Applications and challenges for efficient exploration of omics interventions for the enhancement of nutritional quality in rice (Oryza sativa L.)

Identification of genomic region(s) responsible for high iron and zinc content in rice

(2019) Shilpi Dixit et al.   Scientific Reports

Status and Prospects of Next Generation Sequencing Technologies in Crop Plants

(2018) T.R. Sharma et al.   CURRENT ISSUES IN MOLECULAR BIOLOGY

Discovery of Lineage-Specific Genome Change in Rice Through Analysis of Resequencing Data

(2018) Robert A. Arthur et al.   GENETICS

Genomes of 13 domesticated and wild rice relatives highlight genetic conservation, turnover and innovation across the genus Oryza

(2018) Joshua C. Stein et al.   NATURE GENETICS

Lineage-specific gene acquisition or loss is involved in interspecific hybrid sterility in rice

(2018) Yohei Koide et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Isolation and characterisation of antioxidative peptides from bromelain-hydrolysed brown rice protein by proteomic technique

(2018) Orrapun Selamassakul et al.   PROCESS BIOCHEMISTRY

Comparative whole genome re-sequencing analysis in upland New Rice for Africa: insights into the breeding history and respective genome compositions

(2018) Naoki Yamamoto et al.   Rice

QTL Identification for Cooking and Eating Quality in indica Rice Using Multi-Parent Advanced Generation Intercross (MAGIC) Population

(2018) Kimberly S. Ponce et al.   Frontiers in Plant Science

Discovery of Lineage-Specific Genome Change in Rice Through Analysis of Resequencing Data

(2018) Robert A. Arthur et al.   GENETICS

Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

(2018) Jae-Hyeon Oh et al.   3 Biotech

Whole-genome resequencing and transcriptomic analysis of genes regulating anthocyanin biosynthesis in black rice plants

(2018) Jae-Hyeon Oh et al.   3 Biotech

Genome sequencing of rice subspecies and genetic analysis of recombinant lines reveals regional yield- and quality-associated loci

(2018) Xiukun Li et al.   BMC BIOLOGY

Alternative Splicing Plays a Critical Role in Maintaining Mineral Nutrient Homeostasis in Rice (Oryza sativa)

(2018) Chunlan Dong et al.   PLANT CELL

RNA-binding protein RBP-P is required for glutelin and prolamine mRNA localization in rice endosperm cells

(2018) Li Tian et al.   PLANT CELL

Identification of genomic regions associated with agronomic and biofortification traits in DH populations of rice

(2018) B. P. Mallikarjuna Swamy et al.   PLoS One

Identification of the biochemical characteristics of developing giant embryo rice grains using non-targeted metabolomics

(2018) Guo-Chao Zhao et al.   JOURNAL OF CEREAL SCIENCE

Improvements to the Rice Genome Annotation Through Large-Scale Analysis of RNA-Seq and Proteomics Data Sets

(2018) Zhe Ren et al.   MOLECULAR & CELLULAR PROTEOMICS

Integrating a genome‐wide association study with a large‐scale transcriptome analysis to predict genetic regions influencing the glycaemic index and texture in rice

(2018) Roslen Anacleto et al.   PLANT BIOTECHNOLOGY JOURNAL

Transcriptome monitoring visualizes growth stage-dependent nutrient status dynamics in rice under field conditions

(2018) Hinako Takehisa et al.   PLANT JOURNAL

Genome Based Meta-QTL Analysis of Grain Weight in Tetraploid Wheat Identifies Rare Alleles of GRF4 Associated with Larger Grains

(2018) Raz Avni et al.   Genes

Augmentation of crop productivity through interventions of omics technologies in India: challenges and opportunities

(2018) Rajesh Kumar Pathak et al.   3 Biotech

A comparative UHPLC-QqQ-MS-based metabolomics approach for evaluating Chinese and North American wild rice

