谢为博


姓名



谢为博        
   



性别



男        
   



职称



教授



学位



博士



电话



027-87280350    



邮箱


 

 


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

 

  科研成果


主持课题:

国家自然科学基金优秀青年科学基金 水稻基因组学与分子育种,2020-2022

国家自然科学基金面上项目 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,2018-2021

国家自然科学基金面上项目 整合组学数据剖析水稻籽粒中代谢途径及其调控网络,2016-2019

国家自然科学基金青年基金 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,2012-2014

国家重点研发计划课题 杂种优势预测的新方法和强优势新材料,2016-2020

国家863计划专项子课题 全基因组选择育种技术平台建设,2014-2018

国家863计划专项子课题 水稻组学、资源和生物信息平台的创建,2012-2015

中国科协青年人才托举工程,2015-2017



本课题组依托华中农业大学作物遗传改良国家重点实验室,主要从事杂种优势、种质资源遗传变异和基因组调控元件的挖掘与利用方面的研究。近年来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,获得发明专利3项,已得到推广应用;发布了水稻基因组序列变异的功能效应图谱RiceVarMap V2.0和植物中首个基于深度学习模型预测基因组序列变异调控效应的网络服务PlantDeepSEA,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。

目前课题组主要从事三个方面的研究:(1)开发鉴定作物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,具有很好的就业前景,也适合继续深造;课题组既需要“湿实验”人才,也需要“干实验”人才,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)。


近年发表的论文:

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.com/citations?user=I5zjYOUAAAAJ

# Equal contribution * Corresponding author



1. Zhao H, Li J, Yang L, Qin G, Xia C, Xu X, Su Y, Liu Y, Ming L, Chen L, Xiong L and Xie W*. An inferred functional impact map of genetic variants in rice. Mol Plant, 2021, DOI: 10.1016/j.molp.2021.06.025

2. Zhao H#, Tu Z#, Liu Y, Zong Z, Li J, Liu H, Xiong F, Zhan J, Hu X, Xie W*. PlantDeepSEA, a deep learning-based web service to predict the regulatory effects of genomic variants in plants. Nucleic Acids Res, 2021, 49: W523

3. Tang S#, Zhao H#, Lu S, Yu L, Zhang G, Zhang Y, Yang Q, Zhou Y, Wang X, Ma W, Xie W*, Guo L*. Genome- and transcriptome-wide association studies provide insights into the genetic basis of natural variation of seed oil content in Brassica napus. Mol Plant, 2021, 14: 470

4. Zhu T#, Liao K#, Zhou R#, Xia C, Xie W*. ATAC-seq with unique molecular identifiers improves quantification and footprinting. Commun Biol, 2020, 3: 675

5. Yao W, Li G, Zhao H, Wang G, Lian X, Xie W*. Exploring the rice dispensable genome using a metagenome-like assembly strategy. Genome Biol, 2015, 16: 187
Featured as "Research Highlight" in Genome Biology "Harvesting rice’s dispensable genome"

6. 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 collection. Proc Natl Acad Sci USA, 2015, 112: E5411-E5419
Featured as "Research Highlight" in Nature Plants "Rice breeding: Signature analysis"

7. 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

8. 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 Study. Mol Plant, 2015, 8: 946-957

9. 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 metabolism. Nat Genet, 2014, 46: 714-721

10. Yu H#, Xie W#, Li J, Zhou F*, Zhang Q*. A whole-genome SNP array (RICE6K) for genomic breeding in rice. Plant Biotechnol J, 2014, 12: 28-37

11. 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 Breeding. Mol Plant, 2014, 7: 541-553

12. Cai H#, Xie W#, Zhu T, Lian X*. Transcriptome response to phosphorus starvation in rice. Acta Physiol Plant, 2012, 34: 327-341

13. 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 sequencing. Proc Natl Acad Sci USA, 2010, 119: 151-164

14. 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 rice. Plant J, 2010, 61: 752-766

15. 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 method. Theor Appl Genet, 2009, 119: 151-164

