Upland rice genomic signatures of adaptation to drought resistance and navigation to molecular design breeding

Alpha-Linolenic Acid Mediates Diverse Drought Responses in Maize (Zea mays L.) at Seedling and Flowering Stages

(2022) Xuejing Zi et al.   MOLECULES

SunUp and Sunset genomes revealed impact of particle bombardment mediated transformation and domestication history in papaya

(2022) Jingjing Yue et al.   NATURE GENETICS

Blue Revolution for Food Security under Carbon Neutrality: A Case from the Water-saving and Drought-resistance Rice

(2022) Hui Xia et al.   Molecular Plant

Natural variation of DROT1 confers drought adaptation in upland rice

(2022) Xingming Sun et al.   Nature Communications

Genome sequencing reveals evidence of adaptive variation in the genus Zea

(2022) Lu Chen et al.   NATURE GENETICS

INDITTO2 transposon conveys auxin‐mediated DRO1 transcription for rice drought avoidance

(2021) Yiting Zhao et al.   PLANT CELL AND ENVIRONMENT

Stable and Novel Quantitative Trait Loci (QTL) Confer Narrow Root Cone Angle in an Aerobic Rice (Oryza sativa L.) Production System

(2021) Ricky Vinarao et al.   Rice

Pan-genome analysis of 33 genetically diverse rice accessions reveals hidden genomic variations

(2021) Peng Qin et al.   CELL

Drought tolerance in selected aerobic and upland rice varieties is driven by different metabolic and antioxidative responses

(2021) Giovanni Melandri et al.   PLANTA

Natural alleles of a uridine 5ʹ‐diphospho‐glucosyltransferase gene responsible for differential endosperm development between upland rice and paddy rice

(2021) Zihao Wu et al.   Journal of Integrative Plant Biology

Parallel selection of distinct Tof5 alleles drove the adaptation of cultivated and wild soybean to high latitudes

(2021) Lidong Dong et al.   Molecular Plant

Transcriptional activation of rice CINNAMOYL‐CoA REDUCTASE 10 by OsNAC5, contributes to drought tolerance by modulating lignin accumulation in roots

(2021) Seung Woon Bang et al.   PLANT BIOTECHNOLOGY JOURNAL

Neo-functionalization of a Teosinte branched 1 homologue mediates adaptations of upland rice

(2020) Jun Lyu et al.   Nature Communications

Genomic landscape of parallel domestication of upland rice and its implications

(2020) Mei‐Xia Wang et al.   Journal of Systematics and Evolution

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

(2020) Zhi Luo et al.   Evolutionary Applications

Regulation of phenylpropanoid biosynthesis by MdMYB88 and MdMYB124 contributes to pathogen and drought resistance in apple

(2020) Dali Geng et al.   Horticulture Research

Genome-Wide Analyses Reveal Footprints of Divergent Selection and Drought Adaptive Traits in Synthetic-Derived Wheats

(2019) Fakiha Afzal et al.   G3-Genes Genomes Genetics

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

(2019) Lijun Luo et al.   MOLECULAR BREEDING

Insights into endoplasmic reticulum‐associated degradation in plants

(2019) Qian Chen et al.   NEW PHYTOLOGIST

Accurate detection of complex structural variations using single-molecule sequencing

(2018) Fritz J. Sedlazeck et al.   NATURE METHODS

OsERF71 confers drought tolerance via modulating ABA signaling and proline biosynthesis

(2018) Jinjie Li et al.   PLANT SCIENCE

MUMmer4: A fast and versatile genome alignment system

(2018) Guillaume Marçais et al.   PLoS Computational Biology

Parallel selection on a dormancy gene during domestication of crops from multiple families

(2018) Min Wang et al.   NATURE GENETICS

Natural Variation in OsLG3 Increases Drought Tolerance in Rice by Inducing ROS Scavenging

(2018) Haiyan Xiong et al.   PLANT PHYSIOLOGY

Loci and natural alleles underlying robust roots and adaptive domestication of upland ecotype rice in aerobic conditions

(2018) Yan Zhao et al.   PLoS Genetics

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

Allele-defined genome of the autopolyploid sugarcane Saccharum spontaneum L.

(2018) Jisen Zhang et al.   NATURE GENETICS

eggNOG 5.0: a hierarchical, functionally and phylogenetically annotated orthology resource based on 5090 organisms and 2502 viruses

(2018) Jaime Huerta-Cepas et al.   NUCLEIC ACIDS RESEARCH

Canu: scalable and accurate long-read assembly via adaptivek-mer weighting and repeat separation

(2017) Sergey Koren et al.   GENOME RESEARCH

Transcriptome analysis of drought-responsive genes regulated by hydrogen sulfide in wheat (Triticum aestivum L.) leaves

(2017) Hua Li et al.   MOLECULAR GENETICS AND GENOMICS

Deletion of an Endoplasmic Reticulum Stress Response Element in a ZmPP2C-A Gene Facilitates Drought Tolerance of Maize Seedlings

