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明瑞光教授

PostTime:2019-2-20 11:20 阅读人数:568

明瑞光,教授,博士生导师。现为福建农林大学基因组中心主任。1991-1995年在美国夏威夷大学获得植物遗传育种专业博士学位;1995-1998年在美国德州农工大学从事博士后研究;1998-2005年担任美国夏威夷农业研究中心研究员(Plant Molecular Geneticist);2005-至今为美国伊利诺伊大学香槟校区(University of Illinois at Urbana-Champaign, UIUC)副教授、教授。为《Tropical Plant Biology》共同主编、《Genome Insights》和《Journal of Systematics and Evolution》编委。在植物性染色体研究方面,开创了早期性染色体进化研究领域,并长期处于这个领域的前沿。在甘蔗分子生物学研究方面,主要工作集中在甘蔗的糖分和产量相关数量性状分析、基因组学、分子标记等研究。先后主持美国国家科学基金3项,美国农业部项目3项、美国能源部项目1项,其他项目9项,作为Co-PI参与项目13项,经费累计达1683万美金。先后在《Nature》(3篇)、《Science》(2篇)、《PNAS》(2篇)、《Genome research》(6篇)、《Plant cell》、《Plant Journal》(3篇)、《Plant physiology》等国际学术期刊表文章142篇,著作2部(Springer出版),参与著作9部。

联系方式: rayming10@163.com

主要研究方向

   1.植物性染色体基因组演化 

   2.被子植物的性别决定分子机制 

   3.植物生殖系统的遗传调控,基因网络与互作 

   4.热带、亚热带植物基因组结构与功能

发表论文:

   142.Jisen Zhang,Qing Zhang,Leiting Li,Haibao Tang,Qiong Zhang,Yang Chen,JieArro,Xingtan Zhang,Aiqin Wang,Chenyong Miao,Ray Ming*.2018.Recent Polyploidization Events in Three Saccharum Founding Species.Plant Biotechnology journal.https://doi.org/10.1111/pbi.12962.

   141.Wai, C. M., Zhang, J., Jones, T. C., Nagai, C., & Ming, R. (2017). Cell wall metabolism and hexose allocation contribute to biomass accumulation in high yielding extreme segregants of a saccharum interspecific f2 population. Bmc Genomics, 18(1), 773.

  140. Wai, C.M., R. VanBuren, J. Zhang, L. Huang, W. Miao, P. P. Edger, W.C. Yim, H. Priest, B. Meyers, T.C.Mockler, J.A.C. Smith, J. Cushman, R. Ming.  2017. Temporal and spatial transcriptomic and microRNA dynamics of CAM photosynthesis in pineapple. The Plant Journal. DOI: 10.1111/tpj.13630

  139. Qin, G., C. Xu, R. Ming, H. Tang, R. Guyot, E. M. Kramer, Y. Hu. X. Yi, Y. Qi, X. Xu, Z. Gao, H. Pan, J. Jian, Y. Tian, Z. Yue, Y. Xu.  2017. The pomegranate (Punica granatum L.) genome and the genomics of punicalagin biosynthesis. The Plant Journal. DOI: 10.1111/tpj.13625

  138. Xue, X., Z. Li, M. Cai, Q. Zhang, X. Zhang, R. Ming, J. Zhang 2017. Identification and Characterization of microRNAs from Saccharum officinarum L by Deep Sequencing. Tropical Plant Biology. doi:10.1007/s12042-017-9190-y

  137. Zhang, Q., M. Cai, X. Yu, L. Wang, C. Guo, R. Ming, J. Zhang 2017. Transcriptome dynamics of Camellia sinensis in response to continuous salinity and drought stress. Tree Genetics & Genomes, 13, 78.

  136. Zeng, F., X. Lian, G. Zhang, X. Yu, C.A. Bradley, R. Ming. 2017. A comparative genome analysis of Cercospora sojina with other members of the pathogen genus Mycosphaerella on different plant hosts. Genomics DATA 350.

  135. Zeng, F., C. Wang, G. Zhang, J. Wei, C.A. Bradley, R. Ming. 2017. Draft genome sequence of Cercospora sojina isolate S9, a fungus causing frogeye leaf spot (FLS) disease of soybean. Genomics DATA 12:79-80. 

  134. Chen, Y., Q. Zhang, W. Hu, X. Zhang, L. Wang, X. Hua, Q. Yu, R. Ming, J. Zhang. 2017. Evolution and expression of the fructokinase gene family in Saccharum. BMC Genomics (in press).

  133.  Goldberg,E.E., S.P. Otto, J.C. Vamosi, I. Mayrose, N. Sabath, R. Ming, and T.-L. Ashman. 2017. Macroevolutionary synthesis of flowering plant sexual systems. Evolution. doi:10.1111/evo.13181.