16. Wei J, Xie W, Li R, Wang S, Qu H, Ma R, Zhou X, Jia Z. Analysis of trait heritability in functionally partitioned rice genomes. Heredity (Edinb), 2020, 124: 485-498

17. Yang J, Chang Y, Qin Y, Chen D, Zhu T, Peng K, Wang H, Tang N, Li X, Wang Y, Liu Y, Li X, Xie W, Xiong L. A lamin-like protein OsNMCP1 regulates drought resistance and root growth through chromatin accessibility modulation by interacting with a chromatin remodeller OsSWI3C in rice. New Phytol, 2020, 227: 65-83

18. Yao W, Li Y, Xie W, Wang L. Features of sRNA biogenesis in rice revealed by genetic dissection of sRNA expression level. Comput Struct Biotechnol J, 2020, 18: 3207-3216

19. Chen J, Zhou H, Xie W, Xia D, Gao G, Zhang Q, Wang G, Lian X, Xiao J, He Y. Genome-wide association analyses reveal the genetic basis of combining ability in rice. Plant Biotechnol J, 2019, 17: 2211-2222

20. Hu X, Xie W, Wu C, Xu S. A directed learning strategy integrating multiple omic data improves genomic prediction. Plant Biotechnol J, 2019, 17: 2011-2020

21. Jain R, Jenkins J, Shu S, Chern M, Martin JA, Copetti D, Duong PQ, Pham NT, Kudrna DA, Talag J, Schackwitz WS, Lipzen AM, Dilworth D, Bauer D, Grimwood J, Nelson CR, Xing F, Xie W, Barry KW, Wing RA, Schmutz J, Li G, Ronald PC. Genome sequence of the model rice variety KitaakeX. BMC Genomics, 2019, 20: 905

22. Wang S, Wei J, Li R, Qu H, Chater JM, Ma R, Li Y, Xie W, Jia Z. Identification of optimal prediction models using multi-omic data for selecting hybrid rice. Heredity (Edinb), 2019, 123: 395-406

23. Dong H, Zhao H, Li S, Han Z, Hu G, Liu C, Yang G, Wang G, Xie W, Xing Y. Genome-wide association studies reveal that members of bHLH subfamily 16 share a conserved function in regulating flag leaf angle in rice (Oryza sativa). Plos Genetics, 2018, 14: 20

24. Song J, Lei Y, Shu C, Ding Y, Xing F, Liu H, Wang J, Xie W, Zhang J, Chen L. Rice Information GateWay: A Comprehensive Bioinformatics Platform for Indica Rice Genomes. Mol Plant, 2018, 11: 505-507

25. Sun S, Wang T, Wang L, Li X, Jia Y, Liu C, Huang X, Xie W, Wang X. Natural selection of a GSK3 determines rice mesocotyl domestication by coordinating strigolactone and brassinosteroid signaling. Nature Commun, 2018, 9: 13

26. Yang M, Lu K, Zhao FJ, Xie W, Ramakrishna P, Wang G, Du Q, Liang L, Sun C, Zhao H, Zhang Z, Liu Z, Tian J, Huang XY, Wang W, Dong H, Hu J, Ming L, Xing Y, Wang G, Xiao J, Salt DE, Lian X. Genome-Wide Association Studies Reveal the Genetic Basis of Ionomic Variation in Rice. Plant Cell, 2018, 30: 2720-2740

27. Zhu C, Peng Q, Fu D, Zhuang D, Yu Y, Duan M, Xie W, Cai Y, Ouyan Y, Lian X, Wu C. The E3 Ubiquitin Ligase HAF1 Modulates Circadian Accumulation of EARLY FLOWERING3 to Control Heading Date in Rice under Long-Day Conditions. Plant Cell, 2018, 30: 2352-2367

28. Wang Q, Zhao H, Jiang J, Xu J, Xie W, Fu X, Liu C, He Y, Wang G. Genetic Architecture of Natural Variation in Rice Nonphotochemical Quenching Capacity Revealed by Genome-Wide Association Study. Frontiers in Plant Science, 2017, 8: 13

