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袁道军

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相关介绍
基本信息栏姓名：袁道军出生年月：1979. 07 性别：男硕/博导：硕导民族：汉族开设课程：生物信息学、植物大数据职称：副教授研究方向：基因组与作物驯化学位.：农学博士联系方式办公电话：027-8728 3955 电子邮件：ydj at mail.hzau.edu.cn 个人简介袁道军，男，博士，植物科学技术学院副教授，硕士生导师，主讲《生物信息学》、《植物大数据》和《植物基因组研究进展》等课程。分别于2002年、2005年和2014年于华中农业大学依次获得农学和工学（计算机科学与技术）学士、理学硕士和农学博士学位。2015年4月至2019年8月，先后在美国杨百翰大学（Brigham Young University, Provo, UT）Joshua Udall副教授和爱荷华州立大学（Iowa State University, Ames, IA）Jonathan Wendel教授指导下开展博士后研究，期间前往美国农业部南方平原研究中心（USDA-ARS, College Station, TX）、北卡罗莱纳州立大学（North Carolina State University, Raleigh, NC）和康奈尔大学（Cornel University, Ithaca, NY）等开展合作研究。长期从事棉花基因组及生物信息学方面工作，利用组学大数据，开展棉花的比较基因组学研究，揭示棉花基因组进化与驯化的奥秘，为棉花的遗传改良和从头驯化提供理论基础。先后主持自然科学基金、国家重大专项子课题和中央高校基本科研业务费项目各1项，参与多项国家自然科学基金以及美国国家自然科学基金重点项目。近些年来以第一作者、通讯作者和共同作者在Nature Genetics、Advanced Science、Nature Communication、Nucleic Acids Research、Plant Biotechnology Journal和Scientific Reports等学术杂志上发表论文40余篇，总引用次数超过2300次，H指数22，I10指数26，详情请见Google Scholar链接 https://scholar.google.com/citations?hl=en&user=BjD0NDYAAAAJ 或 https.//orcid.org/0000-0001-6007-5571 。教育经历 2007.09—2014.12 作物遗传育种农学博士华中农业大学 2002.09—2005.06 气象学理学硕士华中农业大学 1999.09—2002.06 计算机科学与技术工学学士华中农业大学 1998.09—2002.06 农学农学学士华中农业大学工作经历 2018.08—2019.08 爱荷华州立大学(Iowa State University, Iowa, USA) 博士后 2015.04—2018.08 杨百翰大学(Brigham Young University, Utah, USA) 博士后 2017.01—至今华中农业大学植物科技学院副教授 2006.01—2016.12 华中农业大学植物科技学院讲师 2005.07—2007.12 华中农业大学植物科技学院助教科研项目 1. 教育部，中央高校基本科研项目，课题编号：2021ZKPY013，项目年限：2021-2024（主持） 2. 农业农村部，国家重大科技专项，课题编号：2018ZX08010-05B，项目年限：2018-2019（子课题主持） 3. 科技部，国家自然科学基金，课题编号：31201251，项目年限：2013-2015（主持） 4. 教育部，中央高校基本科研项目，课题编号：2013JC011，项目年限：2013-2014（主持）教学研究与教学改革 1. 2020年校级教改项目.《生物信息学》课程思政（主持） 2. 2019年校级教改项目.现代农业气象多功能网络教学平台的研制（参与） 3. 2013年湖北省教学研究项目.以科研团队支撑农学类专业本科生综合创新实验教学的探索与实践（参与）发明专利及获得奖励发明专利 1.朱龙付,高巍,龙璐,张献龙,聂以春,袁道军.棉花硬脂酰去饱和化酶GbSSI2基因及应用.专利授权号.ZL201310019959.5 2.张献龙,李阳,涂礼莉,袁道军.棉花细胞壁伸展蛋白基因GbEXPATR 及应用，专利授权号.ZL201410073300.2 软件著作权 1.袁道军,陈进炜,高文辉. 基于参照物法的叶面积计算机测量系统【简称.Leaf】V1.0 2.袁道军,高文辉,王茂军. 基于相似性比较基因组学分析及结果展示工具相似性几何体软件【简称.SimiTriX-SimiQuad】V1.0 主要奖励 1.2020年湖北省自然科学奖一等奖. 棉花纤维发育与品质形成生物学. 2.2020年教育部自然科学奖一等奖. 棉花抗黄萎病的信号调控网络研究. 3.青年教师讲课竞赛优胜奖、教学质量三等奖、招生宣传先进个人和优秀班主任等. 学术论文与著作（*表示共同通讯作者，#表示共同第一作者）. 学术论文(代表作，引用次数来自Google Scholar，更新日期2021年9月) 1. D. Yuan^, C.E. Grover, G. Hu, M. Pan, E. R. Miller, J.L. Conover, S.P. Hunt, J.A. Udall^, J. F. Wendel. Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. *Advanced Science* 2021, 2003634. https.//doi.org/10.1002/advs.202003634 (IF=15.840,Cited:3) 2. Wang M^#, Tu L^#, Yuan D^#, Zhu D, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. *Nature genetics* 2019, 51(2).224–229. https.//www.nature.com/articles/s41588-018-0282-x (IF=27.603, Cited:229) 3. Yuan D^#, Tang Z^#, Wang M^#, Gao W, Tu L, Jin X, Chen L, He Y, Zhang L, Zhu L et al. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. *Scientific reports* 2015, 5.17662. https.//www.nature.com/articles/srep17662 (IF=5.578, Cited:182) 4. Wang M, Yuan D^, Gao W, Li Y, Tan J, Zhang X^. A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls. *PLoS One* 2013, 8(8).e72082. https.//www.ncbi.nlm.nih.gov/pubmed/23951288 (IF=3.730,Cited:85) 5. Yuan D, Tu L, Zhang X. Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. *PLoS One* 2011, 6(7).e22758. https://pubmed.ncbi.nlm.nih.gov/21829504/ (IF=4.411, Cited:29) 其它学术论文 1. Li J, Yuan D, Wang P, Wang Q, Sun M, Liu Z, Si H, Xu Z, Ma Y, Zhang B, Pei L, Tu L, Zhu L, Chen L-L, Lindsey K, Zhang X, Jin S, Wang M: Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biology 2021, 22(1):119. https://doi.org/10.1186/s13059-021-02351-w 2. Grover CE, Yuan D, Arick MA, II,, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA: The Gossypium stocksii genome as a novel resource for cotton improvement. G3 Genes\|Genomes\|Genetics 2021. https://doi.org/10.1093/g3journal/jkab125 3. Ding Y, Zhang R, Zhu L, Wang M, Ma Y, Yuan D, Liu N, Hu H, Min L, Zhang X: An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid ‘Huaza Mian H318’, as revealed by genome-wide gene expression analysis. BMC Genomics 2021, 22(1):277. https://doi.org/10.1186/s12864-021-07580-8 4. Li B, Liang S, Alariqi M, Wang F, Wang G, Wang Q, Xu Z, Yu L, Naeem Zafar M, Sun L, Si H, Yuan D, Guo W, Wang Y, Lindsey K, Zhang X, Jin S: The application of temperature sensitivity CRISPR/LbCpf1 (LbCas12a) mediated genome editing in allotetraploid cotton (G. hirsutum) and creation of nontransgenic, gossypol-free cotton. Plant Biotechnol J 2021, 19(2):221-223. https://www.ncbi.nlm.nih.gov/pubmed/32854160 5. Xiao S, Hu Q, Zhang X, Si H, Liu S, Chen L, Chen K, Berne S, Yuan D, Lindsey K, Zhang X, Zhu L: Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2. Journal of Experimental Botany 2021, 72(13):4721-4743. https://doi.org/10.1093/jxb/erab186 6. Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X: Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Scientific Reports 2021, 11(1):9471. https://doi.org/10.1038/s41598-021-88160-4 7. Grover CE, Pan M, Yuan D, Arick MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG, Wendel JF, Udall JA: The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. G3 (Bethesda) 2020, 10(5):1457-1467. https://www.ncbi.nlm.nih.gov/pubmed/32122962 8. Grover CE, Yoo MJ, Lin M, Murphy MD, Harker DB, Byers RL, Lipka AE, Hu G, Yuan D, Conover JL, Udall JA, Paterson AH, Gore MA, Wendel JF: Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.). G3 (Bethesda) 2020, 10(2):731-754. https://www.ncbi.nlm.nih.gov/pubmed/31843806 9. Bao Y, Hu G, Grover CE, Conover J, Yuan D, Wendel JF: Unraveling cis and trans regulatory evolution during cotton domestication. Nat Commun 2019, 10(1):5399. https://www.ncbi.nlm.nih.gov/pubmed/31776348 10. Hu L, Xu Z, Wang M, Fan R, Yuan D, Wu B, Wu H, Qin X, Yan L, Tan L, Sim S, Li W, Saski CA, Daniell H, Wendel JF, Lindsey K, Zhang X, Hao C, Jin S: The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis. Nat Commun 2019, 10(1):4702. https://www.ncbi.nlm.nih.gov/pubmed/31619678 11. Li B, Rui H, Li Y, Wang Q, Alariqi M, Qin L, Sun L, Ding X, Wang F, Zou J, Wang Y, Yuan D, Zhang X, Jin S: Robust CRISPR/Cpf1 (Cas12a)-mediated genome editing in allotetraploid cotton (Gossypium hirsutum). Plant Biotechnol J 2019, 17(10):1862-1864. https://www.ncbi.nlm.nih.gov/pubmed/31055869 12. Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF: De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri. G3 (Bethesda) 2019, 9(10):3079-3085. https://www.ncbi.nlm.nih.gov/pubmed/31462444 13. Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, 2nd, Masonbrink RE, Peterson DG, Wendel JF: The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Front Plant Sci 2019, 10:1541. https://www.ncbi.nlm.nih.gov/pubmed/31827481 14. Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, Yuan D, Zhang Q, Lindsey K, Zhang X: Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 2017, 49(4):579-587. https://www.ncbi.nlm.nih.gov/pubmed/28263319 15. Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q: GbEXPATR, a species‐specific expansin, enhances cotton fibre elongation through cell wall restructuring. Plant biotechnology journal 2016, 14(3):951-963. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12450 16. Wang M, Wang P, Tu L, Zhu S, Zhang L, Li Z, Zhang Q, Yuan D, Zhang X: Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic Acids Res 2016, 44(9):4067-4079. https://www.ncbi.nlm.nih.gov/pubmed/27067544 17. Wang M, Yuan D, Tu L, Gao W, He Y, Hu H, Wang P, Liu N, Lindsey K, Zhang X: Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytologist 2015, 207(4):1181-1197. https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.13429 18. Wu Y, Min L, Wu Z, Yang L, Zhu L, Yang X, Yuan D, Guo X, Zhang X: Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton. Scientific reports 2015, 5:9608. https://www.ncbi.nlm.nih.gov/pubmed/26043720 19. Jin F, Hu L, Yuan D, Xu J, Gao W, He L, Yang X, Zhang X: Comparative transcriptome analysis between somatic embryos (SE s) and zygotic embryos in cotton: evidence for stress response functions in SE development. Plant biotechnology journal 2014, 12(2):161-173. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12123 20. Liu C, Yuan D, Lin Z: Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. Journal of genetics 2014, 93(3):689-697. https://www.ncbi.nlm.nih.gov/pubmed/25572227 21. Sun L, Zhu L, Xu L, Yuan D, Min L, Zhang X: Cotton cytochrome P450 CYP82D regulates systemic cell death by modulating the octadecanoid pathway. Nature communications 2014, 5:5372. https://www.nature.com/articles/ncomms6372 22. Li X, Yuan D, Zhang J, Lin Z, Zhang X: Genetic mapping and characteristics of genes specifically or preferentially expressed during fiber development in cotton. PLoS One 2013, 8(1):e54444. https://www.ncbi.nlm.nih.gov/pubmed/23372723 23. Liu C, Yuan D, Zhang X, Lin Z: Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP. Journal of genetics 2013, 92(2):175-181. https://pubmed.ncbi.nlm.nih.gov/23970073/ 24. Min L, Zhu L, Tu L, Deng F, Yuan D, Zhang X: Cotton GhCKI disrupts normal male reproduction by delaying tapetum programmed cell death via inactivating starch synthase. The Plant Journal 2013, 75(5):823-835. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12245/ 25. Yang X, Wang L, Yuan D, Lindsey K, Zhang X: Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. Journal of experimental botany 2013, 64(6):1521-1536. https://www.ncbi.nlm.nih.gov/pubmed/23382553 26. Li X, Yuan D, Wang H, Chen X, Wang B, Lin Z, Zhang X: Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP. Genome 2012, 55(6):459-470. https://cdnsciencepub.com/doi/full/10.1139/g2012-032/ 27. Yang X, Zhang X, Yuan D, Jin F, Zhang Y, Xu J: Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC plant biology 2012, 12(1):110. https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-110 28. Yuan D, Liang S, Lin Z, Zhang X: In silico comparative analysis of EST-SSRs in three cotton genomes. African Journal of Biotechnology 2012, 11(69):13269-13371. 29. Hu L, Yang X, Yuan D, Zeng F, Zhang X: GhHmgB3 deficiency deregulates proliferation and differentiation of cells during somatic embryogenesis in cotton. Plant biotechnology journal 2011, 9(9):1038-1048. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1467-7652.2011.00617.x 30. Xu L, Zhu L, Tu L, Liu L, Yuan D, Jin L, Long L, Zhang X: Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. Journal of experimental botany 2011, 62(15):5607-5621. https://academic.oup.com/jxb/article/62/15/5607/561887 31. Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X: Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC 1 population between Gossypium hirsutum and G. barbadense. BMC genomics 2011, 12(1):15. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-15 教材与著作 1. Hu G, Grover CE, Yuan D, Dong Y, Miller E, Conover JL, Wendel JF: Evolution and Diversity of the Cotton Genome. In: Cotton Precision Breeding. Edited by Rahman M-u, Zafar Y, Zhang T. Cham: Springer International Publishing; 2021: 25-78. 2. Maojun Wang, Daojun Yuan, Xianlong Zhang. Genome Sequencing, In. Cotton, 2nd edition, edited by David Fang and Richard G. Percy, published by American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, 2015, P289-302. 3. 《农学概论》参编，2009，中国矿业大学出版社. ISBN:9787564602024.

