Application of high-throughput amplicon sequencing-based SSR genotyping in genetic background screening

[1]  Weixiong Zhang,et al.  Transcriptional insights into the pyramided resistance to rice bacterial blight , 2018, Scientific Reports.

[2]  Tengfei Qin,et al.  Comparative Transcriptome Profiling of Rice Near-Isogenic Line Carrying Xa23 under Infection of Xanthomonas oryzae pv. oryzae , 2018, International journal of molecular sciences.

[3]  J. Muñóz-Valle,et al.  The 3′-UTR (CA)n microsatellite on CD40LG gene as a possible genetic marker for rheumatoid arthritis in Mexican population: impact on CD40LG mRNA expression , 2018, Clinical Rheumatology.

[4]  Wei Wang,et al.  Genome-wide Targeted Mutagenesis in Rice Using the CRISPR/Cas9 System. , 2017, Molecular plant.

[5]  K. Sakthivel,et al.  The host background of rice influences the resistance expression of a three genes pyramid (xa5 + xa13 + Xa21) to bacterial blight (Xanthomonas oryzae pv. oryzae) pathotypes of Indian mainland and Bay islands , 2017 .

[6]  Akihiko Kondo,et al.  Targeted base editing in rice and tomato using a CRISPR-Cas9 cytidine deaminase fusion , 2017, Nature Biotechnology.

[7]  Sheng Ren,et al.  An accurate and efficient method for large-scale SSR genotyping and applications , 2017, Nucleic acids research.

[8]  G. He,et al.  Development and evaluation of near-isogenic lines for brown planthopper resistance in rice cv. 9311 , 2016, Scientific Reports.

[9]  Shaoyan Zheng,et al.  Development of Commercial Thermo-sensitive Genic Male Sterile Rice Accelerates Hybrid Rice Breeding Using the CRISPR/Cas9-mediated TMS5 Editing System , 2016, Scientific Reports.

[10]  ZHU-LIANG Yang,et al.  Genetic diversity and breeding history of Winter Mushroom (Flammulina velutipes) in China uncovered by genomic SSR markers. , 2016, Gene.

[11]  R. Qin,et al.  Rapid improvement of grain weight via highly efficient CRISPR/Cas9-mediated multiplex genome editing in rice. , 2016, Journal of genetics and genomics = Yi chuan xue bao.

[12]  Meiru Li,et al.  Reassessment of the Four Yield-related Genes Gn1a, DEP1, GS3, and IPA1 in Rice Using a CRISPR/Cas9 System , 2016, Front. Plant Sci..

[13]  M. Pilet-Nayel,et al.  Validation of QTL for resistance to Aphanomyces euteiches in different pea genetic backgrounds using near-isogenic lines , 2015, Theoretical and Applied Genetics.

[14]  Weixiong Zhang,et al.  Rice Xa21 primed genes and pathways that are critical for combating bacterial blight infection , 2015, Scientific Reports.

[15]  Paul Medvedev,et al.  Accurate typing of short tandem repeats from genome-wide sequencing data and its applications , 2015, Genome research.

[16]  M. Ebrahimi,et al.  Using SSR Markers For Assessment Genetic Diversity And Detection Drought Escape Candidate Genes In Barley Lines (Hordeum Vulgare L.) , 2014 .

[17]  Benjamin L. Oakes,et al.  Programmable RNA recognition and cleavage by CRISPR/Cas9 , 2014, Nature.

[18]  Jian‐Kang Zhu,et al.  The CRISPR/Cas9 system produces specific and homozygous targeted gene editing in rice in one generation. , 2014, Plant biotechnology journal.

[19]  Yunde Zhao,et al.  Self-processing of ribozyme-flanked RNAs into guide RNAs in vitro and in vivo for CRISPR-mediated genome editing. , 2014, Journal of integrative plant biology.

[20]  A. Nakamura,et al.  Increase in Cellulose Accumulation and Improvement of Saccharification by Overexpression of Arabinofuranosidase in Rice , 2013, PloS one.

[21]  Wenxue Zhai,et al.  Do transgenesis and marker-assisted backcross breeding produce substantially equivalent plants? - A comparative study of transgenic and backcross rice carrying bacterial blight resistant gene Xa21 , 2013, BMC Genomics.

