谢为博 【副教授】
姓名 谢为博 性别
职称 副教授 学位 博士
电话 027-87280350 邮箱 weibo.xie@mail.hzau.edu.cn xwbmail@gmail
工作单位 华中农业大学信息学院
研究方向 基因组学, 系统生物学
教育经历

2004.9-2010.6 华中农业大学 生命科学技术学院 基因组学专业 硕博连读
     1999.9-2003.9 中南民族大学 化学与生命科学学院 生物技术专业 本科

主要职历

2010.7- 华中农业大学 作物遗传改良国家重点实验室 固定研究人员
     2014.8- 华中农业大学 信息学院 副教授
     2013.1-2014.7 华中农业大学 生命科学技术学院 副教授
     2010.7-2012.12 华中农业大学 生命科学技术学院 讲师


承担课题:
     国家自然科学基金    整合组学数据剖析水稻籽粒中代谢途径及其调控网络
     国家自然科学基金    基于新一代测序技术的高通量基因分型方法的开发与完善
     国家自然科学基金    玉米和水稻重要性状的全基因组关联分析
     国家863计划专项    水稻组学、资源和生物信息平台的创建    子项目
     国家863计划专项    全基因组选择育种技术平台建设    子项目

科研成果
本课题组主要以遗传学、生物信息学和各种组学方法为手段,围绕水稻种质资源遗传变异和组学数据的挖掘与利用开展研究。主要贡献如下:
(1)开展了多项挖掘利用水稻种质资源遗传变异的研究。与合作者收集并测序533份具代表性的水稻品种,建立了一个水稻关联分析平台,有效推动了水稻重要农艺性状相关变异位点的鉴定和利用。通过对大量水稻品种的序列分析,系统鉴定了籼稻育种过程中受选择的基因组位点,为进一步改良水稻提供了重要靶点。率先开展了水稻“非必需基因组”研究,发掘了大量不存在于水稻参考基因组中的新序列,初步分析了其组成和形成机制并首次开展了基于泛基因组的关联分析研究。
(2)开发了多种高通量基因分型方法和平台。建立了基于Affymetrix芯片表达谱数据挖掘序列多态性的方法和基于新一代测序技术的低成本的群体基因分型方法。作为主要设计人员之一与中国种子集团、北京大学合作开发了全球第一款水稻育种芯片和后续多款育种芯片,申请发明专利3项,已得到推广应用。
(3)建立了多个水稻生物信息学数据库。包括水稻表达谱数据库CREP(http://crep.ncpgr.cn)、水稻基因组序列变异数据库RiceVarMap(http://ricevarmap.ncpgr.cn)和水稻泛基因组序列数据库PanRice(http://panrice.ncpgr.cn),用户超过5万人次,有效促进了各种水稻组学数据的深度利用。

近年主持和参与国家自然科学基金、国家863、农业部948等科研项目10余项。发表科学研究论文50余篇,被引用超过1800次,h-index超过23;其中作为通讯作者或第一作者在Nature Genetics、PNAS、Genome Biology和Nucleic Acids Res等国际权威SCI杂志上发表论文10余篇。


完整文章列表及引用情况请访问:
ORCID http://orcid.org/0000-0002-2768-3572
Google scholar http://scholar.google.ca/citations?user=I5zjYOUAAAAJ

SIGNED ARTICLES:


# Equal contribution * Corresponding author


  1. Yao W, Li G, Zhao H, Wang G, Lian X, Xie W*. Exploring the rice dispensable genome using a metagenome-like assembly strategyGenome Biology, 2015, 16: 187 (IF 10.8) 
    Featured as "Research Highlight" in Genome Biology "Harvesting rice’s dispensable genome"
  2. Xie W#, Wang G#, Yuan M, Yao W, Lyu K, Zhao H, Yang M, Li P, Zhang X, Yuan J, Wang Q, Liu F, Dong H, Zhang L, Li X, Meng X, Zhang W, Xiong L, He Y, Wang S, Yu S, Xu C, Luo J, Li X, Xiao J, Lian X*, Zhang Q*. Breeding signatures of rice improvement revealed by a genomic variation map from a large germplasm collectionProc Natl Acad Sci USA, 2015, 112: E5411-E5419 (IF 9.7)
    Featured as "Research Highlight" in Nature Plants "Rice breeding: Signature analysis"
  3. Zhao H, Yao W, Ouyang Y, Yang W, Wang G, Lian X, Xing Y, Chen L, Xie W*. RiceVarMap: a comprehensive database of rice genomic variations. Nucleic Acids Res, 2015, 43: D1018-1022 (IF 9.1)
  4. Wang Q#, Xie W#, Xing H, Yan J, Meng X, Li X, Fu X, Xu J, Lian X, Yu S, Xing Y, Wang G*. Genetic Architecture of Natural Variation in Rice Chlorophyll Content Revealed by a Genome-Wide Association StudyMol Plant, 2015, 8: 946-957 (IF 6.3)
  5. Chen W#, Gao Y#, Xie W#, Gong L#, Lu K#, Wang W, Li Y, Liu X, Zhang H, Dong H, Zhang W, Zhang L, Yu S, Wang G, Lian X*, Luo J*. Genome-wide association analyses provide genetic and biochemical insights into natural variation in rice metabolismNat Genet, 2014, 46: 714-721 (IF 29.4)
  6. Yu H#, Xie W#, Li J, Zhou F*, Zhang Q*. A whole-genome SNP array (RICE6K) for genomic breeding in ricePlant Biotechnol J, 2014, 12: 28-37 (IF 5.8)
  7. Chen H#, Xie W#, He H#, Yu H#, Chen W, Li J, Yu R, Yao Y, Zhang W, He Y, Tang X*, Zhou F*, Deng X W*, Zhang Q*. A High-Density SNP Genotyping Array for Rice Biology and Molecular BreedingMol Plant, 2014, 7: 541-553 (IF 6.3)
  8. Cai H#, Xie W#, Zhu T, Lian X*. Transcriptome response to phosphorus starvation in riceActa Physiol Plant, 2012, 34: 327-341 (IF 1.6)
  9. Xie W, Feng Q, Yua H, Huang X, Zhao Q, Xing Y, Yu S, Han B, Zhang Q*. Parent-independent genotyping for constructing an ultrahigh-density linkage map based on population sequencingProc Natl Acad Sci USA, 2010, 119: 151-164 (IF 9.7)
  10. Wang L#, Xie W#, Chen Y, Tang W, Yang J, Ye R, Liu L, Lin Y, Xu C, Xiao J, Zhang Q*. A dynamic gene expression atlas covering the entire life cycle of ricePlant J, 2010, 61: 752-766 (IF 6.0)
  11. Xie W, Chen Y, Zhou G, Wang L, Zhang C, Zhang J, Xiao J, Zhu T, Zhang Q*. Single feature polymorphisms between two rice cultivars detected using a median polish methodTheor Appl Genet, 2009, 119: 151-164 (IF 3.8)
  12. Wu J, Feng F, Lian X, Teng X, Wei H, Yu H, Xie W, Yan M, Fan P, Li Y, Ma X, Liu H, Yu S, Wang G, Zhou F, Luo L, Mei H. Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice. BMC Plant Biol, 2015, 15:218
  13. Zhang L, Mao D, Xing F, Bai X, Zhao H, Yao W, Li G, Xie W, Xing Y. Loss of function of OsMADS3 via the insertion of a novel retrotransposon leads to recessive male sterility in rice (Oryza sativa). Plant Sci, 2015, 238:188-97
  14. Wang J, Yao W, Zhu D, Xie W, Zhang Q. Genetic basis of sRNA quantitative variation analyzed using an experimental population derived from an elite rice hybrid. Elife, 2015, 4: e04250
  15. Yang Z, Ma H, Hong H, Yao W, Xie W, Xiao J, Li X, Wang S. Transcriptome-based analysis of mitogen-activated protein kinase cascades in the rice response to Xanthomonas oryzae infection. Rice (N Y), 2015, 8: 4
