Bin Han

Summary

Affiliation: National Center for Gene Research
Country: China

Publications

  1. pmc Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943
    Tingting Lu
    College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, PR China
    DNA Res 15:285-95. 2008
  2. doi request reprint Sequencing-based genome-wide association study in rice
    Bin Han
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Curr Opin Plant Biol 16:133-8. 2013
  3. pmc Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences
    Zhenhua Peng
    Chinese Academy of Forestry, Wanshou Shan, Beijing, PR China
    BMC Plant Biol 10:116. 2010
  4. pmc Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)
    Jianjun Xu
    Yangzhou University, P R China
    BMC Genomics 11:656. 2010
  5. pmc Rice functional genomics research in China
    Bin Han
    National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, People s Republic of China
    Philos Trans R Soc Lond B Biol Sci 362:1009-21. 2007
  6. ncbi request reprint Genome-wide intraspecific DNA-sequence variations in rice
    Bin Han
    National Centre for Gene Research, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Curr Opin Plant Biol 6:134-8. 2003
  7. pmc Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication
    Yanchun Yu
    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant Cell 20:2946-59. 2008
  8. doi request reprint Dwarf 88, a novel putative esterase gene affecting architecture of rice plant
    Zhenyu Gao
    National Center for Gene Research Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200233 Shanghai, China
    Plant Mol Biol 71:265-76. 2009
  9. pmc High-throughput genotyping by whole-genome resequencing
    Xuehui Huang
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Genome Res 19:1068-76. 2009
  10. pmc Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines
    Lu Wang
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
    Theor Appl Genet 122:327-40. 2011

Collaborators

Detail Information

Publications82

  1. pmc Collection and comparative analysis of 1888 full-length cDNAs from wild rice Oryza rufipogon Griff. W1943
    Tingting Lu
    College of Life Science and Biotechnology, Shanghai Jiaotong University, Shanghai, PR China
    DNA Res 15:285-95. 2008
    ..In conclusion, these FLcDNA clones are a resource for further function verification and could be broadly utilized in rice biological studies...
  2. doi request reprint Sequencing-based genome-wide association study in rice
    Bin Han
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Curr Opin Plant Biol 16:133-8. 2013
    ..We then discuss the sequencing strategies and experimental designs for GWAS of agronomic traits in rice, and the perspective and challenges coupled with GWAS work are further addressed...
  3. pmc Genome-wide characterization of the biggest grass, bamboo, based on 10,608 putative full-length cDNA sequences
    Zhenhua Peng
    Chinese Academy of Forestry, Wanshou Shan, Beijing, PR China
    BMC Plant Biol 10:116. 2010
    ....
  4. pmc Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.)
    Jianjun Xu
    Yangzhou University, P R China
    BMC Genomics 11:656. 2010
    ..Chromosome segment substitution lines (CSSLs) are the most powerful tools for the detection and precise mapping of quantitative trait loci (QTLs), for the analysis of complex traits in plant molecular genetics...
  5. pmc Rice functional genomics research in China
    Bin Han
    National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, People s Republic of China
    Philos Trans R Soc Lond B Biol Sci 362:1009-21. 2007
    ..National and international collaborations on rice functional genomics study are accelerating rice gene discovery and application...
  6. ncbi request reprint Genome-wide intraspecific DNA-sequence variations in rice
    Bin Han
    National Centre for Gene Research, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Curr Opin Plant Biol 6:134-8. 2003
    ..Intraspecific sequence polymorphisms commonly occur in both coding and non-coding regions. These variations often affect gene structures and may contribute to intraspecific phenotypic adaptations...
  7. pmc Independent losses of function in a polyphenol oxidase in rice: differentiation in grain discoloration between subspecies and the role of positive selection under domestication
    Yanchun Yu
    State Key Laboratory of Plant Genomics and National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant Cell 20:2946-59. 2008
    ..This case may hence represent an example of artificial selection driving the differentiation among domesticated varieties...