相关介绍

基本信息栏

姓名：袁道军出生年月：1979. 07

性别：男硕/博导：硕导

民族：汉族开设课程：生物信息学、植物大数据

职称：副教授研究方向：基因组与作物驯化

学位.：农学博士

联系方式

办公电话：027-8728 3955

电子邮件：ydj at mail.hzau.edu.cn

个人简介

袁道军，男，博士，植物科学技术学院副教授，硕士生导师，主讲《生物信息学》、《植物大数据》和《植物基因组研究进展》等课程。分别于2002年、2005年和2014年于华中农业大学依次获得农学和工学（计算机科学与技术）学士、理学硕士和农学博士学位。2015年4月至2019年8月，先后在美国杨百翰大学（Brigham Young University, Provo, UT）Joshua Udall副教授和爱荷华州立大学（Iowa State University, Ames, IA）Jonathan Wendel教授指导下开展博士后研究，期间前往美国农业部南方平原研究中心（USDA-ARS, College Station, TX）、北卡罗莱纳州立大学（North Carolina State University, Raleigh, NC）和康奈尔大学（Cornel University, Ithaca, NY）等开展合作研究。

长期从事棉花基因组及生物信息学方面工作，利用组学大数据，开展棉花的比较基因组学研究，揭示棉花基因组进化与驯化的奥秘，为棉花的遗传改良和从头驯化提供理论基础。先后主持自然科学基金、国家重大专项子课题和中央高校基本科研业务费项目各1项，参与多项国家自然科学基金以及美国国家自然科学基金重点项目。近些年来以第一作者、通讯作者和共同作者在Nature Genetics、Advanced Science、Nature Communication、Nucleic Acids Research、Plant Biotechnology Journal和Scientific Reports等学术杂志上发表论文40余篇，总引用次数超过2300次，H指数22，I10指数26，详情请见Google Scholar链接 https://scholar.google.com/citations?hl=en&user=BjD0NDYAAAAJ 或 https.//orcid.org/0000-0001-6007-5571 。