(2018) Ning Yan et al.   FOOD CHEMISTRY

Comparative proteomics and protein profile related to phenolic compounds and antioxidant activity in germinated Oryza sativa ‘KDML105’ and Thai brown rice ‘Mali Daeng’ for better nutritional value

(2017) Sarunyaporn Maksup et al.   JOURNAL OF THE SCIENCE OF FOOD AND AGRICULTURE

Resequencing and variation identification of whole genome of the japonica rice variety "Longdao24" with high yield

(2017) Shukun Jiang et al.   PLoS One

Rice Bran Metabolome Contains Amino Acids, Vitamins & Cofactors, and Phytochemicals with Medicinal and Nutritional Properties

(2017) Iman Zarei et al.   Rice

Transcriptomics technologies

(2017) Rohan Lowe et al.   PLoS Computational Biology

Regional Association Analysis of MetaQTLs Delineates Candidate Grain Size Genes in Rice

(2017) Anurag V. Daware et al.   Frontiers in Plant Science

Agronomic biofortification of crops to fight hidden hunger in sub-Saharan Africa

(2017) A.W. de Valença et al.   Global Food Security-Agriculture Policy Economics and Environment

Improving nutrition through biofortification: A review of evidence from HarvestPlus, 2003 through 2016

(2017) Howarth E. Bouis et al.   Global Food Security-Agriculture Policy Economics and Environment

Single genetic locus improvement of iron, zinc and β-carotene content in rice grains

(2017) Simrat Pal Singh et al.   Scientific Reports

Editorial (Thematic Issue: Plant Quality Improvement and Nutrigenomics)

(2016) Lam-Son Phan Tran et al.   CURRENT GENOMICS

Analysis of Big Data technologies for use in agro-environmental science

(2016) Rob Lokers et al.   ENVIRONMENTAL MODELLING & SOFTWARE

Comparative nutritional compositions and proteomics analysis of transgenic Xa21 rice seeds compared to conventional rice

(2016) Dipak Gayen et al.   FOOD CHEMISTRY

A 1H HR-MAS NMR-Based Metabolomic Study for Metabolic Characterization of Rice Grain from Various Oryza sativa L. Cultivars

(2016) Eun-Hye Song et al.   JOURNAL OF AGRICULTURAL AND FOOD CHEMISTRY

Plant Ionomics: From Elemental Profiling to Environmental Adaptation

(2016) Xin-Yuan Huang et al.   Molecular Plant

Overexpression of the 16-kDa α-amylase/trypsin inhibitor RAG2 improves grain yield and quality of rice

(2016) Wei Zhou et al.   PLANT BIOTECHNOLOGY JOURNAL

iTRAQ-Based Quantitative Proteomics Analysis of Black Rice Grain Development Reveals Metabolic Pathways Associated with Anthocyanin Biosynthesis

(2016) Linghua Chen et al.   PLoS One

Optimum breeding strategies using genomic selection for hybrid breeding in wheat, maize, rye, barley, rice and triticale

(2016) Jose J. Marulanda et al.   THEORETICAL AND APPLIED GENETICS

Toward integration of genomic selection with crop modelling: the development of an integrated approach to predicting rice heading dates

(2016) Akio Onogi et al.   THEORETICAL AND APPLIED GENETICS

Proteomic and Glycomic Characterization of Rice Chalky Grains Produced Under Moderate and High-temperature Conditions in Field System

(2016) Kentaro Kaneko et al.   Rice

Identification of variability for agronomically important traits in rice mutant families

(2016) Viviane Kopp da Luz et al.   BRAGANTIA

Identification of variability for agronomically important traits in rice mutant families

(2016) Viviane Kopp da Luz et al.   BRAGANTIA

Rice grain nutritional traits and their enhancement using relevant genes and QTLs through advanced approaches

(2016) Anumalla Mahender et al.   SpringerPlus

Worldwide Genetic Diversity for Mineral Element Concentrations in Rice Grain

(2015) Shannon R. M Pinson et al.   CROP SCIENCE

Cultivar specific variations in antioxidative defense system, genome and proteome of two tropical rice cultivars against ambient and elevated ozone