[22]  Paul Medvedev,et al.  Using state machines to model the Ion Torrent sequencing process and to improve read error rates , 2013, Bioinform..

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

[24]  Steven L Salzberg,et al.  Fast gapped-read alignment with Bowtie 2 , 2012, Nature Methods.

[25]  A. Monforte,et al.  High-throughput SNP genotyping in Cucurbita pepo for map construction and quantitative trait loci mapping , 2012, BMC Genomics.

[26]  R. Kaur,et al.  Assessment of genetic diversity in cabbage cultivars using RAPD and SSR markers , 2011, Journal of Crop Science and Biotechnology.

[27]  W. Zhai,et al.  Generation of marker-free, bacterial blight-resistant transgenic sterile line and hybrid rice with Xa21 , 2011 .

[28]  R. Petit,et al.  Current trends in microsatellite genotyping , 2011, Molecular ecology resources.

[29]  Lihuang Zhu,et al.  Transcriptional characteristics of Xa21-mediated defense responses in rice. , 2011, Journal of integrative plant biology.

[30]  Chenwu Xu,et al.  Developing high throughput genotyped chromosome segment substitution lines based on population whole-genome re-sequencing in rice (Oryza sativa L.) , 2010, BMC Genomics.

[31]  S. Jing,et al.  High-resolution mapping of the brown planthopper resistance gene Bph6 in rice and characterizing its resistance in the 9311 and Nipponbare near isogenic backgrounds , 2010, Theoretical and Applied Genetics.

[32]  Cai-guo Xu,et al.  Multiple gene loci affecting genetic background-controlled disease resistance conferred by R gene Xa3/Xa26 in rice , 2009, Theoretical and Applied Genetics.

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

[34]  M. Todesco,et al.  A Genetic Defect Caused by a Triplet Repeat Expansion in Arabidopsis thaliana , 2009, Science.

[35]  W. Zhai,et al.  Introduction of a rice blight resistance gene,Xa21, into five Chinese rice varieties through anAgrobacterium-mediated system , 2000, Science in China Series C: Life Sciences.

[36]  Yunbi Xu,et al.  Pyramiding of Xa7 and Xa21 for the improvement of disease resistance to bacterial blight in hybrid rice , 2006 .

[37]  F. Jin,et al.  Fine mapping of a grain weight quantitative trait locus on rice chromosome 8 using near-isogenic lines derived from a cross between Oryza sativa and Oryza rufipogon , 2006, Theoretical and Applied Genetics.

[38]  P. Shewry,et al.  Transgenesis has less impact on the transcriptome of wheat grain than conventional breeding. , 2006, Plant biotechnology journal.

[39]  E. Hinchliffe,et al.  Improving the nutritional value of Golden Rice through increased pro-vitamin A content , 2005, Nature Biotechnology.

[40]  P. Christou,et al.  Modulation of the polyamine biosynthetic pathway in transgenic rice confers tolerance to drought stress. , 2004, Proceedings of the National Academy of Sciences of the United States of America.

[41]  C. Rodríguez-Gallego,et al.  The dinucleotide repeat polymorphism in the 3′UTR of the CD154 gene has a functional role on protein expression and is associated with systemic lupus erythematosus , 2004, Annals of the rheumatic diseases.

[42]  S. Tanksley,et al.  Genetic and physical analysis of the rice bacterial blight disease resistance locus, Xa21 , 1992, Molecular and General Genetics MGG.

[43]  Thomas D. Schmittgen,et al.  Analysis of relative gene expression data using real-time quantitative PCR and the 2(-Delta Delta C(T)) Method. , 2001, Methods.

[44]  D. Zacharias,et al.  Minimum CAG repeat in the human calmodulin-1 gene 5' untranslated region is required for full expression. , 1998, Biochimica et biophysica acta.

[45]  S Karlin,et al.  Trinucleotide repeats and long homopeptides in genes and proteins associated with nervous system disease and development. , 1996, Proceedings of the National Academy of Sciences of the United States of America.

[46]  Li-li Chen,et al.  A Receptor Kinase-Like Protein Encoded by the Rice Disease Resistance Gene, Xa21 , 1995, Science.

[47]  Thomas D. Schmittgen,et al.  Analysis of Relative Gene Expression Data Using Real-Time Quantitative PCR and the 2 2 DD C T Method , 2022 .