教育经历

2007.09—2014.12 作物遗传育种农学博士华中农业大学

2002.09—2005.06 气象学理学硕士华中农业大学

1999.09—2002.06 计算机科学与技术工学学士华中农业大学

1998.09—2002.06 农学农学学士华中农业大学

工作经历

2018.08—2019.08 爱荷华州立大学(Iowa State University, Iowa, USA) 博士后

2015.04—2018.08 杨百翰大学(Brigham Young University, Utah, USA) 博士后

2017.01—至今华中农业大学植物科技学院副教授

2006.01—2016.12 华中农业大学植物科技学院讲师

2005.07—2007.12 华中农业大学植物科技学院助教

科研项目

1. 教育部，中央高校基本科研项目，课题编号：2021ZKPY013，项目年限：2021-2024（主持）

2. 农业农村部，国家重大科技专项，课题编号：2018ZX08010-05B，项目年限：2018-2019（子课题主持）

3. 科技部，国家自然科学基金，课题编号：31201251，项目年限：2013-2015（主持）

4. 教育部，中央高校基本科研项目，课题编号：2013JC011，项目年限：2013-2014（主持）

教学研究与教学改革

1. 2020年校级教改项目.《生物信息学》课程思政（主持）

2. 2019年校级教改项目.现代农业气象多功能网络教学平台的研制（参与）

3. 2013年湖北省教学研究项目.以科研团队支撑农学类专业本科生综合创新实验教学的探索与实践（参与）

发明专利及获得奖励

发明专利

1.朱龙付,高巍,龙璐,张献龙,聂以春,袁道军.棉花硬脂酰去饱和化酶GbSSI2基因及应用.专利授权号.ZL201310019959.5

2.张献龙,李阳,涂礼莉,袁道军.棉花细胞壁伸展蛋白基因GbEXPATR 及应用，专利授权号.ZL201410073300.2

软件著作权

1.袁道军,陈进炜,高文辉. 基于参照物法的叶面积计算机测量系统【简称.Leaf】V1.0

2.袁道军,高文辉,王茂军. 基于相似性比较基因组学分析及结果展示工具相似性几何体软件【简称.SimiTriX-SimiQuad】V1.0

主要奖励

1.2020年湖北省自然科学奖一等奖. 棉花纤维发育与品质形成生物学.

2.2020年教育部自然科学奖一等奖. 棉花抗黄萎病的信号调控网络研究.

3.青年教师讲课竞赛优胜奖、教学质量三等奖、招生宣传先进个人和优秀班主任等.

学术论文与著作（*表示共同通讯作者，#表示共同第一作者）.

学术论文(代表作，引用次数来自Google Scholar，更新日期2021年9月)

1. D. Yuan^*, C.E. Grover, G. Hu, M. Pan, E. R. Miller, J.L. Conover, S.P. Hunt, J.A. Udall^*, J. F. Wendel. Parallel and Intertwining Threads of Domestication in Allopolyploid Cotton. Advanced Science 2021, 2003634. https.//doi.org/10.1002/advs.202003634 (IF=15.840,Cited:3)

2. Wang M^#, Tu L^#, Yuan D^#, Zhu D, Shen C, Li J, Liu F, Pei L, Wang P, Zhao G et al. Reference genome sequences of two cultivated allotetraploid cottons, Gossypium hirsutum and Gossypium barbadense. Nature genetics 2019, 51(2).224–229. https.//www.nature.com/articles/s41588-018-0282-x (IF=27.603, Cited:229)

3. Yuan D^#, Tang Z^#, Wang M^#, Gao W, Tu L, Jin X, Chen L, He Y, Zhang L, Zhu L et al. The genome sequence of Sea-Island cotton (Gossypium barbadense) provides insights into the allopolyploidization and development of superior spinnable fibres. Scientific reports 2015, 5.17662. https.//www.nature.com/articles/srep17662 (IF=5.578, Cited:182)

