Genome-Wide Association Analysis Dissects the Genetic Basis of the Grain Carbon and Nitrogen Contents in Milled Rice

[1]  M. Gu,et al.  Natural variation of OsGluA2 is involved in grain protein content regulation in rice , 2019, Nature Communications.

[2]  F. Deng,et al.  Polyaspartic acid (PASP)-urea and optimised nitrogen management increase the grain nitrogen concentration of rice , 2019, Scientific Reports.

[3]  Guijun Yang,et al.  Monitoring ratio of carbon to nitrogen (C/N) in wheat and barley leaves by using spectral slope features with branch-and-bound algorithm , 2018, Scientific Reports.

[4]  Xianghua Li,et al.  Genetic Basis of Variation in Rice Seed Storage Protein (Albumin, Globulin, Prolamin, and Glutelin) Content Revealed by Genome-Wide Association Analysis , 2018, Front. Plant Sci..

[5]  Kenneth L. McNally,et al.  Genomic variation in 3,010 diverse accessions of Asian cultivated rice , 2018, Nature.

[6]  Zhikang Li,et al.  Genome-wide and gene-based association mapping for rice eating and cooking characteristics and protein content , 2017, Scientific Reports.

[7]  Dianrong Ma,et al.  Mapping quantitative trait loci associated with starch paste viscosity in rice (Oryza sativa L.) under different environmental conditions , 2017 .

[8]  Yueyun Hong,et al.  The Sulfoquinovosyltransferase-like Enzyme SQD2.2 is Involved in Flavonoid Glycosylation, Regulating Sugar Metabolism and Seed Setting in Rice , 2017, Scientific Reports.

[9]  Wenfu Chen,et al.  Advances and prospects of super rice breeding in China , 2017 .

[10]  Zhikang Li,et al.  Relationship of Rice Grain Amylose, Gelatinization Temperature and Pasting Properties for Breeding Better Eating and Cooking Quality of Rice Varieties , 2016, PloS one.

[11]  Guifu Liu,et al.  Critical roles of soluble starch synthase SSIIIa and granule-bound starch synthase Waxy in synthesizing resistant starch in rice , 2016, Proceedings of the National Academy of Sciences.

[12]  Genome-wide association study of eating and cooking qualities in different subpopulations of rice (Oryza sativa L.) , 2016, BMC Genomics.

[13]  Ling Jiang,et al.  ADP-glucose pyrophosphorylase large subunit 2 is essential for storage substance accumulation and subunit interactions in rice endosperm. , 2016, Plant science : an international journal of experimental plant biology.

[14]  Xin Zhang,et al.  Pyrophosphate: fructose-6-phosphate 1-phosphotransferase (PFP) regulates carbon metabolism during grain filling in rice , 2016, Plant Cell Reports.

[15]  Bo Huang,et al.  Improving power and accuracy of genome-wide association studies via a multi-locus mixed linear model methodology , 2016, Scientific Reports.

[16]  G. An,et al.  Alanine aminotransferase 1 (OsAlaAT1) plays an essential role in the regulation of starch storage in rice endosperm. , 2015, Plant science : an international journal of experimental plant biology.

[17]  W. J. Lucas,et al.  Brassinosteroids promote development of rice pollen grains and seeds by triggering expression of Carbon Starved Anther, a MYB domain protein. , 2015, The Plant journal : for cell and molecular biology.

[18]  T. Hatanaka,et al.  CO2-Responsive CONSTANS, CONSTANS-Like, and Time of Chlorophyll a/b Binding Protein Expression1 Protein Is a Positive Regulator of Starch Synthesis in Vegetative Organs of Rice1[OPEN] , 2015, Plant Physiology.

[19]  Chia-Hung Chien,et al.  EXPath: a database of comparative expression analysis inferring metabolic pathways for plants , 2015, BMC Genomics.

[20]  Wensheng Wang,et al.  SNP-Seek database of SNPs derived from 3000 rice genomes , 2014, Nucleic Acids Res..

[21]  T. Hirose,et al.  Control of grain protein contents through SEMIDWARF1 mutant alleles: sd1 increases the grain protein content in Dee-geo-woo-gen but not in Reimei , 2015, Molecular Genetics and Genomics.

[22]  Cai-guo Xu,et al.  OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice , 2014, Nature Communications.