  16. Zhang L, Li Q, Dong H, He Q, Liang L, Tan C, Han Z, Yao W, Li G, Zhao H, Xie W, Xing Y. Three CCT domain-containing genes were identified to regulate heading date by candidate gene-based association mapping and transformation in rice. Sci Rep, 2015, 5: 7663
  17. Peng B, Kong H, Li Y, Wang L, Zhong M, Sun L, Gao G, Zhang Q, Luo L, Wang G, Xie W, Chen J, Yao W, Peng Y, Lei L, Lian X, Xiao J, Xu C, Li X, He Y. OsAAP6 functions as an important regulator of grain protein content and nutritional quality in rice. Nat Commun, 2014, 5: 4847
  18. Songyikhangsuthor K, Guo Z, Wang N, Zhu X, Xie W, Mou T, Xiong L. Natural variation in the sequence of SNAC1 and its expression level polymorphism in rice Germplasms under drought stress. J Genet Genomics, 2014, 41: 609-612
  19. Wang J, Yu H, Weng X, Xie W, Xu C, Li X, Xiao J, Zhang Q. An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population. J Exp Bot, 2014, 65: 1069-1079
  20. Wang K, Cui K, Liu G, Xie W, Yu H, Pan J, Huang J, Nie L, Shah F, Peng S. Identification of quantitative trait loci for phosphorus use efficiency traits in rice using a high density SNP map. BMC Genet, 2014, 15: 1276
  21. Yang W, Guo Z, Huang C, Duan L, Chen G, Jiang N, Fang W, Feng H, Xie W, Lian X, Wang G, Luo Q, Zhang Q, Liu Q, Xiong L. Combining high-throughput phenotyping and genome-wide association studies to reveal natural genetic variation in rice. Nat Commun, 2014, 5: 5087
  22. Li Y, Fan C, Xing Y, Yun P, Luo L, Yan B, Peng B, Xie W, Wang G, Li X, Xiao J, Xu C, He Y. Chalk5 encodes a vacuolar H(+)-translocating pyrophosphatase influencing grain chalkiness in rice. Nat Genet, 2014, 46: 398-404
  23. Wang J, Yu H, Weng X, Xie W, Xu C, Li X, Xiao J, Zhang Q. An expression quantitative trait loci-guided co-expression analysis for constructing regulatory network using a rice recombinant inbred line population. J Exp Bot, 2014, 65: 1069-1079
  24. Tan C, Han Z, Yu H, Zhan W, Xie W, Chen X, Zhao H, Zhou F, Xing Y. QTL scanning for rice yield using a whole genome SNP array. J Genet Genomics, 2013, 40: 629-638
  25. Yan W, Liu H, Zhou X, Li Q, Zhang J, Lu L, Liu T, Zhang C, Zhang Z, Shen G, Yao W, Chen H, Yu S, Xie W, Xing Y. Natural variation in Ghd7.1 plays an important role in grain yield and adaptation in rice. Cell Res, 2013, 23: 969-971
  26. Cai H, Xie W, Lian X. Comparative Analysis of Differentially Expressed Genes in Rice Under Nitrogen and Phosphorus Starvation Stress Conditions. Plant Molecular Biology Reporter, 2013, 31: 160-173
  27. Zhou G, Chen Y, Yao W, Zhang C, Xie W, Hua J, Xing Y, Xiao J, Zhang Q. Genetic composition of yield heterosis in an elite rice hybrid. Proc Natl Acad Sci USA, 2012, 109: 15847-15852
  28. Huang J, Zhao X, Weng X, Wang L, Xie W. The rice B-box zinc finger gene family: genomic identification, characterization, expression profiling and diurnal analysis. PLoS ONE, 2012, 7: e48242
  29. Cai H, Lu Y, Xie W, Zhu T, Lian X. Transcriptome response to nitrogen starvation in rice. J Biosci, 2012, 37: 731-747
  30. Ding J, Shen J, Mao H, Xie W, Li X, Zhang Q. RNA-directed DNA methylation is involved in regulating photoperiod-sensitive male sterility in rice. Mol Plant, 2012, 5: 1210-1216
  31. Tie W, Zhou F, Wang L, Xie W, Chen H, Li X, Lin Y. Reasons for lower transformation efficiency in indica rice using Agrobacterium tumefaciens-mediated transformation: lessons from transformation assays and genome-wide expression profiling. Plant Mol Biol, 2012, 78:1-18
  32. Jiang Y, Cai Z, Xie W, Long T, Yu H, Zhang Q. Rice functional genomics research: Progress and implications for crop genetic improvement. Biotechnol Adv, 2012, 30:1059-1070