  8. doi request reprint Dwarf 88, a novel putative esterase gene affecting architecture of rice plant
    Zhenyu Gao
    National Center for Gene Research Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 200233 Shanghai, China
    Plant Mol Biol 71:265-76. 2009
    ..The potential relationship between the tiller formation associated genes and D88 is discussed and future identification of the substrate for D88 may lead to the characterization of new pathways regulating plant development...
  9. pmc High-throughput genotyping by whole-genome resequencing
    Xuehui Huang
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Genome Res 19:1068-76. 2009
    ....
  10. pmc Mapping 49 quantitative trait loci at high resolution through sequencing-based genotyping of rice recombinant inbred lines
    Lu Wang
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
    Theor Appl Genet 122:327-40. 2011
    ..Moreover, the RILs developed in this study serve as an excellent system for mapping and studying genetic basis of agricultural and biological traits of rice...
  11. pmc Strand-specific RNA-seq reveals widespread occurrence of novel cis-natural antisense transcripts in rice
    Tingting Lu
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai, 200233, China
    BMC Genomics 13:721. 2012
    ..However, the transcriptomes are yet to be deeply sequenced to comprehensively investigate cis-NATs...
  12. pmc Function annotation of the rice transcriptome at single-nucleotide resolution by RNA-seq
    Tingting Lu
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Genome Res 20:1238-49. 2010
    ..The ratio of SNPs with nonsynonymous/synonymous mutations was nearly 1:1.06. In total, we interrogated and compared transcriptomes of the two rice subspecies to reveal the overall transcriptional landscape at maximal resolution...
  13. doi request reprint Genome-wide association studies of 14 agronomic traits in rice landraces
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Nat Genet 42:961-7. 2010
    ....
  14. doi request reprint Analysis of collinear regions of Oryza AA and CC genomes
    Qi Feng
    College of Life Science and Biotechnology, Shanghai Jiao Tong University, Shanghai 200240, China
    J Genet Genomics 36:667-77. 2009
    ..Particularly, the density of RNA transposable elements was 17.95% and 1.78% in O. officinalis and O. sativa, respectively. This explains why the orthologous region is about 100 kb longer in the CC genome in comparison to the AA genome...
  15. pmc Genetic control of seed shattering in rice by the APETALA2 transcription factor shattering abortion1
    Yan Zhou
    National Center for Gene Research, National Center for Plant Gene Research Shanghai and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Plant Cell 24:1034-48. 2012
    ..qSH1 functioned downstream of SHAT1 and SH4, through maintaining SHAT1 and SH4 expression in AZ, thus promoting AZ differentiation...
  16. ncbi request reprint A collection of 10,096 indica rice full-length cDNAs reveals highly expressed sequence divergence between Oryza sativa indica and japonica subspecies
    Xiaohui Liu
    National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Plant Mol Biol 65:403-15. 2007
    ..These variations might distinguish the phenotypic changes of the two cultivated rice subspecies indica and japonica. Analysis of these cDNAs extends known rice genes and identifies new ones in rice...
  17. ncbi request reprint Microarray analysis reveals similarities and variations in genetic programs controlling pollination/fertilization and stress responses in rice (Oryza sativa L.)
    Lefu Lan
    Institute of Genetics and Development Biology, Laboratory of Molecular and Developmental Biology, Chinese Academy of Science and National Center for Plant Gene Research, 100080, Beijing, China
    Plant Mol Biol 59:151-64. 2005
    ..Taken together, these results provided some clues to elucidate the molecular mechanisms of pollination and fertilization in rice...
  18. doi request reprint Evolutionary and expression study of the aldehyde dehydrogenase (ALDH) gene superfamily in rice (Oryza sativa)
    Chenxi Gao
    National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, PR China
    Gene 431:86-94. 2009
    ..These results suggested that the specific rice ALDH genes might be potentially useful in rice genetic improvement...
  19. pmc Genetic control of a transition from black to straw-white seed hull in rice domestication
    Bo Feng Zhu
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Plant Physiol 155:1301-11. 2011
    ..We propose that the straw-white hull was selected as an important visual phenotype of nonshattered grains during rice domestication...