(2015) Abhijit Sarkar et al.   ECOTOXICOLOGY AND ENVIRONMENTAL SAFETY

Impact of phytic acid on nutrient bioaccessibility and antioxidant properties of dehusked rice

(2015) H. H. Lee et al.   JOURNAL OF FOOD SCIENCE AND TECHNOLOGY-MYSORE

Accuracy of Genomic Selection in a Rice Synthetic Population Developed for Recurrent Selection Breeding

(2015) Cécile Grenier et al.   PLoS One

MAGIC populations in crops: current status and future prospects

(2015) B. Emma Huang et al.   THEORETICAL AND APPLIED GENETICS

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines

(2015) Jennifer Spindel et al.   PLoS Genetics

Expanding Omics Resources for Improvement of Soybean Seed Composition Traits

(2015) Juhi Chaudhary et al.   Frontiers in Plant Science

Whole-Genome Resequencing and Transcriptomic Analysis to Identify Genes Involved in Leaf-Color Diversity in Ornamental Rice Plants

(2015) Chang-Kug Kim et al.   PLoS One

Control of grain protein contents through SEMIDWARF1 mutant alleles: sd1 increases the grain protein content in Dee-geo-woo-gen but not in Reimei

(2014) Tomio Terao et al.   MOLECULAR GENETICS AND GENOMICS

RiceVarMap: a comprehensive database of rice genomic variations

(2014) Hu Zhao et al.   NUCLEIC ACIDS RESEARCH

SNP-Seek database of SNPs derived from 3000 rice genomes

(2014) Nickolai Alexandrov et al.   NUCLEIC ACIDS RESEARCH

Identification of loci governing eight agronomic traits using a GBS-GWAS approach and validation by QTL mapping in soya bean

(2014) Humira Sonah et al.   PLANT BIOTECHNOLOGY JOURNAL

EMS mutagenesis in mature seed-derived rice calli as a new method for rapidly obtaining TILLING mutant populations

(2014) Xavier Serrat et al.   Plant Methods

Genome Wide Association Mapping of Grain Arsenic, Copper, Molybdenum and Zinc in Rice (Oryza sativa L.) Grown at Four International Field Sites

(2014) Gareth J. Norton et al.   PLoS One

Predicting hybrid performance in rice using genomic best linear unbiased prediction

(2014) S. Xu et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Proteomic analysis of seed storage proteins in wild rice species of the Oryza genus

(2014) Chunmiao Jiang et al.   Proteome Science

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

(2014) Longbiao Guo et al.   Rice

OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice

(2014) Bo Peng et al.   Nature Communications

Metabolic variation between japonica and indica rice cultivars as revealed by non-targeted metabolomics

(2014) Chaoyang Hu et al.   Scientific Reports

Integrating omic approaches for abiotic stress tolerance in soybean

(2014) Rupesh Deshmukh et al.   Frontiers in Plant Science

The 3,000 rice genomes project: new opportunities and challenges for future rice research

(2014) Jia-Yang Li et al.   GigaScience

Protein profile of rice (Oryza sativa) seeds

(2013) Yanhua Yang et al.   GENETICS AND MOLECULAR BIOLOGY

Profiling the ionome of rice and its use in discriminating geographical origins at the regional scale, China

(2013) Gang Li et al.   JOURNAL OF ENVIRONMENTAL SCIENCES

Lysine from Cooked White Rice Consumed by Healthy Young Men Is Highly Metabolically Available When Assessed Using the Indicator Amino Acid Oxidation Technique

(2013) Ivo R. D. Prolla et al.   JOURNAL OF NUTRITION

Silicon decreases the arsenic level in rice grain by limiting arsenite transport

(2013) Alexander T. Fleck et al.   JOURNAL OF PLANT NUTRITION AND SOIL SCIENCE

MutMap-Gap: whole-genome resequencing of mutant F2 progeny bulk combined withde novoassembly of gap regions identifies the rice blast resistance genePii

