Genomics-assisted allele mining and its integration into rice breeding

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

[2]  M. Yano,et al.  Control of root system architecture by DEEPER ROOTING 1 increases rice yield under drought conditions , 2013, Nature Genetics.

[3]  M. Yano,et al.  Genome-Wide Haplotype Changes Produced by Artificial Selection during Modern Rice Breeding in Japan , 2012, PloS one.

[4]  M. Yano,et al.  Identification of qSOR1, a major rice QTL involved in soil-surface rooting in paddy fields , 2011, Theoretical and Applied Genetics.

[5]  Paul C. Struik,et al.  Using chromosome introgression lines to map quantitative trait loci for photosynthesis parameters in rice (Oryza sativa L.) leaves under drought and well-watered field conditions , 2011, Journal of experimental botany.

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

[7]  M. Yano,et al.  Molecular distinction in genetic regulation of nonphotochemical quenching in rice , 2011, Proceedings of the National Academy of Sciences.

[8]  M. Yano,et al.  Genetic interactions involved in the inhibition of heading by heading date QTL, Hd2 in rice under long-day conditions , 2011, Theoretical and Applied Genetics.

[9]  L. Xiong,et al.  Evaluation of near-isogenic lines for drought resistance QTL and fine mapping of a locus affecting flag leaf width, spikelet number, and root volume in rice , 2011, Theoretical and Applied Genetics.

[10]  M. Yano,et al.  Dro1, a major QTL involved in deep rooting of rice under upland field conditions. , 2011, Journal of experimental botany.

[11]  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.

[12]  S. Adachi,et al.  Identification and characterization of genomic regions on chromosomes 4 and 8 that control the rate of photosynthesis in rice leaves , 2011, Journal of experimental botany.

[13]  J. Rogers,et al.  Crop genome sequencing: lessons and rationales. , 2011, Trends in plant science.

[14]  M. Yano,et al.  Discovery of Genome-Wide DNA Polymorphisms in a Landrace Cultivar of Japonica Rice by Whole-Genome Sequencing , 2011, Plant & cell physiology.

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

[16]  M. Yano,et al.  Uncovering of major genetic factors generating naturally occurring variation in heading date among Asian rice cultivars , 2011, Theoretical and Applied Genetics.

[17]  M. Yano,et al.  Identification of Chromosomal Regions Controlling the Leaf Photosynthetic Rate in Rice by Using a Progeny from Japonica and High-yielding Indica Varieties , 2011 .

[18]  M. Yano,et al.  Germplasm enhancement by developing advanced plant materials from diverse rice accessions , 2010 .

[19]  M. Yano,et al.  Core single-nucleotide polymorphisms—a tool for genetic analysis of the Japanese rice population , 2010 .

[20]  M. Yano,et al.  Genetic structure revealed by a whole-genome single-nucleotide polymorphism survey of diverse accessions of cultivated Asian rice (Oryza sativa L.) , 2010 .

[21]  Tadashi Hirasawa,et al.  New approach for rice improvement using a pleiotropic QTL gene for lodging resistance and yield , 2010, Nature communications.

[22]  Kenneth L. McNally,et al.  Genetic Variation in Biomass Traits among 20 Diverse Rice Varieties1[W][OA] , 2010, Plant Physiology.

[23]  M. Yano,et al.  Durable panicle blast-resistance gene Pb1 encodes an atypical CC-NBS-LRR protein and was generated by acquiring a promoter through local genome duplication. , 2010, The Plant journal : for cell and molecular biology.

[24]  M. Yano,et al.  Characterization of a rice variety with high hydraulic conductance and identification of the chromosome region responsible using chromosome segment substitution lines. , 2010, Annals of botany.

[25]  M. Yano,et al.  A Quantitative Trait Locus for Chlorophyll Content and its Association with Leaf Photosynthesis in Rice , 2010, Rice.

[26]  M. Yano,et al.  Integration of Genomics into Rice Breeding , 2010, Rice.

[27]  Jianmin Wan,et al.  DTH8 Suppresses Flowering in Rice, Influencing Plant Height and Yield Potential Simultaneously1[W][OA] , 2010, Plant Physiology.

[28]  Makoto Matsuoka,et al.  OsSPL14 promotes panicle branching and higher grain productivity in rice , 2010, Nature Genetics.

[29]  M. Yano,et al.  Fine mapping of Sta1, a quantitative trait locus determining stele transversal area, on rice chromosome 9 , 2010, Molecular breeding.

[30]  M. Yano,et al.  Q-TARO: QTL Annotation Rice Online Database , 2010, Rice.

