Combining GWAS, Genome-Wide Domestication and a Transcriptomic Analysis Reveals the Loci and Natural Alleles of Salt Tolerance in Rice (Oryza sativa L.)

Advances in Sensing, Response and Regulation Mechanism of Salt Tolerance in Rice

(2021) Kimberly S. Ponce et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Twelve years of SAMtools and BCFtools

(2021) Petr Danecek et al.   GigaScience

Rice Shaker potassium channel OsAKT2 positively regulates salt tolerance and grain yield by mediating K + redistribution

(2021) Quanxiang Tian et al.   PLANT CELL AND ENVIRONMENT

Haplotype Analysis of BADH1 by Next-Generation Sequencing Reveals Association with Salt Tolerance in Rice during Domestication

(2021) Myeong-Hyeon Min et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

OsNBL3, a mitochondrion‐localized pentatricopeptide repeat protein, is involved in splicing nad5 intron 4 and its disruption causes lesion mimic phenotype with enhanced resistance to biotic and abiotic stresses

(2021) Tiancheng Qiu et al.   PLANT BIOTECHNOLOGY JOURNAL

Transcriptomic Analysis of Short-Term Salt-Stress Response in Mega Hybrid Rice Seedlings

(2021) Noushin Jahan et al.   Agronomy-Basel

Loci and Natural Alleles for Low-Nitrogen-Induced Growth Response Revealed by the Genome-Wide Association Study Analysis in Rice (Oryza sativa L.)

(2021) Yang Lv et al.   Frontiers in Plant Science

Salt Tolerance Mechanisms of Plants

(2020) Eva van Zelm et al.   Annual Review of Plant Biology

ARGONAUTE2 Enhances Grain Length and Salt Tolerance by Activating BIG GRAIN3 to Modulate Cytokinin Distribution in Rice

(2020) Wenchao Yin et al.   PLANT CELL

Plant abiotic stress response and nutrient use efficiency

(2020) Zhizhong Gong et al.   Science China-Life Sciences

Loci and alleles for submergence responses revealed by GWAS and transcriptional analysis in rice

(2020) Hongsheng Gao et al.   MOLECULAR BREEDING

A Strigolactone Biosynthesis Gene Contributed to the Green Revolution in Rice

(2020) Yuexing Wang et al.   Molecular Plant

TBtools: An Integrative Toolkit Developed for Interactive Analyses of Big Biological Data

(2020) Chengjie Chen et al.   Molecular Plant

PHYTOCHROME-INTERACTING FACTOR-LIKE14 and SLENDER RICE1 interaction controls seedling growth under salt stress

(2020) Weiping Mo et al.   PLANT PHYSIOLOGY

Salt Tolerance Mechanisms and Approaches: Future Scope of Halotolerant Genes and Rice Landraces

(2020) Tarun Bhatt et al.   Rice Science

Clock component OsPRR73 positively regulates rice salt tolerance by modulating OsHKT2;1 ‐mediated sodium homeostasis

(2020) Hua Wei et al.   EMBO JOURNAL

Predicting long-term dynamics of soil salinity and sodicity on a global scale

(2020) Amirhossein Hassani et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A Critical Role of Sodium Flux via the Plasma Membrane Na+/H+ Exchanger SOS1 in the Salt Tolerance of Rice

(2019) Houda El Mahi et al.   PLANT PHYSIOLOGY

A rice RING H2‐type E3 ligase, OsSIRH2‐14, enhances salinity tolerance via ubiquitin/26S proteasome‐mediated degradation of salt‐related proteins

(2019) Yong Chan Park et al.   PLANT CELL AND ENVIRONMENT

QTL analysis for rice salinity tolerance and fine mapping of a candidate locus qSL7 for shoot length under salt stress

(2019) Noushin Jahan et al.   PLANT GROWTH REGULATION

Identification of genes for salt tolerance and yield-related traits in rice plants grown hydroponically and under saline field conditions by genome-wide association study

(2019) Chen Liu et al.   Rice

A Genome-Wide Association Study Reveals Candidate Genes Related to Salt Tolerance in Rice (Oryza sativa) at the Germination Stage

(2018) Jie Yu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Stress Management: OsIDS1 Modulates Histone Deacetylation to Repress Salt Tolerance Genes

(2018) Magdalena M. Julkowska   PLANT PHYSIOLOGY

Domestication history and geographical adaptation inferred from a SNP map of African rice

(2016) Rachel S Meyer et al.   NATURE GENETICS

Suppression of OsVPE3 Enhances Salt Tolerance by Attenuating Vacuole Rupture during Programmed Cell Death and Affects Stomata Development in Rice

(2016) Wenyun Lu et al.   Rice

HKT transporters mediate salt stress resistance in plants: from structure and function to the field