[23]  Xin-qiang Liang,et al.  Carbon, Nitrogen and Phosphorus Accumulation and Partitioning, and C:N:P Stoichiometry in Late-Season Rice under Different Water and Nitrogen Managements , 2014, PloS one.

[24]  rice genomes The 3,000 rice genomes project , 2014, GigaScience.

[25]  Stephen D. Turner,et al.  qqman: an R package for visualizing GWAS results using Q-Q and manhattan plots , 2014, bioRxiv.

[26]  Haiyang Wang,et al.  GLUTELIN PRECURSOR ACCUMULATION3 Encodes a Regulator of Post-Golgi Vesicular Traffic Essential for Vacuolar Protein Sorting in Rice Endosperm[W][OPEN] , 2014, Plant Cell.

[27]  Zhikang Li,et al.  Identification of Stably Expressed Quantitative Trait Loci for Grain Yield and Protein Content Using Recombinant Inbred Line and Reciprocal Introgression Line Populations in Rice , 2013 .

[28]  Z. Yin,et al.  Small GTPase Sar1 is crucial for proglutelin and α-globulin export from the endoplasmic reticulum in rice endosperm , 2013, Journal of experimental botany.

[29]  S. S. Sun,et al.  Metabolic engineering and profiling of rice with increased lysine. , 2013, Plant biotechnology journal.

[30]  Yoshiaki Nagamura,et al.  RiceXPro Version 3.0: expanding the informatics resource for rice transcriptome , 2012, Nucleic Acids Res..

[31]  Aijun Sun,et al.  Functions of the CCCH type zinc finger protein OsGZF1 in regulation of the seed storage protein GluB-1 from rice , 2013, Plant Molecular Biology.

[32]  D. Schwartz,et al.  Improvement of the Oryza sativa Nipponbare reference genome using next generation sequence and optical map data , 2013, Rice.

[33]  Yong-Jin Park,et al.  An SNP downstream of the OsBEIIb gene is significantly associated with amylose content and viscosity properties in rice (Oryza sativa L.) , 2012 .

[34]  Ling Jiang,et al.  Genetic relationship between grain chalkiness, protein content, and paste viscosity properties in a backcross inbred population of rice , 2012 .

[35]  Chunlong Sun,et al.  A Putative Gene sbe3-rs for Resistant Starch Mutated from SBE3 for Starch Branching Enzyme in Rice (Oryza sativa L.) , 2012, PloS one.

[36]  Kunisuke Tanaka,et al.  Formation mechanism of the internal structure of type I protein bodies in rice endosperm: relationship between the localization of prolamin species and the expression of individual genes. , 2012, The Plant journal : for cell and molecular biology.

[37]  Stacey S. Cherny,et al.  Evaluating the effective numbers of independent tests and significant p-value thresholds in commercial genotyping arrays and public imputation reference datasets , 2011, Human Genetics.

[38]  G. Wang,et al.  Opaque7 Encodes an Acyl-Activating Enzyme-Like Protein That Affects Storage Protein Synthesis in Maize Endosperm , 2011, Genetics.

[39]  H. Zhai,et al.  Dynamic QTL Analysis of Rice Protein Content and Protein Index Using Recombinant Inbred Lines , 2011, Journal of Plant Biology.

[40]  P. Visscher,et al.  GCTA: a tool for genome-wide complex trait analysis. , 2011, American journal of human genetics.

[41]  J. Wan,et al.  Dissecting the genetic basis for the effect of rice chalkiness, amylose content, protein content, and rapid viscosity analyzer profile characteristics on the eating quality of cooked rice using the chromosome segment substitution line population across eight environments. , 2011, Genome.

[42]  Taiji Kawakatsu,et al.  Cereal seed storage protein synthesis: fundamental processes for recombinant protein production in cereal grains. , 2010, Plant biotechnology journal.

[43]  F. Liu,et al.  OsRab5a regulates endomembrane organization and storage protein trafficking in rice endosperm cells. , 2010, The Plant journal : for cell and molecular biology.

[44]  H. Yasuda,et al.  Reducing Rice Seed Storage Protein Accumulation Leads to Changes in Nutrient Quality and Storage Organelle Formation1[W][OA] , 2010, Plant Physiology.

[45]  M. Yano,et al.  A Novel Factor FLOURY ENDOSPERM2 Is Involved in Regulation of Rice Grain Size and Starch Quality[W] , 2010, Plant Cell.

