Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters

[1]  Namrata Singh,et al.  Corrigendum: Open access resources for genome-wide association mapping in rice , 2016, Nature communications.

[2]  A. Henry,et al.  Action of multiple intra-QTL genes concerted around a co-localized transcription factor underpins a large effect QTL , 2015, Scientific Reports.

[3]  F. Taguchi-Shiobara,et al.  Natural Variation in the Flag Leaf Morphology of Rice Due to a Mutation of the NARROW LEAF 1 Gene in Oryza sativa L. , 2015, Genetics.

[4]  Xueyong Li,et al.  Characterization of a Null Allelic Mutant of the Rice NAL1 Gene Reveals Its Role in Regulating Cell Division , 2015, PloS one.

[5]  D. Akdemir,et al.  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, PLoS genetics.

[6]  Li Wang,et al.  LSCHL4 from Japonica Cultivar, Which Is Allelic to NAL1, Increases Yield of Indica Super Rice 93-11 , 2014, Molecular plant.

[7]  Dabing Zhang,et al.  Molecular control of grass inflorescence development. , 2014, Annual review of plant biology.

[8]  A. Greenberg,et al.  High-Resolution Inflorescence Phenotyping Using a Novel Image-Analysis Pipeline, PANorama1[W][OPEN] , 2014, Plant Physiology.

[9]  M. Stephens,et al.  fastSTRUCTURE: Variational Inference of Population Structure in Large SNP Data Sets , 2014, Genetics.

[10]  Doreen Ware,et al.  Regulatory modules controlling maize inflorescence architecture , 2014, Genome research.

[11]  Zhi-xing Zhang,et al.  A Proteomic Study on Molecular Mechanism of Poor Grain-Filling of Rice (Oryza sativa L.) Inferior Spikelets , 2014, PloS one.

[12]  R Core Team,et al.  R: A language and environment for statistical computing. , 2014 .

[13]  D. Fujita,et al.  NAL1 allele from a rice landrace greatly increases yield in modern indica cultivars , 2013, Proceedings of the National Academy of Sciences.

[14]  Joseph L. Gage,et al.  Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations , 2013, TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik.

[15]  F. Taguchi-Shiobara,et al.  A natural variant of NAL1, selected in high-yield rice breeding programs, pleiotropically increases photosynthesis rate , 2013, Scientific Reports.

[16]  R. Terauchi,et al.  OsLG1 regulates a closed panicle trait in domesticated rice , 2013, Nature Genetics.

[17]  Jun-ichi Itoh,et al.  RiceFREND: a platform for retrieving coexpressed gene networks in rice , 2012, Nucleic Acids Res..

[18]  A. Fujiyama,et al.  A map of rice genome variation reveals the origin of cultivated rice , 2012, Nature.

[19]  S. Fujioka,et al.  Rice CYP90D2 and CYP90D3 catalyze C-23 hydroxylation of brassinosteroids in vitro. , 2012, Plant physiology and biochemistry : PPB.

[20]  A. Auton,et al.  Genome-wide patterns of genetic variation in worldwide Arabidopsis thaliana accessions from the RegMap panel , 2011, Nature Genetics.

[21]  Qian Qian,et al.  Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm , 2011, Nature Genetics.

[22]  Edward S. Buckler,et al.  Distinct Genetic Architectures for Male and Female Inflorescence Traits of Maize , 2011, PLoS genetics.

[23]  Justin O Borevitz,et al.  Genome-wide association studies in plants: the missing heritability is in the field , 2011, Genome Biology.

[24]  H. Yoshida,et al.  Flower development in rice. , 2011, Journal of experimental botany.

[25]  Mark H. Wright,et al.  Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa , 2011, Nature communications.

[26]  Keyan Zhao,et al.  Genetic Architecture of Aluminum Tolerance in Rice (Oryza sativa) Determined through Genome-Wide Association Analysis and QTL Mapping , 2011, PLoS genetics.

[27]  Peng Wang,et al.  A major QTL, Ghd8, plays pleiotropic roles in regulating grain productivity, plant height, and heading date in rice. , 2011, Molecular plant.

[28]  Yonghong Wang,et al.  Branching in rice. , 2011, Current opinion in plant biology.

[29]  M. Yano,et al.  Evaluation of yield performance in rice near-isogenic lines with increased spikelet number , 2011 .

[30]  Yutaka Sato,et al.  Field transcriptome revealed critical developmental and physiological transitions involved in the expression of growth potential in japonica rice , 2011, BMC Plant Biology.

[31]  H. Kitano,et al.  Diversity of panicle branching patterns in wild relatives of rice , 2010 .

[32]  Qifa Zhang,et al.  Genome-wide association studies of 14 agronomic traits in rice landraces , 2010, Nature Genetics.

[33]  C. Bustamante,et al.  Genomic Diversity and Introgression in O. sativa Reveal the Impact of Domestication and Breeding on the Rice Genome , 2010, PloS one.

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

[35]  Bjarni J. Vilhjálmsson,et al.  Genome-wide association study of 107 phenotypes in Arabidopsis thaliana inbred lines , 2010 .

[36]  G. An,et al.  Map-based cloning of the ERECT PANICLE 3 gene in rice , 2009, Theoretical and Applied Genetics.