  20. ncbi request reprint Diversity of centromeric repeats in two closely related wild rice species, Oryza officinalis and Oryza rhizomatis
    Weidong Bao
    State Key Laboratory of Plant Genomics, National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, 100101, Beijing, PR China
    Mol Genet Genomics 275:421-30. 2006
    ..Therefore, these data reveal the evolutionary diversification pattern of centromere DNA within/or between close related species, and could provide an insight into the dynamic evolutionary processes of rice centromere...
  21. pmc Genome-wide analysis of transposon insertion polymorphisms reveals intraspecific variation in cultivated rice
    Xuehui Huang
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, China
    Plant Physiol 148:25-40. 2008
    ..These analyses provide genome-wide insights into evolutionary history and genetic variation of rice...
  22. doi request reprint A map of rice genome variation reveals the origin of cultivated rice
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Nature 490:497-501. 2012
    ..The domestication-associated traits are analysed through high-resolution genetic mapping. This study provides an important resource for rice breeding and an effective genomics approach for crop domestication research...
  23. doi request reprint Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Nat Genet 44:32-9. 2012
    ..This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice...
  24. pmc RICD: a rice indica cDNA database resource for rice functional genomics
    Tingting Lu
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, PR China
    BMC Plant Biol 8:118. 2008
    ..A database of the rice indica cDNAs was therefore built to provide a comprehensive web data source for searching and retrieving the indica cDNA clones...
  25. pmc Molecular cytogenetic characterization of the Antirrhinum majus genome
    Dongfen Zhang
    Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, 100101, China
    Genetics 169:325-35. 2005
    ..These genetically anchored TAC clones were labeled as FISH probes to hybridize to pachytene chromosomes of A. majus. As a result, the relationship between chromosomes and the linkage groups (LGs) in Antirrhinum has been established...
  26. doi request reprint Genomic architecture of heterosis for yield traits in rice
    Xuehui Huang
    National Center for Gene Research, CAS Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Nature 537:629-633. 2016
    ..These results inform on the genomic architecture of heterosis and rice hybrid breeding...
  27. doi request reprint An-2 Encodes a Cytokinin Synthesis Enzyme that Regulates Awn Length and Grain Production in Rice
    Benguo Gu
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Mol Plant 8:1635-50. 2015
    ..We therefore propose that the selection of genetic variation in An-2 was due to reduced awn length and increased grain yield in cultivated rice...
  28. doi request reprint A pyramid breeding of eight grain-yield related quantitative trait loci based on marker-assistant and phenotype selection in rice (Oryza sativa L.)
    Guo Zong
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    J Genet Genomics 39:335-50. 2012
    ..This scheme allowed pyramiding of as many as 24 QTLs at a single hybridization without massive cross work. This study provided insights into the molecular basis of rice grain yield for direct wealth for high-yielding rice breeding...
  29. pmc Structural features of the rice chromosome 4 centromere
    Yu Zhang
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Nucleic Acids Res 32:2023-30. 2004
    ..The presence of three intact retrotransposons in the centromere suggests that they may be responsible for functional centromere initiation through a transcription-mediated mechanism...
  30. doi request reprint Resequencing rice genomes: an emerging new era of rice genomics
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Trends Genet 29:225-32. 2013
    ..Here, we review the recent advances in rice genomics and discuss the future of this line of research...
  31. ncbi request reprint Sequence and analysis of rice chromosome 4
    Qi Feng
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Nature 420:316-20. 2002
    ..By contrast, there is little conservation in gene order between rice and Arabidopsis...
  32. doi request reprint The rice OsLTP6 gene promoter directs anther-specific expression by a combination of positive and negative regulatory elements
    Xiaohui Liu
    National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai, 200233, People s Republic of China
    Planta 238:845-57. 2013
    ..Two negative regulatory elements were also found in two distinct regions within this promoter. They repressed the expression in leaf and stem, respectively. These results revealed the regulating complexity of anther-specific expression. ..