  132.  Liao, Z., Q. Yu, R. Ming. 2017. Development of male specific markers and identification of sex reversal mutants in papaya. Euphytica. 213:1-12

  131.  VanBuren, R., C. M. Wai, J. Zhang, J. Han, J. Arro, Z. Lin, Z. Liao, Q. Yu, M.-L. Wang, F. Zee, R. C. Moore, D. Charlesworth, R. Ming 2016. Extremely low nucleotide diversity in the X-linked region of papaya caused by a strong selective sweep.  Gneome Biology.  17(1), 230.

  130. Ming, R., C.M. Wai, R. Guyot. 2016. Pineapple genome: a reference for monocots and CAM photosynthesis. Trends in Genetics. 32:690-696.

  129. Paull, R.E., Chen, N.J., Ming, R., Wai, C.M., Shirley, N., Schwerdt, J. and Bulone, V., 2016. Carbon Flux and Carbohydrate Gene Families in Pineapple. Tropical Plant Biology. 9:200-213.

  128. Zhang, X., Liang, P. and Ming, R., 2016. Genome-Wide Identification and Characterization of Nucleotide-Binding Site (NBS) Resistance Genes in Pineapple. Tropical Plant Biology. 9:187-199.

  127. Zheng, Y., Li, T., Xu, Z., Wai, C.M., Chen, K., Zhang, X., Wang, S., Ji, B., Ming, R. and Sunkar, R., 2016. Identification of microRNAs, phasiRNAs and Their Targets in Pineapple. Tropical Plant Biology. 9:176-186.

  126. Wai, C.M., Powell, B., Ming, R. and Min, X.J., 2016. Genome-Wide Identification and Analysis of Genes Encoding Proteolytic Enzymes in Pineapple. Tropical Plant Biology. 9:161-175.

  125. Wai, C.M., Powell, B., Ming, R. and Min, X.J., 2016. Analysis of Alternative Splicing Landscape in Pineapple (Ananas comosus). Tropical Plant Biology. 9:150-160.

  124. Singh, R., Ming, R. and Yu, Q., 2016. Comparative Analysis of GC Content Variations in Plant Genomes. Tropical Plant Biology. 9:136-149.

  123. Zhang, J., A. Sharma, Q. Yu, J. Wang, L. Li, L. Zhu, X. Zhang, Y, Chen, R. Ming. 2016 Comparative structural analysis of Bru1 region homeologs in Saccharum spontaneum and S. officinarum. BMC Genomics. 17:446.

  122. Fang, J., A. Lin,W. Qiu,H. Cai,M. Umar,R.i Chen,R. Ming. 2016. Transcriptome profiling revealed stress-induced and disease resistance genes up-regulated in PRSV resistant transgenic papaya. Frontiers in Plant Science. 7:855.

  121. Zhang, Q., Hu, W., Zhu, F., Wang, L., Yu, Q., Ming, R. and Zhang, J., 2016. Structure, phylogeny, allelic haplotypes and expression of sucrose transporter gene families in Saccharum. BMC genomics, 17:1.

  120. Fang, J., C. Miao, R. Chen, R. Ming. 2016. Genome-wide comparative analysis of microsatellites in pineapple. Tropical Plant Biology. 9:117-135.

  119. Arro, J., J.-W. Park, C. M. Wai, R. VanBuren, Y.-B. Pan, C. Nagai, J. da Silva, R. Ming. 2016. Balancing selection contributed to domestication of autopolyploid sugarcane (Saccharum officinarum L.). Euphytica (in press).

  118. Fang, J., A. Woods, R. Chen, R. Ming. 2016. Molecular basis of off-type microsatellite markers in papaya. Euphytica. doi:10.1007/s10681-015-1630

  117. Zhang, L., Ming, R., Zhang, J., Tao, A., Fang, P., & Qi, J. 2015. De novo transcriptome sequence and identification of major bast-related genes involved in cellulose biosynthesis in jute (Corchorus capsularis L.). BMC genomics, 16(1), 1062.

  116. Ming, R., R. VanBuren, C. M. Wai, H. Tang, M.C. Schatz, J. E. Bowers, E. Lyons, M.-L. Wang, J. Chen, E. Biggers, J. Zhang, L. Huang, L. Zhang, W. Miao, J. Zhang, Z. Ye, C. Miao, Z. Lin, H. Wang, H. Zhou, W. C. Yim, H. D. Priest, C. Zheng, M. Woodhouse, P. P. Edger, R. Guyot, H.-B. Guo, H. Guo, G. Zheng, R. Singh, A. Sharma, X. Min, Y. Zheng, H. Lee, J. Gurtowski, F. J. Sedlazeck, A. Harkess, M. R. McKain, Z. Liao, J. Fang, J. Liu, X. Zhang, Q. Zhang, W. Hu, Y. Qin, K. Wang, L.-Y. Chen, N. Shirley, Y.-R. Lin, L.-Y. Liu, A. G. Hernandez, C. L. Wright, V. Bulone, G. A. Tuskan, K. Heath, F. Zee, P. H. Moore, R. Sunkar, J. H. Leebens-Mack, T. Mockler, J. L. Bennetzen, M. Freeling, D. Sankoff, A. H. Paterson, X. Zhu, X. Yang,J. A. C. Smith, J. C. Cushman, R.E. Paull, Q. Yu. 2015. The pineapple genome and the evolution of CAM photosynthesis. Nature Genetics. 47:1435-1442.