(2013) Hiroki Takagi et al.   NEW PHYTOLOGIST

The advantages and limitations of trait analysis with GWAS: a review

(2013) Arthur Korte et al.   Plant Methods

MutMap+: Genetic Mapping and Mutant Identification without Crossing in Rice

(2013) Rym Fekih et al.   PLoS One

Genetic analysis of the metabolome exemplified using a rice population

(2013) L. Gong et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

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

Mapping and validation of quantitative trait loci associated with concentrations of 16 elements in unmilled rice grain

(2013) Min Zhang et al.   THEORETICAL AND APPLIED GENETICS

Resequencing rice genomes: an emerging new era of rice genomics

(2013) Xuehui Huang et al.   TRENDS IN GENETICS

Environmental effects on mineral accumulation in rice grains and identification of ecological specific QTLs

(2012) Juan Du et al.   ENVIRONMENTAL GEOCHEMISTRY AND HEALTH

Mapping QTLs and candidate genes for iron and zinc concentrations in unpolished rice of Madhukar×Swarna RILs

(2012) K. Anuradha et al.   GENE

Effects of White Rice, Brown Rice and Germinated Brown Rice on Antioxidant Status of Type 2 Diabetic Rats

(2012) Mustapha Umar Imam et al.   INTERNATIONAL JOURNAL OF MOLECULAR SCIENCES

Comparative analysis of the proteomic and nutritional composition of transgenic rice seeds with Cry1ab/ac genes and their non-transgenic counterparts

(2012) Yan Wang et al.   JOURNAL OF CEREAL SCIENCE

Comparative metabolic profiling of pigmented rice (Oryza sativa L.) cultivars reveals primary metabolites are correlated with secondary metabolites

(2012) Jae Kwang Kim et al.   JOURNAL OF CEREAL SCIENCE

Comparisons and selection of rice mutants with high iron and zinc contents in their polished grains that were mutated from the indica type cultivar IR64

(2012) Toong Long Jeng et al.   JOURNAL OF FOOD COMPOSITION AND ANALYSIS

Genome sequencing reveals agronomically important loci in rice using MutMap

(2012) Akira Abe et al.   NATURE BIOTECHNOLOGY

Fortifying plants with the essential amino acids lysine and methionine to improve nutritional quality

(2012) Gad Galili et al.   PLANT BIOTECHNOLOGY JOURNAL

Vacuolar membrane transporters OsVIT1 and OsVIT2 modulate iron translocation between flag leaves and seeds in rice

(2012) Yu Zhang et al.   PLANT JOURNAL

Dissection of genotype-phenotype associations in rice grains using metabolome quantitative trait loci analysis

(2012) Fumio Matsuda et al.   PLANT JOURNAL

Genomic Selection in Plant Breeding: A Comparison of Models

(2011) Nicolas Heslot et al.   CROP SCIENCE

Fine mapping of grain length QTLs on chromosomes 1 and 7 in Basmati rice (Oryza sativa L.)

(2011) Rakesh Singh et al.   JOURNAL OF PLANT BIOCHEMISTRY AND BIOTECHNOLOGY

A genomics and multi-platform metabolomics approach to identify new traits of rice quality in traditional and improved varieties

(2011) M. N. Calingacion et al.   Metabolomics

Improved antioxidant activity of BKOS Thai jasmine rice

(2011) N. Semsang et al.   NATURAL PRODUCT RESEARCH

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

(2011) Xun Xu et al.   NATURE BIOTECHNOLOGY

A Role for the Cysteine-Rich 10 kDa Prolamin in Protein Body I Formation in Rice

(2011) Ai Nagamine et al.   PLANT AND CELL PHYSIOLOGY

Application of Gene Targeting to Designed Mutation Breeding of High-Tryptophan Rice