4. Wang M, Yuan D^*, Gao W, Li Y, Tan J, Zhang X^*. A comparative genome analysis of PME and PMEI families reveals the evolution of pectin metabolism in plant cell walls. PLoS One 2013, 8(8).e72082. https.//www.ncbi.nlm.nih.gov/pubmed/23951288 (IF=3.730,Cited:85)

5. Yuan D, Tu L, Zhang X. Generation, annotation and analysis of first large-scale expressed sequence tags from developing fiber of Gossypium barbadense L. PLoS One 2011, 6(7).e22758. https://pubmed.ncbi.nlm.nih.gov/21829504/ (IF=4.411, Cited:29)

其它学术论文

1. Li J, Yuan D, Wang P, Wang Q, Sun M, Liu Z, Si H, Xu Z, Ma Y, Zhang B, Pei L, Tu L, Zhu L, Chen L-L, Lindsey K, Zhang X, Jin S, Wang M: Cotton pan-genome retrieves the lost sequences and genes during domestication and selection. Genome Biology 2021, 22(1):119. https://doi.org/10.1186/s13059-021-02351-w

2. Grover CE, Yuan D, Arick MA, II,, Miller ER, Hu G, Peterson DG, Wendel JF, Udall JA: The Gossypium stocksii genome as a novel resource for cotton improvement. G3 Genes|Genomes|Genetics 2021. https://doi.org/10.1093/g3journal/jkab125

3. Ding Y, Zhang R, Zhu L, Wang M, Ma Y, Yuan D, Liu N, Hu H, Min L, Zhang X: An enhanced photosynthesis and carbohydrate metabolic capability contributes to heterosis of the cotton (Gossypium hirsutum) hybrid ‘Huaza Mian H318’, as revealed by genome-wide gene expression analysis. BMC Genomics 2021, 22(1):277. https://doi.org/10.1186/s12864-021-07580-8

4. Li B, Liang S, Alariqi M, Wang F, Wang G, Wang Q, Xu Z, Yu L, Naeem Zafar M, Sun L, Si H, Yuan D, Guo W, Wang Y, Lindsey K, Zhang X, Jin S: The application of temperature sensitivity CRISPR/LbCpf1 (LbCas12a) mediated genome editing in allotetraploid cotton (G. hirsutum) and creation of nontransgenic, gossypol-free cotton. Plant Biotechnol J 2021, 19(2):221-223. https://www.ncbi.nlm.nih.gov/pubmed/32854160

5. Xiao S, Hu Q, Zhang X, Si H, Liu S, Chen L, Chen K, Berne S, Yuan D, Lindsey K, Zhang X, Zhu L: Orchestration of plant development and defense by indirect crosstalk of salicylic acid and brassinosteorid signaling via transcription factor GhTINY2. Journal of Experimental Botany 2021, 72(13):4721-4743. https://doi.org/10.1093/jxb/erab186

6. Zhou J, Zhang S, Wang J, Shen H, Ai B, Gao W, Zhang C, Fei Q, Yuan D, Wu Z, Tembrock LR, Li S, Gu C, Liao X: Chloroplast genomes in Populus (Salicaceae): comparisons from an intensively sampled genus reveal dynamic patterns of evolution. Scientific Reports 2021, 11(1):9471. https://doi.org/10.1038/s41598-021-88160-4

7. Grover CE, Pan M, Yuan D, Arick MA, Hu G, Brase L, Stelly DM, Lu Z, Schmitz RJ, Peterson DG, Wendel JF, Udall JA: The Gossypium longicalyx Genome as a Resource for Cotton Breeding and Evolution. G3 (Bethesda) 2020, 10(5):1457-1467. https://www.ncbi.nlm.nih.gov/pubmed/32122962

8. Grover CE, Yoo MJ, Lin M, Murphy MD, Harker DB, Byers RL, Lipka AE, Hu G, Yuan D, Conover JL, Udall JA, Paterson AH, Gore MA, Wendel JF: Genetic Analysis of the Transition from Wild to Domesticated Cotton (Gossypium hirsutum L.). G3 (Bethesda) 2020, 10(2):731-754. https://www.ncbi.nlm.nih.gov/pubmed/31843806