  33. ncbi request reprint Transcript abundance of rml1, encoding a putative GT1-like factor in rice, is up-regulated by Magnaporthe grisea and down-regulated by light
    Rong Wang
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Gene 324:105-15. 2004
    ..grisea and light). The putative RML1 protein, encoded by this single copy gene, is thus identified as a new member of the plant-specific GT family of transcription factors in rice...
  34. ncbi request reprint Preparation of single rice chromosome for construction of a DNA library using a laser microbeam trap
    Xiaohui Liu
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    J Biotechnol 109:217-26. 2004
    ..These results suggest the possible application of this method for the preparation of other subcellular structures and for the cloning of single macromolecule through a laser microbeam trap...
  35. pmc Computational identification of 69 retroposons in Arabidopsis
    Yujun Zhang
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Plant Physiol 138:935-48. 2005
    ..In addition, we reported the first plant functional chimeric gene that adapts to intercompartmental transport by capturing two additional exons after retroposition...
  36. doi request reprint The Magnaporthe oryzae avirulence gene AvrPiz-t encodes a predicted secreted protein that triggers the immunity in rice mediated by the blast resistance gene Piz-t
    Wei Li
    National Center for Gene Research and Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, China
    Mol Plant Microbe Interact 22:411-20. 2009
    ..Additionally, we found that AvrPiz-t can suppress the programmed cell death triggered by mouse BAX protein in Nicotiana benthamiana, identifying a mechanism by which AvrPiz-t may contribute virulence of M. oryzae...
  37. doi request reprint OsSPL13 controls grain size in cultivated rice
    Lizhen Si
    National Center for Gene Research, Chinese Academy of Sciences Center for Excellence of Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Nat Genet 48:447-56. 2016
    ..Our study demonstrates that new genes can be effectively identified on the basis of genome-wide association data. ..
  38. pmc Transcriptome-wide investigation of circular RNAs in rice
    Tingting Lu
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes of Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    RNA 21:2076-87. 2015
    ..This suggested that circRNA and its linear form might act as a negative regulator of its parental gene. Overall, these analyses reveal the prevalence of circRNAs in rice and provide new biological insights into rice circRNAs. ..
  39. pmc BRITTLE CULM1, which encodes a COBRA-like protein, affects the mechanical properties of rice plants
    Yunhai Li
    Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Plant Cell 15:2020-31. 2003
    ....
  40. doi request reprint Identification of OsbZIP72 as a positive regulator of ABA response and drought tolerance in rice
    Guojun Lu
    Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Planta 229:605-15. 2009
    ..These results suggest that OsbZIP72 plays a positive role in drought resistance through ABA signaling, and is potential useful for engineering drought tolerant rice...
  41. ncbi request reprint Sequence variations of simple sequence repeats on chromosome-4 in two subspecies of the Asian cultivated rice
    Can Li
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Theor Appl Genet 108:392-400. 2004
    ..These results provide a great opportunity for SSR-based marker development and comparative genome analysis of the two subspecies of the Asian cultivated rice...
  42. ncbi request reprint [The structural, transcriptional and homology analysis of two frr genes in rice]
    Xin Hu
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Zhi Wu Sheng Li Yu Fen Zi Sheng Wu Xue Xue Bao 30:105-14. 2004
    ....
  43. ncbi request reprint Control of tillering in rice
    Xueyong Li
    Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
    Nature 422:618-21. 2003
    ..MOC1 encodes a putative GRAS family nuclear protein that is expressed mainly in the axillary buds and functions to initiate axillary buds and to promote their outgrowth...
  44. doi request reprint The draft genome of the grass carp (Ctenopharyngodon idellus) provides insights into its evolution and vegetarian adaptation
    Yaping Wang
    State Key Laboratory of Freshwater Ecology and Biotechnology, Institute of Hydrobiology, Chinese Academy of Sciences, Wuhan, China
    Nat Genet 47:625-31. 2015
    ..We believe that the grass carp genome could serve as an initial platform for breeding better-quality fish using a genomic approach. ..