(2017) Yanli Xiang et al.   Molecular Plant

De novo assembly of the Aedes aegypti genome using Hi-C yields chromosome-length scaffolds

(2017) Olga Dudchenko et al.   SCIENCE

Sequencing and de novo assembly of a near complete indica rice genome

(2017) Huilong Du et al.   Nature Communications

BUSCO: assessing genome assembly and annotation completeness with single-copy orthologs

(2015) Felipe A. Simão et al.   BIOINFORMATICS

qRT9, a quantitative trait locus controlling root thickness and root length in upland rice

(2015) Junzhou Li et al.   JOURNAL OF EXPERIMENTAL BOTANY

De Novo Plant Genome Assembly Based on Chromatin Interactions: A Case Study of Arabidopsis thaliana

(2015) Ting Xie et al.   Molecular Plant

At14a-Like1 participates in membrane-associated mechanisms promoting growth during drought inArabidopsis thaliana

(2015) M. Nagaraj Kumar et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Genetic Variation, Heritability, and Diversity Analysis of Upland Rice (Oryza sativaL.) Genotypes Based on Quantitative Traits

(2015) Mst. Tuhina-Khatun et al.   Biomed Research International

Trimmomatic: a flexible trimmer for Illumina sequence data

(2014) Anthony M. Bolger et al.   BIOINFORMATICS

RAxML version 8: a tool for phylogenetic analysis and post-analysis of large phylogenies

(2014) Alexandros Stamatakis   BIOINFORMATICS

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

(2014) Jun Lyu et al.   BMC PLANT BIOLOGY

Breeding high-yielding drought-tolerant rice: genetic variations and conventional and molecular approaches

(2014) Arvind Kumar et al.   JOURNAL OF EXPERIMENTAL BOTANY

Pilon: An Integrated Tool for Comprehensive Microbial Variant Detection and Genome Assembly Improvement

(2014) Bruce J. Walker et al.   PLoS One

Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions

(2013) Yusaku Uga et al.   NATURE GENETICS

De novo transcript sequence reconstruction from RNA-seq using the Trinity platform for reference generation and analysis

(2013) Brian J Haas et al.   Nature Protocols

Analysis of elite variety tag SNPs reveals an important allele in upland rice

(2013) Jun Lyu et al.   Nature Communications

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions

(2013) Daehwan Kim et al.   GENOME BIOLOGY

A program for annotating and predicting the effects of single nucleotide polymorphisms, SnpEff

(2012) Pablo Cingolani et al.   FLY

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

MCScanX: a toolkit for detection and evolutionary analysis of gene synteny and collinearity

(2012) Y. Wang et al.   NUCLEIC ACIDS RESEARCH

OsMIOX, a myo-inositol oxygenase gene, improves drought tolerance through scavenging of reactive oxygen species in rice (Oryza sativa L.)

(2012) Junzhi Duan et al.   PLANT SCIENCE

The variant call format and VCFtools

(2011) P. Danecek et al.   BIOINFORMATICS

Root biology and genetic improvement for drought avoidance in rice

(2011) Veeresh R.P. Gowda et al.   FIELD CROPS RESEARCH

Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions

(2011) Junfei Gu et al.   JOURNAL OF EXPERIMENTAL BOTANY

Dro1, a major QTL involved in deep rooting of rice under upland field conditions

(2011) Yusaku Uga et al.   JOURNAL OF EXPERIMENTAL BOTANY

Development of upland rice introgression lines and identification of QTLs for basal root thickness under different water regimes

(2011) Junzhou Li et al.   Journal of Genetics and Genomics

A framework for variation discovery and genotyping using next-generation DNA sequencing data

(2011) Mark A DePristo et al.   NATURE GENETICS

Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice

(2011) Xipeng Ding et al.   THEORETICAL AND APPLIED GENETICS

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

(2010) A. McKenna et al.   GENOME RESEARCH

Population resequencing reveals local adaptation of Arabidopsis lyrata to serpentine soils

(2010) Thomas L Turner et al.   NATURE GENETICS

TEclass--a tool for automated classification of unknown eukaryotic transposable elements

(2009) G. Abrusan et al.   BIOINFORMATICS

The Sequence Alignment/Map format and SAMtools

(2009) H. Li et al.   BIOINFORMATICS

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

BLAST+: architecture and applications

(2009) Christiam Camacho et al.   BMC BIOINFORMATICS

Comparative transcriptional profiling under drought stress between upland and lowland rice (Oryza sativa L.) using cDNA-AFLP

(2009) FengHua Gao et al.   Science Bulletin

Evo-Devo and an Expanding Evolutionary Synthesis: A Genetic Theory of Morphological Evolution

(2008) Sean B. Carroll   CELL

Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice

(2008) Guojun Lu et al.   PLANTA

Automated eukaryotic gene structure annotation using EVidenceModeler and the Program to Assemble Spliced Alignments

(2008) Brian J Haas et al.   GENOME BIOLOGY