華中農業大學信息學院生物信息研究生導師：謝為博

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姓名:謝為博

性別:男

職稱:教授

學位:博士

電話:027-87280350

郵箱:weibo.xie@mail.hzau.edu.cn

xwbmail@gmail.com

工作單位:

華中農業大學信息學院

研究方向:

水稻基因組學, 系統生物學

教育經歷：

2004.9 - 2010.6 華中農業大學 生命科學技術學院 基因組學專業  碩博連讀

1999.9 - 2003.9 中南民族大學 化學與生命科學學院 生物技術專業 本科

主要職歷

2018.1 - 華中農業大學 信息學院 教授，博士生導師

2014.8 - 2017.12 華中農業大學 信息學院 副教授，博士生導師

2013.1 - 2014.7 華中農業大學 生命科學技術學院 副教授

2010.7 - 2012.12 華中農業大學 生命科學技術學院 講師

2010.7  - 華中農業大學 作物遺傳改良國家重點實驗室 固定研究人員

科研成果

主持課題：

國家重點研發計劃 雜種優勢預測的新方法和強優勢新材料 課題，1126萬元，2016-2020

國家863計劃專項 全基因組選擇育種技術平臺建設 子課題，240萬元，2014-2018

國家863計劃專項 水稻組學、資源和生物信息平臺的創建 子課題，80萬元，2012-2015

國家自然科學基金 基于比較基因組和ATAC-seq注釋水稻基因組染色質開放區及其序列變異 面上項目，56萬元，2018-2021

國家自然科學基金 整合組學數據剖析水稻籽粒中代謝途徑及其調控網絡 面上項目，74萬元，2016-2019

國家自然科學基金 基于新一代測序技術的高通量基因分型方法的開發與完善 青年基金，24萬元，2012-2014

中國科協青年人才托舉工程，45萬元，2015-2017

本課題組主要以水稻為研究對象。近年來系統開展了多項挖掘利用水稻種質資源遺傳變異的工作，鑒定了秈稻育種過程中受選擇的基因組位點，為進一步改良水稻提供了重要靶點；并首次在水稻中開展了“非必需基因組”研究，揭示了其組成及對表型的影響，這些研究為進一步挖掘利用水稻優異遺傳變異開辟了新途徑。同時，作為主要設計人員之一開發了全球第一款水稻育種芯片和后續多款育種芯片，獲得發明專利3項，已得到推廣應用，并建立了多個水稻生物信息學數據庫，為進一步研究與利用水稻種質資源提供了新的平臺和工具。相關研究被Nature Plants、Genome Biology等雜志列為研究亮點，予以高度評價。

目前課題組主要從事三個方面的研究：（1）開發鑒定水稻非編碼調控元件的組學和計算方法；（2）整合多組學數據開展水稻系統生物學研究；（3）將上述研究結果應用于解析雜種優勢的機理。研究方向兼顧基礎與應用，具有很好的就業前景，也適合繼續深造；課題組既需要“濕實驗”人才，也需要“干實驗”人才，歡迎生物、數學、物理和計算機相關專業的青年朋友加入（作為碩博生、博士后和科研助理）。

近年發表的論文：

完整文章列表及引用情況請訪問：

ORCID http://orcid.org/0000-0002-2768-3572

Google scholar http://scholar.google.com/citations?user=I5zjYOUAAAAJ

# 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 strategy. Genome 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 collection. Proc 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 Study. Mol 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 metabolism. Nat Genet, 2014, 46: 714-721 (IF 29.4)

6. Yu H#, Xie W#, Li J, Zhou F*, Zhang Q*. A whole-genome SNP (RICE6K) for genomic breeding in rice. Plant 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 for Rice Biology and Molecular Breeding. Mol Plant, 2014, 7: 541-553 (IF 6.3)

8. Cai H#, Xie W#, Zhu T, Lian X*. Transcriptome response to phosphorus starvation in rice. Acta 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 sequencing. Proc 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 rice. Plant 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 method. Theor 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 . 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

已批準專利：

1. 周發松,謝為博,喻輝輝,李菁,張啟發. 一種水稻全基因組SNP芯片及其應用. 專利號：201210055775

2. 周發松,陳浩東,謝為博,何航,喻輝輝,唐曉艷,李菁,周君莉,何予卿,陳偉,張啟發,鄧興旺. 水稻全基因組育種芯片及其應用. 專利號：201380056318

3. 謝為博,張啟發,練興明,王功偉. 一種基于受選擇位點指數評估動植物品種育種潛力的方法及其應用. 專利號：201510551134

備注入選首批中國科協青年人才托舉工程

2012年全國優秀博士學位論文提名論文

2011年湖北省優秀博士學位論文

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