  45. ncbi request reprint [The association of single nucleotide P-selectin gene polymorphism with IgA nephropathy]
    Zhao Hui Wang
    Department of Nephrology, Ruijin Hospital, Shanghai Jiaotong University, Shanghai 200025, China
    Zhonghua Nei Ke Za Zhi 45:559-64. 2006
    ..P-selectin plays an important role in the pathogenesis and development of IgA nephropathy. The purpose of this study is to find a possible relationship between P-selectin gene polymorphism and IgA nephropathy...
  46. pmc An-1 encodes a basic helix-loop-helix protein that regulates awn development, grain size, and grain number in rice
    Jianghong Luo
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Plant Cell 25:3360-76. 2013
    ..Thus, we propose that awn loss was favored and strongly selected by humans, as genetic variations at the An-1 locus that cause awn loss would increase grain numbers and subsequently improve grain yield in cultivated rice. ..
  47. doi request reprint Overexpression of a NAC transcription factor enhances rice drought and salt tolerance
    Xingnan Zheng
    National Center for Gene Research and Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Biochem Biophys Res Commun 379:985-9. 2009
    ..Together, these results suggest that ONAC045 encodes a novel stress-responsive NAC transcription factor and is potential useful for engineering drought and salt tolerant rice...
  48. doi request reprint Evolutionary conservation of neighbouring gene pairs in plants
    Xiling Liu
    National Center for Gene Research Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    Gene 437:71-9. 2009
    ..Moreover, a co-expressed signal was detected in conserved divergent pairs, which might be determined by intergenic distance...
  49. ncbi request reprint Structural Analysis of a Gene Cluster Encoding Two Cationic and Three Anionic Peroxidases from Rice Chromosome 4
    Ze hua Chen
    National Center for Gene Research, Chinese Academy of Sciences, Shanghai 200233, China
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 33:163-172. 2001
    ....
  50. pmc Genomic analysis of hybrid rice varieties reveals numerous superior alleles that contribute to heterosis
    Xuehui Huang
    National Center for Gene Research, Collaborative Innovation Center for Genetics and Development, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Nat Commun 6:6258. 2015
    ..We conclude that the accumulation of numerous rare superior alleles with positive dominance is an important contributor to the heterotic phenomena. ..
  51. doi request reprint Natural variations and genome-wide association studies in crop plants
    Xuehui Huang
    National Center for Gene Research, Shanghai Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China Email
    Annu Rev Plant Biol 65:531-51. 2014
    ..We then review sequencing-based crop domestication studies and offer a perspective on genomics-driven crop designs. ..
  52. ncbi request reprint [Identification and analysis of a group of highly conserved trs-like genes in rice]
    Xin Hu
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Yi Chuan Xue Bao 31:822-9. 2004
    ..All of the ten genes are constitutively expressed in rice tissues and share phylogenetic homology to some extent with other eukaryotic trs-like genes in their gene structures and protein sequences...
  53. ncbi request reprint Dampable waves along nucleic acid sequences mediating nucleotides' interactions
    Tao Li
    National Centre for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, 500 Caobao Road, Shanghai 200233, China
    DNA Seq 15:135-9. 2004
    ..Based on the results we daringly make some hypotheses on several biological topics. Further, studies on the wave may provide new clues for gene prediction and genome structure study...
  54. ncbi request reprint Anaerobic induction of isocitrate lyase and malate synthase in submerged rice seedlings indicates the important metabolic role of the glyoxylate cycle
    Ying Lu
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Acta Biochim Biophys Sin (Shanghai) 37:406-14. 2005
    ..Consequently, we concluded that the glyoxylate cycle was involved in acetate metabolism under anaerobic conditions...
  55. ncbi request reprint An F-box gene linked to the self-incompatibility (S) locus of Antirrhinum is expressed specifically in pollen and tapetum
    Zhao Lai
    Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing
    Plant Mol Biol 50:29-42. 2002
    ..The possibility that Sp encodes an F-box protein and the implications of this for the operation of self-incompatibility are discussed...