[31]  M. Yano,et al.  Fine definition of the pedigree haplotypes of closely related rice cultivars by means of genome-wide discovery of single-nucleotide polymorphisms , 2010, BMC Genomics.

[32]  M. Yano,et al.  Fine-mapping of qRL6.1, a major QTL for root length of rice seedlings grown under a wide range of NH4+ concentrations in hydroponic conditions , 2010, Theoretical and Applied Genetics.

[33]  Toshiyuki Takai,et al.  Canopy temperature on clear and cloudy days can be used to estimate varietal differences in stomatal conductance in rice , 2010 .

[34]  B. Courtois,et al.  Rice Root Genetic Architecture: Meta-analysis from a Drought QTL Database , 2009, Rice.

[35]  Norikuni Saka,et al.  Loss of Function of a Proline-Containing Protein Confers Durable Disease Resistance in Rice , 2009, Science.

[36]  Peter J. Bradbury,et al.  Genetic Properties of the Maize Nested Association Mapping Population , 2009, Science.

[37]  Kenneth L. McNally,et al.  Genomewide SNP variation reveals relationships among landraces and modern varieties of rice , 2009, Proceedings of the National Academy of Sciences.

[38]  Xuehui Huang,et al.  High-throughput genotyping by whole-genome resequencing. , 2009, Genome research.

[39]  R. Fernando,et al.  Factors Affecting Accuracy From Genomic Selection in Populations Derived From Multiple Inbred Lines: A Barley Case Study , 2009, Genetics.

[40]  M. Yano,et al.  Towards the Understanding of Complex Traits in Rice: Substantially or Superficially? , 2009, DNA research : an international journal for rapid publication of reports on genes and genomes.

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

[42]  Roberto Tuberosa,et al.  Genome studies and molecular genetics-from sequence to crops: genomics comes of age. , 2009, Current opinion in plant biology.

[43]  M. Yano,et al.  Variation in root morphology and anatomy among accessions of cultivated rice (Oryza sativa L.) with different genetic backgrounds , 2009 .

[44]  M. Yano,et al.  Detection of a quantitative trait locus controlling carbon isotope discrimination and its contribution to stomatal conductance in japonica rice , 2009, Theoretical and Applied Genetics.

[45]  Yunbi Xu,et al.  Leaf-level water use efficiency determined by carbon isotope discrimination in rice seedlings: genetic variation associated with population structure and QTL mapping , 2009, Theoretical and Applied Genetics.

[46]  M. Goddard,et al.  Invited review: Genomic selection in dairy cattle: progress and challenges. , 2009, Journal of dairy science.

[47]  Detlef Weigel,et al.  Next-generation genetics in plants , 2008, Nature.

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

[49]  Shojiro Tamaki,et al.  Florigen and the Photoperiodic Control of Flowering in Rice , 2008, Rice.

[50]  Kaworu Ebana,et al.  Deletion in a gene associated with grain size increased yields during rice domestication , 2008, Nature Genetics.

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

[52]  R R Mir,et al.  Array-based high-throughput DNA markers for crop improvement , 2008, Heredity.

[53]  W. Powell,et al.  From mutations to MAGIC: resources for gene discovery, validation and delivery in crop plants. , 2008, Current opinion in plant biology.

[54]  M. Yano,et al.  QTLs underlying natural variation in stele and xylem structures of rice root , 2008 .

[55]  R. Bernardo,et al.  Prospects for genomewide selection for quantitative traits in maize , 2007 .

[56]  Wei Huang,et al.  A QTL for rice grain width and weight encodes a previously unknown RING-type E3 ubiquitin ligase , 2007, Nature Genetics.

[57]  A. Price,et al.  Marker-assisted selection to introgress rice QTLs controlling root traits into an Indian upland rice variety , 2006, Theoretical and Applied Genetics.

[58]  L. Xiong,et al.  Genetic Basis of Drought Resistance at Reproductive Stage in Rice: Separation of Drought Tolerance From Drought Avoidance , 2006, Genetics.

[59]  M. Kawase,et al.  Development of an RFLP-based Rice Diversity Research Set of Germplasm , 2005 .

[60]  Takuji Sasaki,et al.  The map-based sequence of the rice genome , 2005, Nature.

[61]  L. Xiong,et al.  Genetic analysis for drought resistance of rice at reproductive stage in field with different types of soil , 2005, Theoretical and Applied Genetics.