29. Zhou H, Li P, Xie W, Hussain S, Li Y, Xia D, Zhao H, Sun S, Chen J, Ye H, Hou J, Zhao D, Gao G, Zhang Q, Wang G, Lian X, Xiao J, Yu S, Li X, He Y. Genome-wide Association Analyses Reveal the Genetic Basis of Stigma Exsertion in Rice. Mol Plant, 2017, 10: 634-644

30. Bai X, Zhao H, Huang Y, Xie W, Han Z, Zhang B, Guo Z, Yang L, Dong H, Xue W, Li G, Hu G, Hu Y, Xing Y. Genome-Wide Association Analysis Reveals Different Genetic Control in Panicle Architecture Between Indica and Japonica Rice. Plant Genome, 2016, 9:

31. Dong H, Zhao H, Xie W, Han Z, Li G, Yao W, Bai X, Hu Y, Guo Z, Lu K, Yang L, Xing Y. A Novel Tiller Angle Gene, TAC3, together with TAC1 and D2 Largely Determine the Natural Variation of Tiller Angle in Rice Cultivars. PLoS Genet, 2016, 12: e1006412

32. Jin M, Liu H, He C, Fu J, Xiao Y, Wang Y, Xie W, Wang G, Yan J. Maize pan-transcriptome provides novel insights into genome complexity and quantitative trait variation. Sci Rep, 2016, 6: 18936

33. Magwa RA, Zhao H, Yao W, Xie W, Yang L, Xing Y, Bai X. Genomewide association analysis for awn length linked to the seed shattering gene qSH1 in rice. J Genet, 2016, 95: 639-646

34. Ouyang Y, Li G, Mi J, Xu C, Du H, Zhang C, Xie W, Li X, Xiao J, Song H, Zhang Q. Origination and Establishment of a Trigenic Reproductive Isolation System in Rice. Mol Plant, 2016, 9: 1542-1545

35. Zhang J, Chen L, Sun S, Kudrna D, Copetti D, Li W, Mu T, Jiao W, Xing F, Lee S, Talag J, Song J, Du B, Xie W, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou DX, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Hurtado B, Danowitz A, Wing R, Zhang Q. Building two indica rice reference genomes with PacBio long-read and Illumina paired-end sequencing data. Sci Data, 2016, 3: 160076

36. Zhang J, Chen L, Xing F, Kudrna D, Yao W, Copetti D, Mu T, Li W, Song J, Xie W, Lee S, Talag J, Shao L, An Y, Zhang C, Ouyang Y, Sun S, Jiao W, Lv F, Du B, Luo M, Maldonado C, Goicoechea J, Xiong L, Wu C, Xing Y, Zhou D, Yu S, Zhao Y, Wang G, Yu Y, Luo Y, Zhou Z, Hurtado B, Danowitz A, Wing R, Zhang Q. Extensive sequence divergence between the reference genomes of two elite indica rice varieties Zhenshan 97 and Minghui 63. Proc Natl Acad Sci USA, 2016, 113: E5163-5171

37. 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

38. 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

39. 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

40. 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

41. 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

42. 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

43. 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

44. 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

45. 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

46. 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

47. 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

48. 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

49. 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

50. 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

51. 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

52. 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

53. 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

54. Cai H, Lu Y, Xie W, Zhu T, Lian X. Transcriptome response to nitrogen starvation in rice. J Biosci, 2012, 37: 731-747

55. 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

56. 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

57. 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

58. 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

59. 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

60. 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

61. 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

62. 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

63. 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

64. 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

65. 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

66. 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

67. 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

68. 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

69. 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

70. 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

71. 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

72. 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



已批准专利:

1. 周发,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

获国家自然科学基金优秀青年科学基金

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PNASNature CommunicationsBioinformaticsScientific ReportsPLoS ONEBMC GenomicsTAG等杂志审稿人