  56. pmc Gene duplication confers enhanced expression of 27-kDa γ-zein for endosperm modification in quality protein maize
    Hongjun Liu
    National Key Laboratory of Plant Molecular Genetics, Chinese Academy of Sciences Center for Excellence in Molecular Plant Sciences, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200032, China
    Proc Natl Acad Sci U S A 113:4964-9. 2016
    ..This discovery provides a useful molecular marker that can be used to accelerate QPM breeding...
  57. ncbi request reprint Identification and Structural Analysis of a Class of Potentially Transposable Solo-LTR in Rice Genome
    Bo Zhou
    National Ceneter for Gene Research, The Chinese Academy of Sciences, Shanghai 200233, China
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 33:158-162. 2001
    ..Obviously, SLTR1 and SLTR2 reported here came from different loci of the genome by the transposition. These solo-LTRs may be useful for our rice genome studies...
  58. doi request reprint Functional analysis of promoter mutations in the ACTN4 and SYNPO genes in focal segmental glomerulosclerosis
    Shengchuan Dai
    Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
    Nephrol Dial Transplant 25:824-35. 2010
    ..To investigate the promoter mutations of ACTN4 and SYNPO genes in patients with idiopathic focal segmental glomerulosclerosis (FSGS), and to provide functional analysis of these mutations in the role of FSGS occurrence...
  59. ncbi request reprint [Characterization of the copy number of RIRE10 retrotransposon and transcriptional activity of its LTR in rice genome]
    Rong Wang
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, The Chinese Academy of Sciences, Shanghai 200233, China
    Sheng Wu Hua Xue Yu Sheng Wu Wu Li Xue Bao (Shanghai) 35:768-73. 2003
    ..Based on the experimental results, the retrotransposition of RIRE10 was speculated to be influenced by two factors: transcriptional activity of LTR region and homologous recombination resulting in solo-LTR...
  60. doi request reprint Development and high-throughput genotyping of substitution lines carring the chromosome segments of indica 9311 in the background of japonica Nipponbare
    Hua Zhang
    Jiangsu Key Laboratory of Crop Genetics and Physiology Key Laboratory of the Ministry of Education for Plant Functional Genomics, College of Agriculture, Yangzhou University, Yangzhou 225009, China
    J Genet Genomics 38:603-11. 2011
    ..These CSSLs with a background of Nipponbare may provide powerful tools for future whole-genome discovery and functional study of essential genes/QTLs in rice, and offer ideal materials and foundations for japonica breeding...
  61. doi request reprint Antennal proteome comparison of sexually mature drone and forager honeybees
    Mao Feng
    Key Laboratory of Pollinating Insect Biology, Ministry of Agriculture Institute of Apicultural Research, Chinese Academy of Agricultural Science, Beijing, China
    J Proteome Res 10:3246-60. 2011
    ..It also provides a new angle for future detailed functional analysis of the antennae of the honeybee castes...
  62. pmc A fine physical map of the rice chromosome 4
    Qiang Zhao
    National Center for Gene Research, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai 200233, China
    Genome Res 12:817-23. 2002
    ..To our knowledge, this map provides the first example of a rapid and reliable physical mapping on the basis of the integration of the data from two taxonomically related subspecies...
  63. doi request reprint ACTN4 gene mutations and single nucleotide polymorphisms in idiopathic focal segmental glomerulosclerosis
    Shengchuan Dai
    Department of Nephrology, Ruijin Hospital, School of Medicine, Shanghai Jiaotong University, Shanghai, China
    Nephron Clin Pract 111:c87-94. 2009
    ..To investigate the association between mutations or single nucleotide polymorphisms (SNPs) of the gene ACTN4 in Chinese patients with idiopathic focal segmental glomerulosclerosis (FSGS)...
  64. ncbi request reprint A crop of maize variants
    Xuehui Huang
    National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China
    Nat Genet 44:734-5. 2012
    ..The authors conducted a comprehensive characterization of sequence variation in maize genomes and identified signals of selection in maize domestication and breeding...