(2015) Shin Hamamoto et al.   CURRENT OPINION IN BIOTECHNOLOGY

OsSIDP366, a DUF1644 gene, positively regulates responses to drought and salt stresses in rice

(2015) Chiming Guo et al.   Journal of Integrative Plant Biology

MutMap accelerates breeding of a salt-tolerant rice cultivar

(2015) Hiroki Takagi et al.   NATURE BIOTECHNOLOGY

Elevated Levels of CYP94 Family Gene Expression Alleviate the Jasmonate Response and Enhance Salt Tolerance in Rice

(2015) Ken-ichi Kurotani et al.   PLANT AND CELL PHYSIOLOGY

MAOHUZI6/ETHYLENE INSENSITIVE3-LIKE1andETHYLENE INSENSITIVE3-LIKE2Regulate Ethylene Response of Roots and Coleoptiles and Negatively Affect Salt Tolerance in Rice

(2015) Chao Yang et al.   PLANT PHYSIOLOGY

The Rice High-Affinity Potassium Transporter1;1 Is Involved in Salt Tolerance and Regulated by an MYB-Type Transcription Factor

(2015) Rong Wang et al.   PLANT PHYSIOLOGY

The R2R3-type MYB gene OsMYB91 has a function in coordinating plant growth and salt stress tolerance in rice

(2015) Ning Zhu et al.   PLANT SCIENCE

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

Conserved miR164-targeted NAC genes negatively regulate drought resistance in rice

(2014) Yujie Fang et al.   JOURNAL OF EXPERIMENTAL BOTANY

The mitogen-activated protein kinase cascade MKK1–MPK4 mediates salt signaling in rice

(2014) Fuzheng Wang et al.   PLANT SCIENCE

An S-Domain Receptor-Like Kinase, OsSIK2, Confers Abiotic Stress Tolerance and Delays Dark-Induced Leaf Senescence in Rice

(2013) L.-J. Chen et al.   PLANT PHYSIOLOGY

Five Years of GWAS Discovery

(2012) Peter M. Visscher et al.   AMERICAN JOURNAL OF HUMAN GENETICS

Effects of salt stress on ion balance and nitrogen metabolism of old and young leaves in rice (Oryza sativa L.)

(2012) Huan Wang et al.   BMC PLANT BIOLOGY

Overexpression of OsHsp17.0 and OsHsp23.7 enhances drought and salt tolerance in rice

(2012) Jie Zou et al.   JOURNAL OF PLANT PHYSIOLOGY

A map of rice genome variation reveals the origin of cultivated rice

(2012) Xuehui Huang et al.   NATURE

Fast gapped-read alignment with Bowtie 2

(2012) Ben Langmead et al.   NATURE METHODS

Differential gene and transcript expression analysis of RNA-seq experiments with TopHat and Cufflinks

(2012) Cole Trapnell et al.   Nature Protocols

The overexpression ofOsNAC9alters the root architecture of rice plants enhancing drought resistance and grain yield under field conditions

(2012) Mark C.F.R. Redillas et al.   PLANT BIOTECHNOLOGY JOURNAL

OsNAC5overexpression enlarges root diameter in rice plants leading to enhanced drought tolerance and increased grain yield in the field

(2012) Jin Seo Jeong et al.   PLANT BIOTECHNOLOGY JOURNAL

OsLEA3-2, an Abiotic Stress Induced Gene of Rice Plays a Key Role in Salt and Drought Tolerance

(2012) Jianli Duan et al.   PLoS One

QTL Analysis of Na+ and K+ Concentrations in Roots and Shoots under Different Levels of NaCl Stress in Rice (Oryza sativa L.)

(2012) Zhoufei Wang et al.   PLoS One

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Molecular characterization and functional analysis by heterologous expression in E. coli under diverse abiotic stresses for OsLEA5, the atypical hydrophobic LEA protein from Oryza sativa L.

(2011) Shuai He et al.   MOLECULAR GENETICS AND GENOMICS

Activation of the plasma membrane Na/H antiporter Salt-Overly-Sensitive 1 (SOS1) by phosphorylation of an auto-inhibitory C-terminal domain

(2011) F. J. Quintero et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Functional analysis of a novel Cys2/His2-type zinc finger protein involved in salt tolerance in rice

(2010) S.-J. Sun et al.   JOURNAL OF EXPERIMENTAL BOTANY

Variance component model to account for sample structure in genome-wide association studies

(2010) Hyun Min Kang et al.   NATURE GENETICS

Association and Linkage Analysis of Aluminum Tolerance Genes in Maize

(2010) Allison M. Krill et al.   PLoS One

TheOsDHODH1Gene is Involved in Salt and Drought Tolerance in Rice

(2009) Wen-Ying Liu et al.   Journal of Integrative Plant Biology

New changes in the plasma-membrane-associated proteome of rice roots under salt stress

(2009) Yanwei Cheng et al.   PROTEOMICS