谢为博 【教授】
姓名 谢为博 性别
职称 教授 学位 博士
电话 027-87280350 邮箱 weibo.xie@mail.hzau.edu.cn xwbmail@gmail.com
工作单位 华中农业大学信息学院
研究方向 水稻基因组学, 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  2018.1 - 华中农业大学 信息学院 教授,博士生导师
     2014.8 - 2017.12 华中农业大学 信息学院 副教授,博士生导师
     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
   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


承担课题:
     国家自然科学基金    基于比较基因组和ATAC-seq注释水稻基因组染色质开放区及其序列变异    面上项目,2018-2021
     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    面上项目,2016-2019
     国家重点研发计划    杂种优势预测的新方法和强优势新材料    课题,2016-2020
     国家863计划专项    全基因组选择育种技术平台建设    子课题,2014-2018
     国家863计划专项    水稻组学、资源和生物信息平台的创建    子课题,2012-2015
     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    青年基金,2012-2014
科研成果
实验室主旨: 水稻是世界上最重要的粮食作物之一,品种改良是水稻研究永恒的主题。种质资源遗传变异的挖掘与利用是品种改良的基础,然而目前只有3-5%的种质被有效利用。组学技术的应用能极大加速种质资源遗传变异的鉴定和表型变异分子机理的解析,但目前尚存在很多方法学上的挑战。本实验室以所建立的水稻品种群体为基础,致力于建立遗传学和高通量组学平台和分析方法,挖掘优异遗传变异,系统解析表型变异的分子机理,为分子设计育种提供基因和方法学基础。

近年来,我们系统开展了多项挖掘利用水稻种质资源遗传变异的工作,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;并首次在水稻中系统开展了“ 非必需基因组”研究,揭示了其组成及对表型的影响,这些研究为进一步挖掘利用水稻优异遗传变异开辟了新途径。同时,作为主要设计人员之一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,并建立了多个水稻生物信息学数据库,为进一步研究与利用水稻种质资源提供了新的平台和工具。相关研究被Nature Plants、Genome Biology等杂志列为研究亮点,予以高度评价。

近年主持和参与国家自然科学基金、国家863、国家重点研发计划等科研项目10余项。发表科学研究论文50余篇,被引用超过2800次,h-index超过28;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。

目前实验室主要从事三个方面的研究:(1)开发鉴定水稻非编码调控元件的组学和计算方法;(2)整合多组学数据开展水稻系统生物学研究;(3)将上述研究结果应用于解析杂种优势的机理。研究方向兼顾基础与应用研究,具有很好的就业前景,也适合继续深造;欢迎生物、数学、物理和计算机相关专业的青年朋友加入(作为硕博生、博士后和科研助理)。


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. 专利号:201380056318
  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. 专利号:201510551134

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