  65. doi request reprint Protein separation using free-flow electrophoresis microchip etched in a single step
    Pingli Wang
    Key Lab of Separation Science for Analytical Chemistry, National Chromatographic R and A Center, Dalian Institute of Chemical Physics, Chinese Academy of Sciences, Dalian, P R China
    J Sep Sci 33:2039-44. 2010
    ....
  66. ncbi request reprint A pilot study of transcription unit analysis in rice using oligonucleotide tiling-path microarray
    Viktor Stolc
    Department of Molecular Cellular and Developmental Biology, Yale University, New Haven, CT 06520, USA
    Plant Mol Biol 59:137-49. 2005
    ..These preliminary results demonstrate the utility of genome tiling microarrays in evaluating annotated rice gene models and in identifying novel transcription units that will facilitate rice genome annotation...
  67. pmc A tiling microarray expression analysis of rice chromosome 4 suggests a chromosome-level regulation of transcription
    Yuling Jiao
    Department of Molecular, Cellular, and Developmental Biology, Yale University, New Haven, Conecticut 06520 8014, USA
    Plant Cell 17:1641-57. 2005
    ..These results suggest a close correlation between transcriptional activity and chromosome organization and the developmental regulation of transcription activity at the chromosome level...
  68. ncbi request reprint Monitoring of gene expression profiles and isolation of candidate genes involved in pollination and fertilization in rice ( Oryza sativa L.) with a 10K cDNA microarray
    Lefu Lan
    Institute of Genetics and Development Biology, Chinese Academy of Science and National Center for Plant Gene Research, Beijing 100080, China
    Plant Mol Biol 54:471-87. 2004
    ..In addition, the genes that differentially expressed during pollination represent candidate genes for dissecting molecular mechanism of this important biological process in rice...
  69. ncbi request reprint Genome-wide analysis of the auxin response factors (ARF) gene family in rice (Oryza sativa)
    Dekai Wang
    Crop Molecular Breeding Center, Institute of Crop and Nuclear Technology Utilization, Zhejiang Academy of Agricultural Sciences, Hangzhou 310021, P R China
    Gene 394:13-24. 2007
    ..The outcome of the present study provides basic genomic information for the rice ARF gene family and will pave the way for elucidating the precise role of OsARFs in plant growth and development in the future...
  70. pmc The Rice Annotation Project Database (RAP-DB): 2008 update
    Tsuyoshi Tanaka
    National Institute of Agrobiological Sciences, Ibaraki 305 8602, Japan
    Nucleic Acids Res 36:D1028-33. 2008
    ..We have also developed a new keyword search system to allow the user to access useful information. The RAP-DB is available at: http://rapdb.dna.affrc.go.jp/ and http://rapdb.lab.nig.ac.jp/...
  71. pmc Mutations of genes in synthesis of the carotenoid precursors of ABA lead to pre-harvest sprouting and photo-oxidation in rice
    Jun Fang
    State Key Laboratory of Plant Genomics and National Centre for Plant Gene Research, Beijing 100101, China
    Plant J 54:177-89. 2008
    ..These results suggest that the impairment of carotenoid biosynthesis causes photo-oxidation and ABA-deficiency phenotypes, of which the latter is a major factor controlling the PHS trait in rice...
  72. ncbi request reprint GS3, a major QTL for grain length and weight and minor QTL for grain width and thickness in rice, encodes a putative transmembrane protein
    Chuchuan Fan
    National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, 430070 Wuhan, China
    Theor Appl Genet 112:1164-71. 2006
    ..Cloning of such a gene provided the opportunity for fully characterizing the regulatory mechanism and related processes during grain development...
  73. ncbi request reprint Expression profiles of 10,422 genes at early stage of low nitrogen stress in rice assayed using a cDNA microarray
    Xingming Lian
    National Key Laboratory of Crop Genetic Improvement, National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China
    Plant Mol Biol 60:617-31. 2006
    ..The challenges for future studies are to characterize the functional roles of the low N stress responsive genes in N metabolisms, including the large number of genes presently with unknown functions...