9. Bao Y, Hu G, Grover CE, Conover J, Yuan D, Wendel JF: Unraveling cis and trans regulatory evolution during cotton domestication. Nat Commun 2019, 10(1):5399. https://www.ncbi.nlm.nih.gov/pubmed/31776348

10. Hu L, Xu Z, Wang M, Fan R, Yuan D, Wu B, Wu H, Qin X, Yan L, Tan L, Sim S, Li W, Saski CA, Daniell H, Wendel JF, Lindsey K, Zhang X, Hao C, Jin S: The chromosome-scale reference genome of black pepper provides insight into piperine biosynthesis. Nat Commun 2019, 10(1):4702. https://www.ncbi.nlm.nih.gov/pubmed/31619678

11. Li B, Rui H, Li Y, Wang Q, Alariqi M, Qin L, Sun L, Ding X, Wang F, Zou J, Wang Y, Yuan D, Zhang X, Jin S: Robust CRISPR/Cpf1 (Cas12a)-mediated genome editing in allotetraploid cotton (Gossypium hirsutum). Plant Biotechnol J 2019, 17(10):1862-1864. https://www.ncbi.nlm.nih.gov/pubmed/31055869

12. Udall JA, Long E, Hanson C, Yuan D, Ramaraj T, Conover JL, Gong L, Arick MA, Grover CE, Peterson DG, Wendel JF: De Novo Genome Sequence Assemblies of Gossypium raimondii and Gossypium turneri. G3 (Bethesda) 2019, 9(10):3079-3085. https://www.ncbi.nlm.nih.gov/pubmed/31462444

13. Udall JA, Long E, Ramaraj T, Conover JL, Yuan D, Grover CE, Gong L, Arick MA, 2nd, Masonbrink RE, Peterson DG, Wendel JF: The Genome Sequence of Gossypioides kirkii Illustrates a Descending Dysploidy in Plants. Front Plant Sci 2019, 10:1541. https://www.ncbi.nlm.nih.gov/pubmed/31827481

14. Wang M, Tu L, Lin M, Lin Z, Wang P, Yang Q, Ye Z, Shen C, Li J, Zhang L, Zhou X, Nie X, Li Z, Guo K, Ma Y, Huang C, Jin S, Zhu L, Yang X, Min L, Yuan D, Zhang Q, Lindsey K, Zhang X: Asymmetric subgenome selection and cis-regulatory divergence during cotton domestication. Nat Genet 2017, 49(4):579-587. https://www.ncbi.nlm.nih.gov/pubmed/28263319

15. Li Y, Tu L, Pettolino FA, Ji S, Hao J, Yuan D, Deng F, Tan J, Hu H, Wang Q: GbEXPATR, a species‐specific expansin, enhances cotton fibre elongation through cell wall restructuring. Plant biotechnology journal 2016, 14(3):951-963. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12450

16. Wang M, Wang P, Tu L, Zhu S, Zhang L, Li Z, Zhang Q, Yuan D, Zhang X: Multi-omics maps of cotton fibre reveal epigenetic basis for staged single-cell differentiation. Nucleic Acids Res 2016, 44(9):4067-4079. https://www.ncbi.nlm.nih.gov/pubmed/27067544

17. Wang M, Yuan D, Tu L, Gao W, He Y, Hu H, Wang P, Liu N, Lindsey K, Zhang X: Long noncoding RNAs and their proposed functions in fibre development of cotton (Gossypium spp.). New Phytologist 2015, 207(4):1181-1197. https://nph.onlinelibrary.wiley.com/doi/full/10.1111/nph.13429

18. Wu Y, Min L, Wu Z, Yang L, Zhu L, Yang X, Yuan D, Guo X, Zhang X: Defective pollen wall contributes to male sterility in the male sterile line 1355A of cotton. Scientific reports 2015, 5:9608. https://www.ncbi.nlm.nih.gov/pubmed/26043720

