Combined strategy employing MutMap and RNA-seq reveals genomic regions and genes associated with complete panicle exsertion in rice

High-performance pipeline for MutMap and QTL-seq

(2022) Yu Sugihara et al.   PeerJ

Down regulation of transcripts involved in selective metabolic pathways as an acclimation strategy in nitrogen use efficient genotypes of rice under low nitrogen

(2021) C. N. Neeraja et al.   3 Biotech

Transcriptome analysis of rice response to blast fungus identified core genes involved in immunity

(2021) Dewei Yang et al.   PLANT CELL AND ENVIRONMENT

RNA-Seq-Based Profiling of pl Mutant Reveals Transcriptional Regulation of Anthocyanin Biosynthesis in Rice (Oryza sativa L.)

(2021) Ruonan Xu et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

RNA-Seq based global transcriptome analysis of rice unravels the key players associated with brown planthopper resistance

(2021) Vanisri Satturu et al.   INTERNATIONAL JOURNAL OF BIOLOGICAL MACROMOLECULES

Mutation resource of Samba Mahsuri revealed the presence of high extent of variations among key traits for rice improvement

(2021) Gopi Potupureddi et al.   PLoS One

Differential Expression of Genes at Panicle Initiation and Grain Filling Stages Implied in Heterosis of Rice Hybrids

(2020) Jawahar Lal Katara et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Transcriptome Analysis of Early Defenses in Rice against Fusarium fujikuroi

(2020) An-Po Cheng et al.   Rice

Genome Wide Analysis of the Transcriptional Profiles in Different Regions of the Developing Rice Grains

(2020) Ting-Ying Wu et al.   Rice

Comparative transcriptome analysis of two rice genotypes differing in their tolerance to saline-alkaline stress

(2020) Qian Li et al.   PLoS One

Gene Expression Dynamics in Rice Peduncles at the Heading Stage

(2020) Manu Kandpal et al.   Frontiers in Genetics

Gene identification and transcriptome analysis of low cadmium accumulation rice mutant (lcd1) in response to cadmium stress using MutMap and RNA-seq

(2019) Zhen Zhen Cao et al.   BMC PLANT BIOLOGY

Graph-based genome alignment and genotyping with HISAT2 and HISAT-genotype

(2019) Daehwan Kim et al.   NATURE BIOTECHNOLOGY

Genome-wide association analysis of panicle exsertion and uppermost internode in rice (Oryza sativa L.)

(2019) Chengfang Zhan et al.   Rice

OUP accepted manuscript

(2018)   BIOINFORMATICS

Characterization and fine mapping of qPE12, a new locus controlling rice panicle exsertion

(2018) Chunfang Zhao et al.   EUPHYTICA

Transcriptome analysis of near-isogenic line provides novel insights into genes associated with panicle traits regulation in rice

(2018) Wuhan Zhang et al.   PLoS One

WB1, a Regulator of Endosperm Development in Rice, Is Identified by a Modified MutMap Method

(2018) Hong Wang et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

The RNA-seq transcriptome analysis identified genes related to rice seed dormancy

(2018) K. Xie et al.   BIOLOGIA PLANTARUM

08SG2/OsBAK1 regulates grain size and number, and functions differently in Indica and Japonica backgrounds in rice

(2017) Hua Yuan et al.   Rice

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

(2017) Huilong Du et al.   Nature Communications

RNA-Seq Analysis of Diverse Rice Genotypes to Identify the Genes Controlling Coleoptile Growth during Submerged Germination

(2017) Sheng-Kai Hsu et al.   Frontiers in Plant Science

Favorable Marker Alleles for Panicle Exsertion Length in Rice (Oryza sativa L.) Mined by Association Mapping and the RSTEP-LRT Method

(2017) Xiaojing Dang et al.   Frontiers in Plant Science

Analysis of QTLs for panicle exsertion and its relationship with yield and yield-related traits in rice (Oryza sativa L.)

(2016) C.F. Zhao et al.   GENETICS AND MOLECULAR RESEARCH

MutMap accelerates breeding of a salt-tolerant rice cultivar

(2015) Hiroki Takagi et al.   NATURE BIOTECHNOLOGY

Data quality aware analysis of differential expression in RNA-seq with NOISeq R/Bioc package

(2015) Sonia Tarazona et al.   NUCLEIC ACIDS RESEARCH

featureCounts: an efficient general purpose program for assigning sequence reads to genomic features

(2013) Y. Liao et al.   BIOINFORMATICS

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

clusterProfiler: an R Package for Comparing Biological Themes Among Gene Clusters

(2012) Guangchuang Yu et al.   OMICS-A JOURNAL OF INTEGRATIVE BIOLOGY

Transcriptomic Analysis of Rice (Oryza sativa) Developing Embryos Using the RNA-Seq Technique

(2012) Hong Xu et al.   PLoS One

Genetic Analysis and Mapping of an Enclosed Panicle Mutant Locus esp1 in Rice (Oryza sativa L.)

(2012) Yuan-lin DUAN et al.   Journal of Integrative Agriculture

Rice Ethylene-Response AP2/ERF Factor OsEATB Restricts Internode Elongation by Down-Regulating a Gibberellin Biosynthetic Gene

(2011) Weiwei Qi et al.   PLANT PHYSIOLOGY

Fast and accurate short read alignment with Burrows-Wheeler transform

(2009) H. Li et al.   BIOINFORMATICS

Inheritance of pinacle exsertion in rice

(2008) Renata Pereira da Cruz et al.   SCIENTIA AGRICOLA