(2011) H. Saika et al.   PLANT PHYSIOLOGY

Low-affinity cation transporter (OsLCT1) regulates cadmium transport into rice grains

(2011) S. Uraguchi et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

A label-free quantitative shotgun proteomics analysis of rice grain development

(2011) Joohyun Lee et al.   Proteome Science

Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping

(2011) Adam N. Famoso et al.   PLoS Genetics

Genomic resources in horticultural crops: Status, utility and challenges

(2010) Humira Sonah et al.   BIOTECHNOLOGY ADVANCES

Ionomics: The functional genomics of elements

(2010) I. Baxter   Briefings in Functional Genomics

Identification of candidate genes for grain number in rice (Oryza sativa L.)

(2010) Rupesh Deshmukh et al.   FUNCTIONAL & INTEGRATIVE GENOMICS

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

(2010) T. Lu et al.   GENOME RESEARCH

Identification of putative target genes to manipulate Fe and Zn concentrations in rice grains

(2010) Raul A. Sperotto et al.   JOURNAL OF PLANT PHYSIOLOGY

Differences in Transcriptional Regulatory Mechanisms Functioning for Free Lysine Content and Seed Storage Protein Accumulation in Rice Grain

(2010) Taiji Kawakatsu et al.   PLANT AND CELL PHYSIOLOGY

OsMADS6 plays an essential role in endosperm nutrient accumulation and is subject to epigenetic regulation in rice (Oryza sativa)

(2010) Jian Zhang et al.   PLANT JOURNAL

Rice metal-nicotianamine transporter, OsYSL2, is required for the long-distance transport of iron and manganese

(2010) Yasuhiro Ishimaru et al.   PLANT JOURNAL

Metabolomic and Functional Genomic Analyses Reveal Varietal Differences in Bioactive Compounds of Cooked Rice

(2010) Adam L. Heuberger et al.   PLoS One

QTL mapping of protein content in rice using single chromosome segment substitution lines

(2010) Guoyou Ye et al.   THEORETICAL AND APPLIED GENETICS

Detection of genomic deletions in rice using oligonucleotide microarrays

(2009) Myron Bruce et al.   BMC GENOMICS

High-throughput genotyping by whole-genome resequencing

(2009) X. Huang et al.   GENOME RESEARCH

Quantitative trait loci controlling Cu, Ca, Zn, Mn and Fe content in rice grains

(2009) Kaiyang Lu et al.   JOURNAL OF GENETICS

A transcriptome atlas of rice cell types uncovers cellular, functional and developmental hierarchies

(2009) Yuling Jiao et al.   NATURE GENETICS

Differential Effects of a Transgene to Confer Low Phytic Acid in Caryopses Located at Different Positions in Rice Panicles

(2009) Mio Kuwano et al.   PLANT AND CELL PHYSIOLOGY

Genetic mapping of the rice ionome in leaves and grain: identification of QTLs for 17 elements including arsenic, cadmium, iron and selenium

(2009) Gareth J. Norton et al.   PLANT AND SOIL

Mutant Resources in Rice for Functional Genomics of the Grasses

(2009) A. Krishnan et al.   PLANT PHYSIOLOGY

Iron fortification of rice seeds through activation of the nicotianamine synthase gene

(2009) S. Lee et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database

(2009) Brigitte Courtois et al.   Rice

QTL mapping for crude protein and protein fraction contents in rice (Oryza sativa L.)

(2008) Wenwei Zhang et al.   JOURNAL OF CEREAL SCIENCE

Isolation and characterization of a low phytic acid rice mutant reveals a mutation in the rice orthologue of maize MIK

(2008) S. I. Kim et al.   THEORETICAL AND APPLIED GENETICS

The rice OsLpa1 gene encodes a novel protein involved in phytic acid metabolism

(2008) S. I. Kim et al.   THEORETICAL AND APPLIED GENETICS