19. Jin F, Hu L, Yuan D, Xu J, Gao W, He L, Yang X, Zhang X: Comparative transcriptome analysis between somatic embryos (SE s) and zygotic embryos in cotton: evidence for stress response functions in SE development. Plant biotechnology journal 2014, 12(2):161-173. https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.12123

20. Liu C, Yuan D, Lin Z: Construction of an EST-SSR-based interspecific transcriptome linkage map of fibre development in cotton. Journal of genetics 2014, 93(3):689-697. https://www.ncbi.nlm.nih.gov/pubmed/25572227

21. Sun L, Zhu L, Xu L, Yuan D, Min L, Zhang X: Cotton cytochrome P450 CYP82D regulates systemic cell death by modulating the octadecanoid pathway. Nature communications 2014, 5:5372. https://www.nature.com/articles/ncomms6372

22. Li X, Yuan D, Zhang J, Lin Z, Zhang X: Genetic mapping and characteristics of genes specifically or preferentially expressed during fiber development in cotton. PLoS One 2013, 8(1):e54444. https://www.ncbi.nlm.nih.gov/pubmed/23372723

23. Liu C, Yuan D, Zhang X, Lin Z: Isolation, characterization and mapping of genes differentially expressed during fibre development between Gossypium hirsutum and G. barbadense by cDNA-SRAP. Journal of genetics 2013, 92(2):175-181. https://pubmed.ncbi.nlm.nih.gov/23970073/

24. Min L, Zhu L, Tu L, Deng F, Yuan D, Zhang X: Cotton GhCKI disrupts normal male reproduction by delaying tapetum programmed cell death via inactivating starch synthase. The Plant Journal 2013, 75(5):823-835. https://onlinelibrary.wiley.com/doi/full/10.1111/tpj.12245/

25. Yang X, Wang L, Yuan D, Lindsey K, Zhang X: Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis. Journal of experimental botany 2013, 64(6):1521-1536. https://www.ncbi.nlm.nih.gov/pubmed/23382553

26. Li X, Yuan D, Wang H, Chen X, Wang B, Lin Z, Zhang X: Increasing cotton genome coverage with polymorphic SSRs as revealed by SSCP. Genome 2012, 55(6):459-470. https://cdnsciencepub.com/doi/full/10.1139/g2012-032/

27. Yang X, Zhang X, Yuan D, Jin F, Zhang Y, Xu J: Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC plant biology 2012, 12(1):110. https://bmcplantbiol.biomedcentral.com/articles/10.1186/1471-2229-12-110

28. Yuan D, Liang S, Lin Z, Zhang X: In silico comparative analysis of EST-SSRs in three cotton genomes. African Journal of Biotechnology 2012, 11(69):13269-13371.

29. Hu L, Yang X, Yuan D, Zeng F, Zhang X: GhHmgB3 deficiency deregulates proliferation and differentiation of cells during somatic embryogenesis in cotton. Plant biotechnology journal 2011, 9(9):1038-1048. https://onlinelibrary.wiley.com/doi/full/10.1111/j.1467-7652.2011.00617.x

30. Xu L, Zhu L, Tu L, Liu L, Yuan D, Jin L, Long L, Zhang X: Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliae as revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. Journal of experimental botany 2011, 62(15):5607-5621. https://academic.oup.com/jxb/article/62/15/5607/561887

31. Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X: Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC 1 population between Gossypium hirsutum and G. barbadense. BMC genomics 2011, 12(1):15. https://bmcgenomics.biomedcentral.com/articles/10.1186/1471-2164-12-15

教材与著作

1. Hu G, Grover CE, Yuan D, Dong Y, Miller E, Conover JL, Wendel JF: Evolution and Diversity of the Cotton Genome. In: Cotton Precision Breeding. Edited by Rahman M-u, Zafar Y, Zhang T. Cham: Springer International Publishing; 2021: 25-78.

2. Maojun Wang, Daojun Yuan, Xianlong Zhang. Genome Sequencing, In. Cotton, 2nd edition, edited by David Fang and Richard G. Percy, published by American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America, 2015, P289-302.

3. 《农学概论》参编，2009，中国矿业大学出版社. ISBN:9787564602024.