  74. ncbi request reprint Features of the expressed sequences revealed by a large-scale analysis of ESTs from a normalized cDNA library of the elite indica rice cultivar Minghui 63
    Jianwei Zhang
    National Key Laboratory of Crop Genetic Improvement, Huazhong Agricultural University, Wuhan 430070, China
    Plant J 42:772-80. 2005
    ....
  75. ncbi request reprint [Association of single nucleotide polymorphism of megsin gene with IgA nephropathy]
    Zhao Hui Wang
    Department of Nephrology, Ruijin Hospital, Shanghai Jiaotong University School of Medical, Shanghai 200025, China
    Zhonghua Yi Xue Za Zhi 86:1337-41. 2006
    ..To investigate whether the single nucleotide polymorphisms (SNPs) in the gene of megsin, a novel serine protease inhibitor, account for the pathogenicity of IgA nephropathy (IgAN)...
  76. pmc Curated genome annotation of Oryza sativa ssp. japonica and comparative genome analysis with Arabidopsis thaliana
    Takeshi Itoh
    Division of Genome and Biodiversity Research, National Institute of Agrobiological Sciences, Tsukuba, Ibaraki 305 8602, Japan
    Genome Res 17:175-83. 2007
    ..Our results suggest that natural selection may have played a role for duplicated genes in both species, so that duplication was suppressed or favored in a manner that depended on the function of a gene...
  77. ncbi request reprint Economic espionage. Researcher acquitted of lab theft charge
    Andrew Lawler
    Science 297:1463. 2002
  78. ncbi request reprint Non-random distribution of T-DNA insertions at various levels of the genome hierarchy as revealed by analyzing 13 804 T-DNA flanking sequences from an enhancer-trap mutant library
    Jian Zhang
    National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research Wuhan, Huazhong Agricultural University, Wuhan 430070, China
    Plant J 49:947-59. 2007
    ..It was estimated that 365 380 insertions are needed to saturate the genome with P = 0.95, and that the 45 441 FSTs that have been isolated so far by various groups tagged 14 287 of the 42 653 non-TE related genes...
  79. pmc Gene expression phenotypes of Arabidopsis associated with sensitivity to low temperatures
    Nicholas J Provart
    Torrey Mesa Research Institute, Syngenta Research and Technology, 3115 Merryfield Row, San Diego, California 92121, USA
    Plant Physiol 132:893-906. 2003
    ..The comparison of transcriptome profiles after transfer of Arabidopsis plants from 22 degrees C to 13 degrees C versus transfer to 4 degrees C suggests that quantitative and temporal differences exist between these molecular responses...
  80. ncbi request reprint Isolation and annotation of 10828 putative full length cDNAs from indica rice
    Kabin Xie
    National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research, Wuhan, Huazhong Agricultural University, Wuhan 430070, China
    Sci China C Life Sci 48:445-51. 2005
    ..More than 60% of the new cDNAs isolated in this study had no homology to the known proteins. This set of FL-cDNAs should be useful for functional genomics and proteomics studies...
  81. pmc Quantitative nature of Arabidopsis responses during compatible and incompatible interactions with the bacterial pathogen Pseudomonas syringae
    Yi Tao
    Torrey Mesa Research Institute, Syngenta Research and Technology, San Diego, California 92121, USA
    Plant Cell 15:317-30. 2003
    ..This finding is consistent with the resistance phenotypes of these plants. We propose a simple quantitative model with a saturating response curve that approximates the overall behavior of this plant-pathogen system...
  82. ncbi request reprint The oryza map alignment project: the golden path to unlocking the genetic potential of wild rice species
    Rod A Wing
    Arizona Genomics Institute, The University of Arizona, Tucson, AZ, USA
    Plant Mol Biol 59:53-62. 2005
    ..In this paper we describe our strategy to construct robust physical maps of all 12 rice species with an emphasis on the AA diploid O. nivara--thought to be the progenitor of modern cultivated rice...