Application of resequencing to rice genomics, functional genomics and evolutionary analysis

Use of Major Quantitative Trait Loci to Improve Grain Yield of Rice

(2014) Long-biao GUO et al.   Rice Science

Genes offering the potential for designing yield-related traits in rice

(2013) Mayuko Ikeda et al.   CURRENT OPINION IN PLANT BIOLOGY

Sequencing-based genome-wide association study in rice

(2013) Bin Han et al.   CURRENT OPINION IN PLANT BIOLOGY

A BAC physical map ofausrice cultivar ‘Kasalath’, and the map-based genomic sequence of ‘Kasalath’ chromosome 1

(2013) Hiroyuki Kanamori et al.   PLANT JOURNAL

QTL-seq: rapid mapping of quantitative trait loci in rice by whole genome resequencing of DNA from two bulked populations

(2013) Hiroki Takagi et al.   PLANT JOURNAL

Dissecting yield-associated loci in super hybrid rice by resequencing recombinant inbred lines and improving parental genome sequences

(2013) Z.-Y. Gao et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

Photoperiod- and thermo-sensitive genic male sterility in rice are caused by a point mutation in a novel noncoding RNA that produces a small RNA

(2012) Hai Zhou et al.   CELL RESEARCH

Recent Progress Using High-throughput Sequencing Technologies in Plant Molecular BreedingF

(2012) Qiang Gao et al.   Journal of Integrative Plant Biology

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

(2012) Xuehui Huang et al.   NATURE

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Genomic dissection of small RNAs in wild rice (Oryza rufipogon): lessons for rice domestication

(2012) Yu Wang et al.   NEW PHYTOLOGIST

Efficacy of Microarray Profiling Data Combined with QTL Mapping for the Identification of a QTL Gene Controlling the Initial Growth Rate in Rice

(2012) Kenji Yano et al.   PLANT AND CELL PHYSIOLOGY

Genome-wide DNA polymorphisms in eliteindicarice inbreds discovered by whole-genome sequencing

(2012) Gopala K. Subbaiyan et al.   PLANT BIOTECHNOLOGY JOURNAL

OsGA20ox1, a candidate gene for a major QTL controlling seedling vigor in rice

(2012) Akira Abe et al.   THEORETICAL AND APPLIED GENETICS

Dynamic Intra-Japonica Subspecies Variation and Resource Application

(2011) Haiyan Lin et al.   Molecular Plant

Resequencing 50 accessions of cultivated and wild rice yields markers for identifying agronomically important genes

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

(2011) Xuehui Huang et al.   NATURE GENETICS

Massive Analysis of Rice Small RNAs: Mechanistic Implications of Regulated MicroRNAs and Variants for Differential Target RNA Cleavage

(2011) D.-H. Jeong et al.   PLANT CELL

Next-generation mapping of Arabidopsis genes

(2011) Ryan S. Austin et al.   PLANT JOURNAL

Genetic Control of a Transition from Black to Straw-White Seed Hull in Rice Domestication

(2011) B.-F. Zhu et al.   PLANT PHYSIOLOGY

Gains in QTL Detection Using an Ultra-High Density SNP Map Based on Population Sequencing Relative to Traditional RFLP/SSR Markers

(2011) Huihui Yu et al.   PLoS One

Molecular evidence for a single evolutionary origin of domesticated rice

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

The role of QTLs in the breeding of high-yielding rice

(2011) Kotaro Miura et al.   TRENDS IN PLANT SCIENCE

Fast-forward genetics enabled by new sequencing technologies

(2011) Korbinian Schneeberger et al.   TRENDS IN PLANT SCIENCE

Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa

(2011) Keyan Zhao et al.   Nature Communications

High-throughput DNA sequencing - concepts and limitations

(2010) Martin Kircher et al.   BIOESSAYS

Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)

(2010) Jianjun Xu et al.   BMC GENOMICS

Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms

(2010) Toshio Yamamoto et al.   BMC GENOMICS

Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq

(2010) T. Lu et al.   GENOME RESEARCH

Deep RNA sequencing at single base-pair resolution reveals high complexity of the rice transcriptome

(2010) G. Zhang et al.   GENOME RESEARCH

Regulation of OsSPL14 by OsmiR156 defines ideal plant architecture in rice

(2010) Yongqing Jiao et al.   NATURE GENETICS

Genome-wide association studies of 14 agronomic traits in rice landraces

(2010) Xuehui Huang et al.   NATURE GENETICS

Limitations of next-generation genome sequence assembly

(2010) Can Alkan et al.   NATURE METHODS

Global Epigenetic and Transcriptional Trends among Two Rice Subspecies and Their Reciprocal Hybrids

(2010) G. He et al.   PLANT CELL

Rice structural variation: a comparative analysis of structural variation between rice and three of its closest relatives in the genus Oryza

(2010) Bonnie L. Hurwitz et al.   PLANT JOURNAL

Identification and characterization of NARROW AND ROLLED LEAF 1, a novel gene regulating leaf morphology and plant architecture in rice

(2010) Jiang Hu et al.   PLANT MOLECULAR BIOLOGY

DTH8 Suppresses Flowering in Rice, Influencing Plant Height and Yield Potential Simultaneously

(2010) X. Wei et al.   PLANT PHYSIOLOGY

Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencing

(2010) W. Xie et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines

(2010) Lu Wang et al.   THEORETICAL AND APPLIED GENETICS

Crop genome sequencing: lessons and rationales

(2010) Catherine Feuillet et al.   TRENDS IN PLANT SCIENCE

Next-generation DNA sequencing of paired-end tags (PET) for transcriptome and genome analyses

(2009) M. J. Fullwood et al.   GENOME RESEARCH

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

RNA-Seq—quantitative measurement of expression through massively parallel RNA-sequencing

(2009) Brian T. Wilhelm et al.   METHODS

Next-generation DNA sequencing techniques

(2009) Wilhelm J. Ansorge   New Biotechnology

Genomewide SNP variation reveals relationships among landraces and modern varieties of rice

(2009) K. L. McNally et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Advantages and limitations of next-generation sequencing technologies: A comparison of electrophoresis and non-electrophoresis methods

(2008) Daniel G. Hert et al.   ELECTROPHORESIS

Rice 2020: A Call For An International Coordinated Effort In Rice Functional Genomics

(2008) Qifa Zhang et al.   Molecular Plant

Dynamic repertoire of a eukaryotic transcriptome surveyed at single-nucleotide resolution

(2008) Brian T. Wilhelm et al.   NATURE

Control of a key transition from prostrate to erect growth in rice domestication

(2008) Lubin Tan et al.   NATURE GENETICS

Genetic control of rice plant architecture under domestication

(2008) Jian Jin et al.   NATURE GENETICS

Deletion in a gene associated with grain size increased yields during rice domestication

(2008) Ayahiko Shomura et al.   NATURE GENETICS

RNA-Seq: a revolutionary tool for transcriptomics

(2008) Zhong Wang et al.   NATURE REVIEWS GENETICS

Mutation of the Rice Narrow leaf1 Gene, Which Encodes a Novel Protein, Affects Vein Patterning and Polar Auxin Transport

(2008) J. Qi et al.   PLANT PHYSIOLOGY