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

[63]  Zhikang Li,et al.  QTL mapping of root traits in a doubled haploid population from a cross between upland and lowland japonica rice in three environments , 2005, Theoretical and Applied Genetics.

[64]  F Alex Feltus,et al.  An SNP resource for rice genetics and breeding based on subspecies indica and japonica genome alignments. , 2004, Genome research.

[65]  B. Courtois,et al.  Locating QTLs controlling constitutive root traits in the rice population IAC 165 × Co39 , 2003, Euphytica.

[66]  Feiyan Liu,et al.  Mapping QTLs and candidate genes for rice root traits under different water-supply conditions and comparative analysis across three populations , 2003, Theoretical and Applied Genetics.

[67]  S. Hittalmani,et al.  Tagging quantitative trait loci associated with grain yield and root morphological traits in rice (Oryza sativa L.) under contrasting moisture regimes , 2002, Euphytica.

[68]  A. Price,et al.  Upland rice grown in soil-filled chambers and exposed to contrasting water-deficit regimes: II. Mapping quantitative trait loci for root morphology and distribution , 2002 .

[69]  G. S. Khush,et al.  Green revolution: A mutant gibberellin-synthesis gene in rice , 2002, Nature.

[70]  J. Zhang,et al.  Mapping QTLs for root morphology of a rice population adapted to rainfed lowland conditions , 2002, Theoretical and Applied Genetics.

[71]  S. Fukuoka,et al.  QTL analysis and mapping of pi21, a recessive gene for field resistance to rice blast in Japanese upland rice , 2001, Theoretical and Applied Genetics.

[72]  Honggang Zheng,et al.  Locating genomic regions associated with components of drought resistance in rice: comparative mapping within and across species , 2001, Theoretical and Applied Genetics.

[73]  Kenneth L. McNally,et al.  Evaluation of near-isogenic lines of rice introgressed with QTLs for root depth through marker-aided selection , 2001, Theoretical and Applied Genetics.

[74]  G. McLaren,et al.  Rice root morphological traits are related to isozyme group and adaptation , 2001 .

[75]  M. Goddard,et al.  Prediction of total genetic value using genome-wide dense marker maps. , 2001, Genetics.

[76]  M. L. Ali,et al.  Mapping QTLs for root traits in a recombinant inbred population from two indica ecotypes in rice , 2000, Theoretical and Applied Genetics.

[77]  B. Courtois,et al.  Quantitative trait loci for root-penetration ability and root thickness in rice: comparison of genetic backgrounds. , 2000, Genome.

[78]  D. S. Virk,et al.  Genetic dissection of root growth in rice (Oryza sativa L.) I: a hydrophonic screen , 1997, Theoretical and Applied Genetics.

[79]  A. D. Tomos,et al.  Genetic dissection of root growth in rice (Oryza sativa L.). II: mapping quantitative trait loci using molecular markers , 1997, Theoretical and Applied Genetics.

[80]  B. Courtois,et al.  Mapping genes controlling root morphology and root distribution in a doubled-haploid population of rice , 1997, Theoretical and Applied Genetics.

[81]  D. Zamir,et al.  An introgression line population of Lycopersicon pennellii in the cultivated tomato enables the identification and fine mapping of yield-associated QTL. , 1995, Genetics.

[82]  D. Mackill,et al.  Locating genes associated with root morphology and drought avoidance in rice via linkage to molecular markers , 1995, Theoretical and Applied Genetics.

[83]  S. Fukai,et al.  Development of drought-resistant cultivars using physiomorphological traits in rice , 1995 .

[84]  M. Lorieux,et al.  A universal core genetic map for rice , 2009, Theoretical and Applied Genetics.

[85]  T. Izawa Daylength measurements by rice plants in photoperiodic short-day flowering. , 2007, International review of cytology.

[86]  Jing-xia Zhang,et al.  Effects of Phenotyping Environment on Identification of Quantitative Trait Loci for Rice Root Morphology under Anaerobic Conditions. , 2002, Crop science.

[87]  A. Price,et al.  A combined RFLP and AFLP linkage map of upland rice (Oryza sativa L.) used to identify QTLs for root-penetration ability , 2000, Theoretical and Applied Genetics.

[88]  W. L. Bland,et al.  Genotypic variation in crop plant root systems , 1987 .

[89]  M. Kirkham Book reviewDrought resistance in crops with emphasis on rice: International Rice Research Institute, Los Baños, Laguna/Manila, The Philippines, 1982. 414 pp., US$16.25 plus airmail (US$14.50) or surface mail (US$1.75) postage. ISBN 971-104-078-6 , 1984 .