemistry
Biotechnology
Cell Biology
Molecular Biology

Access to Document

10.1016/j.xplc.2022.100333Licence: CC BY

Final Published VersionFinal published version, 3.99 MBLicence: CC BY

Cite this

Kuang, L., Shen, Q., Chen, L., Ye, L., Yan, T., Chen, Z.-H., Waugh, R., Li, Q., Huang, L., Cai, S., Fu, L., Xing, P., Wang, K., Shao, J., Wu, F., Jiang, L., Wu, D., & Zhang, G. (2022). The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies. Plant Communications, 3(5), Article 100333. https://doi.org/10.1016/j.xplc.2022.100333

@article{c1701872bb624a50bd4d648366931830,

title = "The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies",

abstract = "The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8\%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.",

keywords = "divergence, genome, salt tolerance, sea barleygrass, transcriptome",

author = "Liuhui Kuang and Qiufang Shen and Liyang Chen and Lingzhen Ye and Tao Yan and Zhong-Hua Chen and Robbie Waugh and Qi Li and Lu Huang and Shengguan Cai and Liangbo Fu and Pengwei Xing and Kai Wang and Jiari Shao and Feibo Wu and Lixi Jiang and Dezhi Wu and Guoping Zhang",

note = "Funding Information: This research was supported by The National Key Research and Development Program of China (2018YFD1000704), the National Natural Science Foundation of China (32071934), the key research project of Zhejiang (2020C02002, 2021C02064-3), the China Agriculture Research System of MOF and MARA, and the Jiangsu Collaborative Innovation Center for Modern Crop Production Copyright Information: {\textcopyright} 2022 The Author(s).",

year = "2022",

month = sep,

day = "12",

doi = "10.1016/j.xplc.2022.100333",

language = "English",

volume = "3",

journal = "Plant Communications",

issn = "2590-3462",

publisher = "Elsevier",

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Kuang, L, Shen, Q, Chen, L, Ye, L, Yan, T, Chen, Z-H, Waugh, R, Li, Q, Huang, L, Cai, S, Fu, L, Xing, P, Wang, K, Shao, J, Wu, F, Jiang, L, Wu, D & Zhang, G 2022, 'The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies', Plant Communications, vol. 3, no. 5, 100333. https://doi.org/10.1016/j.xplc.2022.100333

TY - JOUR

T1 - The genome and gene editing system of sea barleygrass provide a novel platform for cereal domestication and stress tolerance studies

AU - Kuang, Liuhui

AU - Shen, Qiufang

AU - Chen, Liyang

AU - Ye, Lingzhen

AU - Yan, Tao

AU - Chen, Zhong-Hua

AU - Waugh, Robbie

AU - Li, Qi

AU - Huang, Lu

AU - Cai, Shengguan

AU - Fu, Liangbo

AU - Xing, Pengwei

AU - Wang, Kai

AU - Shao, Jiari

AU - Wu, Feibo

AU - Jiang, Lixi

AU - Wu, Dezhi

AU - Zhang, Guoping

N1 - Funding Information: This research was supported by The National Key Research and Development Program of China (2018YFD1000704), the National Natural Science Foundation of China (32071934), the key research project of Zhejiang (2020C02002, 2021C02064-3), the China Agriculture Research System of MOF and MARA, and the Jiangsu Collaborative Innovation Center for Modern Crop Production Copyright Information: © 2022 The Author(s).

PY - 2022/9/12

Y1 - 2022/9/12

N2 - The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.

AB - The tribe Triticeae provides important staple cereal crops and contains elite wild species with wide genetic diversity and high tolerance to abiotic stresses. Sea barleygrass (Hordeum marinum Huds.), a wild Triticeae species, thrives in saline marshlands and is well known for its high tolerance to salinity and waterlogging. Here, a 3.82-Gb high-quality reference genome of sea barleygrass is assembled de novo, with 3.69 Gb (96.8%) of its sequences anchored onto seven chromosomes. In total, 41 045 high-confidence (HC) genes are annotated by homology, de novo prediction, and transcriptome analysis. Phylogenetics, non-synonymous/synonymous mutation ratios (Ka/Ks), and transcriptomic and functional analyses provide genetic evidence for the divergence in morphology and salt tolerance among sea barleygrass, barley, and wheat. The large variation in post-domestication genes (e.g. IPA1 and MOC1) may cause interspecies differences in plant morphology. The extremely high salt tolerance of sea barleygrass is mainly attributed to low Na+ uptake and root-to-shoot translocation, which are mainly controlled by SOS1, HKT, and NHX transporters. Agrobacterium-mediated transformation and CRISPR/Cas9-mediated gene editing systems were developed for sea barleygrass to promote its utilization for exploration and functional studies of hub genes and for the genetic improvement of cereal crops.

KW - divergence

KW - genome

KW - salt tolerance

KW - sea barleygrass

KW - transcriptome

UR - https://www.scopus.com/pages/publications/85131130188

U2 - 10.1016/j.xplc.2022.100333

DO - 10.1016/j.xplc.2022.100333

M3 - Article

C2 - 35643085

SN - 2590-3462

VL - 3

JO - Plant Communications

JF - Plant Communications

IS - 5

M1 - 100333

ER -