[46]  Zhenghui Liu,et al.  Distribution of proteins and amino acids in milled and brown rice as affected by nitrogen fertilization and genotype , 2010 .

[47]  J. Matic,et al.  Rapid method for determination of protein content in cereals and oilseeds: validation, measurement uncertainty and comparison with the Kjeldahl method , 2010 .

[48]  Yasunori Nakamura,et al.  Starch biosynthesis in cereal endosperm. , 2010, Plant physiology and biochemistry : PPB.

[49]  J. Wan,et al.  QTL mapping of protein content in rice using single chromosome segment substitution lines , 2010, Theoretical and Applied Genetics.

[50]  H. Kang,et al.  Variance component model to account for sample structure in genome-wide association studies , 2010, Nature Genetics.

[51]  Qian Qian,et al.  Allelic diversities in rice starch biosynthesis lead to a diverse array of rice eating and cooking qualities , 2009, Proceedings of the National Academy of Sciences.

[52]  Hiroshi Yasuda,et al.  Compensation and interaction between RISBZ1 and RPBF during grain filling in rice. , 2009, The Plant journal : for cell and molecular biology.

[53]  M. Gu,et al.  Variation and distribution of seed storage protein content and composition among different rice varieties. , 2009 .

[54]  F. Liu,et al.  The vacuolar processing enzyme OsVPE1 is required for efficient glutelin processing in rice. , 2009, The Plant journal : for cell and molecular biology.

[55]  M. Yano,et al.  Characterization of a new rice glutelin gene GluD-1 expressed in the starchy endosperm , 2008, Journal of experimental botany.

[56]  Wei He,et al.  Control of rice grain-filling and yield by a gene with a potential signature of domestication , 2008, Nature Genetics.

[57]  Zhen Zhu,et al.  Inheritance Analysis and QTL Mapping of Rice Starch Viscosity (Rapid Visco Analyzer Profile) Characteristics , 2008 .

[58]  Manuel A. R. Ferreira,et al.  PLINK: a tool set for whole-genome association and population-based linkage analyses. , 2007, American journal of human genetics.

[59]  Jinko Graham,et al.  LDheatmap: An R Function for Graphical Display of Pairwise Linkage Disequilibria Between Single Nucleotide Polymorphisms , 2006 .

[60]  Albert J. Vilella,et al.  VariScan: Analysis of evolutionary patterns from large-scale DNA sequence polymorphism data , 2005, Bioinform..

[61]  G. An,et al.  White-core endosperm floury endosperm-4 in rice is generated by knockout mutations in the C-type pyruvate orthophosphate dikinase gene (OsPPDKB). , 2005, The Plant journal : for cell and molecular biology.

[62]  Ines Hilke,et al.  Determination of total organic carbon: an overview of current methods , 2004 .

[63]  Jianguo G. Wu,et al.  Genetic analysis for protein content in indica rice , 1999, Euphytica.

[64]  M. Yano,et al.  Chromosomal location of genes conditioning low amylose content of endosperm starches in rice, Oryza sativa L. , 1988, Theoretical and Applied Genetics.

[65]  T. Nishio,et al.  Low glutelin content1: A Dominant Mutation That Suppresses the Glutelin Multigene Family via RNA Silencing in Rice Online version contains Web-only data. Article, publication date, and citation information can be found at www.plantcell.org/cgi/doi/10.1105/tpc.011452. , 2003, The Plant Cell Online.

[66]  M. Martín,et al.  Proteins in Rice Grains Influence Cooking Properties , 2002 .

[67]  S. Gabriel,et al.  The Structure of Haplotype Blocks in the Human Genome , 2002, Science.

[68]  Yasunori Nakamura,et al.  The fine Structure of Amylopectin in Endosperm from Asian Cultivated Rice can be largely Classified into two Classes , 2002 .

[69]  K. Harada,et al.  Quantitative nature of the Prolamin-box, ACGT and AACA motifs in a rice glutelin gene promoter: minimal cis-element requirements for endosperm-specific gene expression. , 2000, The Plant journal : for cell and molecular biology.

[70]  Yasunori Nakamura,et al.  Differences in Amylopectin Structure Between Two Rice Varieties in Relation to the Effects of Temperature During Grain‐Filling , 1999 .