Transcriptomic divergence between upland and lowland ecotypes contributes to rice adaptation to a drought‐prone agroecosystem

Water-saving and drought-resistance rice: from the concept to practice and theory

(2019) Lijun Luo et al.   MOLECULAR BREEDING

GOATOOLS: A Python library for Gene Ontology analyses

(2018) D. V. Klopfenstein et al.   Scientific Reports

Gene Regulatory Divergence Between Locally Adapted Ecotypes in Their Native Habitats

(2018) Billie A. Gould et al.   MOLECULAR ECOLOGY

Bi-directional selection in upland rice leads to its adaptive differentiation from lowland rice on drought resistance and productivity

(2018) Hui Xia et al.   Molecular Plant

Plant hormone-mediated regulation of stress responses

(2016) Vivek Verma et al.   BMC PLANT BIOLOGY

Genome-assisted Breeding For Drought Resistance

(2016) Awais Khan et al.   CURRENT GENOMICS

Drought responsive gene expression regulatory divergence between upland and lowland ecotypes of a perennial C4grass

(2016) John T. Lovell et al.   GENOME RESEARCH

A Drought-Inducible Transcription Factor Delays Reproductive Timing in Rice

(2016) Chunyu Zhang et al.   PLANT PHYSIOLOGY

Comparative transcriptome analysis highlights the crucial roles of photosynthetic system in drought stress adaptation in upland rice

(2016) Zheng-Feng Zhang et al.   Scientific Reports

Transcriptomic and Metabolomic Studies Disclose Key Metabolism Pathways Contributing to Well-maintained Photosynthesis under the Drought and the Consequent Drought-Tolerance in Rice

(2016) Xiaosong Ma et al.   Frontiers in Plant Science

Adaptive Epigenetic Differentiation between Upland and Lowland Rice Ecotypes Revealed by Methylation-Sensitive Amplified Polymorphism

(2016) Hui Xia et al.   PLoS One

Population transcriptomics uncovers the regulation of gene expression variation in adaptation to changing environment

(2016) Qin Xu et al.   Scientific Reports

Widespread and Adaptive Alterations in Genome-Wide Gene Expression Associated with Ecological Divergence of TwoOryzaSpecies

(2015) Jie Guo et al.   MOLECULAR BIOLOGY AND EVOLUTION

Phenotypic plasticity in gene expression contributes to divergence of locally adapted populations ofFundulus heteroclitus

(2015) David I. Dayan et al.   MOLECULAR ECOLOGY

Genomic, Transcriptomic, and Phenomic Variation Reveals the Complex Adaptation of Modern Maize Breeding

(2015) Haijun Liu et al.   Molecular Plant

OsIAA6, a member of the rice Aux/IAA gene family, is involved in drought tolerance and tiller outgrowth

(2015) Harin Jung et al.   PLANT SCIENCE

Recent advances in the dissection of drought-stress regulatory networks and strategies for development of drought-tolerant transgenic rice plants

(2015) Daisuke Todaka et al.   Frontiers in Plant Science

Drought susceptibility of modern rice varieties: an effect of linkage of drought tolerance with undesirable traits

(2015) Prashant Vikram et al.   Scientific Reports

A genomic perspective on the important genetic mechanisms of upland adaptation of rice

(2014) Jun Lyu et al.   BMC PLANT BIOLOGY

General mechanisms of drought response and their application in drought resistance improvement in plants

(2014) Yujie Fang et al.   CELLULAR AND MOLECULAR LIFE SCIENCES

Population transcriptomics reveals a potentially positive role of expression diversity in adaptation

(2014) Qin Xu et al.   Journal of Integrative Plant Biology

Natural Variation in Abiotic Stress Responsive Gene Expression and Local Adaptation to Climate in Arabidopsis thaliana

(2014) Jesse R. Lasky et al.   MOLECULAR BIOLOGY AND EVOLUTION

Induced over-expression of AtDREB2A CA improves drought tolerance in sugarcane

(2014) Rafaela Ribeiro Reis et al.   PLANT SCIENCE

Genetic Differentiation Revealed by Selective Loci of Drought-Responding EST-SSRs between Upland and Lowland Rice in China

(2014) Hui Xia et al.   PLoS One

Gene Coexpression Networks Reveal Key Drivers of Phenotypic Divergence in Lake Whitefish

(2013) Marie Filteau et al.   MOLECULAR BIOLOGY AND EVOLUTION

Comparative transcriptomics reveals patterns of selection in domesticated and wild tomato

(2013) D. Koenig et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Comparative studies of gene expression and the evolution of gene regulation

(2012) Irene Gallego Romero et al.   NATURE REVIEWS GENETICS

A Selection Index for Gene Expression Evolution and Its Application to the Divergence between Humans and Chimpanzees

(2012) Maria Warnefors et al.   PLoS One

Cis- and trans-regulatory divergence between progenitor species determines gene-expression novelty in Arabidopsis allopolyploids

(2012) Xiaoli Shi et al.   Nature Communications

Epigenetic transgenerational inheritance of somatic transcriptomes and epigenetic control regions

(2012) Michael K Skinner et al.   GENOME BIOLOGY

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

The role of gene expression in ecological speciation

(2010) Scott A. Pavey et al.   Annals of the New York Academy of Sciences

The Genome Analysis Toolkit: A MapReduce framework for analyzing next-generation DNA sequencing data

(2010) A. McKenna et al.   GENOME RESEARCH

Breeding for water-saving and drought-resistance rice (WDR) in China

(2010) L. J. Luo   JOURNAL OF EXPERIMENTAL BOTANY

ANNOVAR: functional annotation of genetic variants from high-throughput sequencing data

(2010) K. Wang et al.   NUCLEIC ACIDS RESEARCH

Progress studies of drought-responsive genes in rice

(2010) Toto Hadiarto et al.   PLANT CELL REPORTS

Robust control of the seasonal expression of the Arabidopsis FLC gene in a fluctuating environment

(2010) S. Aikawa et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Advances in Drought Resistance of Rice

(2009) Muhammad Farooq et al.   CRITICAL REVIEWS IN PLANT SCIENCES

Divergent selection and heterogeneous genomic divergence

(2009) PATRIK NOSIL et al.   MOLECULAR ECOLOGY

WGCNA: an R package for weighted correlation network analysis

(2008) Peter Langfelder et al.   BMC BIOINFORMATICS

Breeding upland rice for drought resistance

(2008) Jérôme Bernier et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Gene Regulation in Primates Evolves under Tissue-Specific Selection Pressures

(2008) Ran Blekhman et al.   PLoS Genetics