  33. Zhang C, Wang J, Xie W, Zhou G, Long M, Zhang Q. Dynamic programming procedure for searching optimal models to estimate substitution rates based on the maximum-likelihood method. Proc Natl Acad Sci USA, 2011, 108: 7860-7865
  34. Yu H, Xie W, Wang J, Xing Y, Xu C, Li X, Xiao J, Zhang Q. Gains in QTL detection using an ultra-high density SNP map based on population sequencing relative to traditional RFLP/SSR markers. PLoS ONE, 2011, 6: e17595
  35. Wang J, Yu H, Xie W, Xing Y, Yu S, Xu C, Li X, Xiao J, Zhang Q. A global analysis of QTLs for expression variations in rice shoot at early seedling stage. Plant J, 2010, 63: 1063-1074
  36. Zhao X, Huang J, Yu H, Wang L, Xie W. Genomic survey, characterization and expression profile analysis of the peptide transporter family in rice (Oryza sativa L.). BMC Plant Biol, 2010, 10: 92
  37. Zhou Y, Cao Y, Huang Y, Xie W, Xu C, Li X, Wang S. Multiple gene loci affecting genetic background-controlled disease resistance conferred by R gene Xa3/Xa26 in rice. Theor Appl Genet, 2009, 120: 127-138
  38. Ye S, Wang L, Xie W, Wan B, Li X, Lin Y. Expression profile of calcium-dependent protein kinase (CDPKs) genes during the whole lifespan and under phytohormone treatment conditions in rice (Oryza sativa L. ssp. indica). Plant Mol Biol, 2009, 70: 311-325
  39. Qiu X, Xie W, Lian X, Zhang Q. Molecular analyses of the rice glutamate dehydrogenase gene family and their response to nitrogen and phosphorous deprivation. Plant Cell Rep, 2009, 28: 1115-1126
  40. Qiu D, Xiao J, Xie W, Cheng H, Li X, Wang S. Exploring transcriptional signalling mediated by OsWRKY13, a potential regulator of multiple physiological processes in rice. BMC Plant Biol, 2009, 9: 74
  41. Ouyang Y, Chen J, Xie W, Wang L, Zhang Q. Comprehensive sequence and expression profile analysis of Hsp20gene family in rice. Plant Mol Biol, 2009, 70: 341-357
  42. Chen J, Ouyang Y, Wang L, Xie W, Zhang Q. Aspartic proteases gene family in rice: Gene structure and expression, predicted protein features and phylogenetic relation. Gene, 2009, 442: 108-118
  43. Qiu D, Xiao J, Xie W, Liu H, Li X, Xiong L, Wang S. Rice gene network inferred from expression profiling of plants overexpressing OsWRKY13, a positive regulator of disease resistance. Mol Plant, 2008, 1: 538-551
  44. Nuruzzaman M, Gupta M, Zhang C, Wang L, Xie W, Xiong L, Zhang Q, Lian X. Sequence and expression analysis of the thioredoxin protein gene family in rice. Mol Genet Genomics, 2008, 280: 139-151
  45. Nayidu N K, Wang L, Xie W, Zhang C, Fan C, Lian X, Zhang Q, Xiong L. Comprehensive sequence and expression profile analysis of PEX11 gene family in rice. Gene, 2008, 412: 59-70
  46. Gupta M, Qiu X, Wang L, Xie W, Zhang C, Xiong L, Lian X, Zhang Q. KT/HAK/KUP potassium transporters gene family and their whole-life cycle expression profile in rice (Oryza sativa). Mol Genet Genomics, 2008, 280: 437-452
  47. Fang Y, You J, Xie K, Xie W, Xiong L. Systematic sequence analysis and identification of tissue-specific or stress-responsive genes of NAC transcription factor family in rice. Mol Genet Genomics, 2008, 280: 547-563


PATENTS:


  1. 周发松,谢为博,喻辉辉,李菁,张启发. 一种水稻全基因组SNP芯片及其应用. 专利号:201210055775
  2. 周发松,陈浩东,谢为博,何航,喻辉辉,唐晓艳,李菁,周君莉,何予卿,陈伟,张启发,邓兴旺. 水稻全基因组育种芯片及其应用. 申请号:CN201380056318
  3. 谢为博,张启发,练兴明,王功伟. 一种基于受选择位点指数评估动植物品种育种潜力的方法及其应用. 申请号:2015105511347
备注 入选首批中国科协青年人才托举工程
2012年全国优秀博士学位论文提名论文
2011年湖北省优秀博士学位论文
担任PNAS、Nature Communications、Bioinformatics、Scientific Reports、PLoS ONE、BMC Genomics和TAG等杂志审稿人