[37]  Qian Qian,et al.  Natural variation at the DEP1 locus enhances grain yield in rice , 2009, Nature Genetics.

[38]  Kosuke M. Teshima,et al.  Variations in Hd1 proteins, Hd3a promoters, and Ehd1 expression levels contribute to diversity of flowering time in cultivated rice , 2009, Proceedings of the National Academy of Sciences.

[39]  L. Liang,et al.  Mapping complex disease traits with global gene expression , 2009, Nature Reviews Genetics.

[40]  M. Yano,et al.  Ehd2, a Rice Ortholog of the Maize INDETERMINATE1 Gene, Promotes Flowering by Up-Regulating Ehd11[C][W] , 2008, Plant Physiology.

[41]  Gurdev S. Khush,et al.  Progress in ideotype breeding to increase rice yield potential , 2008 .

[42]  Lei Wang,et al.  Natural variation in Ghd7 is an important regulator of heading date and yield potential in rice , 2008, Nature Genetics.

[43]  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.

[44]  K. Chong,et al.  Functions of OsBZR1 and 14-3-3 proteins in brassinosteroid signaling in rice , 2007, Proceedings of the National Academy of Sciences.

[45]  K. Asano,et al.  Molecular Interactions of a Soluble Gibberellin Receptor, GID1, with a Rice DELLA Protein, SLR1, and Gibberellin[W] , 2007, The Plant Cell Online.

[46]  Christian A. Ross,et al.  The WRKY Gene Family in Rice (Oryza sativa) , 2007 .

[47]  A. Doust.  Architectural Evolution and its Implications for Domestication in Grasses , 2007, Annals of botany.

[48]  Ashutosh Kumar Singh,et al.  MADS-box gene family in rice: genome-wide identification, organization and expression profiling during reproductive development and stress , 2007, BMC Genomics.

[49]  J. Kyozuka,et al.  Genome-wide analysis of spatial and temporal gene expression in rice panicle development. , 2006, The Plant journal : for cell and molecular biology.

[50]  Qian Qian,et al.  EUI1, encoding a putative cytochrome P450 monooxygenase, regulates internode elongation by modulating gibberellin responses in rice. , 2006, Plant & cell physiology.

[51]  Q. Qian,et al.  Cytokinin Oxidase Regulates Rice Grain Production , 2005, Science.

[52]  Amanda J. Garris,et al.  Genetic Structure and Diversity in Oryza sativa L. , 2005, Genetics.

[53]  Mark Daly,et al.  Haploview: analysis and visualization of LD and haplotype maps , 2005, Bioinform..

[54]  Masatomo Kobayashi,et al.  An Overview of Gibberellin Metabolism Enzyme Genes and Their Related Mutants in Rice1[w] , 2004, Plant Physiology.

[55]  Y. Nagato,et al.  Developmental Course of Inflorescence and Spikelet in Rice , 2004 .

[56]  Z. Li,et al.  Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two backcross populations , 2003, Theoretical and Applied Genetics.

[57]  J. Li,et al.  Identification of QTLs affecting traits of agronomic importance in a recombinant inbred population derived from a subspecific rice cross , 1996, Theoretical and Applied Genetics.

[58]  N. Rosenberg.  distruct: a program for the graphical display of population structure , 2003 .

[59]  P. Shannon,et al.  Cytoscape: a software environment for integrated models of biomolecular interaction networks. , 2003, Genome research.

[60]  G. S. Khush,et al.  QTL × environment interactions in rice. I. Heading date and plant height , 2003, Theoretical and Applied Genetics.

[61]  K. Shimamoto,et al.  FRIZZY PANICLE is required to prevent the formation of axillary meristems and to establish floral meristem identity in rice spikelets , 2003, Development.

[62]  M. Osaki,et al.  Molecular marker dissection of rice (Oryza sativa L.) plant architecture under temperate and tropical climates , 2003, Theoretical and Applied Genetics.

[63]  Peter Hedden,et al.  The genes of the Green Revolution. , 2003, Trends in genetics : TIG.

[64]  A. Paterson,et al.  Gene actions of QTLs affecting several agronomic traits resolved in a recombinant inbred rice population and two testcross populations , 2003, Theoretical and Applied Genetics.

[65]  Masatomo Kobayashi,et al.  Loss-of-function of a Rice Gibberellin Biosynthetic Gene, GA20 oxidase (GA20ox-2), Led to the Rice ‘Green Revolution’ , 2002 .

[66]  F. Taguchi-Shiobara,et al.  Mapping quantitative trait loci for days-to-heading, and culm, panicle and internode lengths in a BC1F3 population using an elite rice variety, Koshihikari, as the recurrent parent , 2001 .

[67]  Lishuang Shen,et al.  Comparison of Molecular Linkage Maps and Agronomic Trait Loci between DH and RIL Populations Derived from the Same Rice Cross , 2001 .

[68]  S. S. Virmani,et al.  Yield Potential Trends of Tropical Rice since the Release of IR8 and the Challenge of Increasing Rice Yield Potential , 1999 .

[69]  S. Tanksley,et al.  Identification of trait-improving quantitative trait loci alleles from a wild rice relative, Oryza rufipogon. , 1998, Genetics.

[70]  G. Khush.  Breaking the yield frontier of rice , 1995 .