  115.Sabath, N, E. Goldberg, L. Glick, M. Einhorn, T.-L. Ashman, R.Ming, S.P. Otto, J. Vamosi, I. Mayrose. 2015 Dioecy does not consistently accelerate or slow lineage diversification across multiple genera of angiosperms. New Phytologist. DOI: 10.1111/nph.13696

  114. Davis, S.C., R. Ming, D. LeBauer, and S.P. Long 2015. Toward systems-level analysis of agricultural production from crassulacean acid metabolism (CAM): scaling from cell to commercial production. New Phytologist. DOI: 10.1111/nph.13522.

  113. Yang, X., Cushman, J. C., Borland, A. M., Edwards, E. J., Wullschleger, S. D., Tuskan, G. A., Griffiths, H., Smith, J.A.C., De Paoli, H.C., Weston, D.J., Cottingham, R., Hartwell, J., Davis, S.C., Silveria, K., Ming, R., Schlaugh, K., Abraham, P., Stewart, R. J., Guo, H.-B., Albion, R., Ha, J., Lim, Sung D., Wone, B.W.M., Yim, W.C., Garcia, T., Mayer, J.A., Petereit, J., Nair, S. S., Casey, E., Hettich, R.L., Ceusters, J., Ranjan, P., Palla, K..J., Yin, H., Reyes-Garcia, C., Andrade, J. L., Freschi, L., Dever, L.V., Boxall, S.F., Walker, J., Davies, J., Bupphada, P., Kadu, N., Winter, K., Sage, R. F., Aguilar, C.N., Schmutz, J., Jenkins, J. & Holtum, J. A. (2015). A roadmap for research on crassulacean acid metabolism (CAM) to enhance. New Phytologist. doi:10.1111/nph.13393

  112. VanBuren, R., F. Zeng, C. Chen, J Zhang, C.M. Wai, J. Han, R. Aryal, A.R. Gschwend, J. Wang, J.K. Na, L. Huang, L. Zhang, W. Miao, J. Gou, J. Arro, R. Guyot, R.C. Moore, M. Wang, F. Zee, D. Charlesworth, P.H. Moore, Q. Yu, R. Ming. 2015. Origin and domestication of papaya Yh chromosome. Genome Research, doi/10.1101/gr.183905.114.

  111. Tang, H, X Zhang, C Miao, J. ZhangR. Ming, JC Schnable, PS Schnable, E Lyons, J Lu 2015. ALLMAPS: Robust scaffold ordering based on multiple maps. Genome Biology. 16:3  

  110. Ming, R. C.M. Wai 2015. Assembling allopolyploid genomes: no longer formidable. Genome Biology. 16:27

  109. Leisner, C, R. Ming, and E.A. Ainsworth. 2015. Distinct transcriptional profiles of ozone stress in soybean flowers, pods and leaves. BMC Plant Biology. 14:335.

  108. Iovene, M, Q. Yu, R. Ming, and J. Jiang. 2015. Independent sex chromosome evolution from the same pair of autosomes inCarica papaya and Vasconcellea parviflora. Genetics doi:10.1534/genetics.114.173021.

  107. Zeng, F., G. Zhang,G. Olaya, J. Wullschleger, H. Sierotzki, R. Ming, C. A. Bradley. 2014. Characterization of quinone outside inhibitor fungicide resistance in Cercospora sojinaand development of diagnostic tools for its identification. Plant Disease doi: 10.1094/PDIS-05-14-0460-RE.

  106. Zeng, F., Q. Yu, S. Hou, P. H. Moore, M. Alam, R. Ming. 2014. Features of transcriptome in trioecious papaya revealed by a large-scale sequencing of ESTs and comparative analysis of higher plants. Plant Omics. 7:450-460.

  105. F. Denoeud, L. Carretero-Paulet, A. Dereeper, G. Droc, R. Guyot, M. Pietrella, C. Zheng, A. Alberti, F. Anthony, G. Aprea, JM. Aury, P. Bento, M. Bernard, S. Bocs, C. Campa, A. Cenci, M. Combes, D. Crouzillat, C. Da Silva, L. Daddiego, F. De Bellis, S. Dussert, O. Garsmeur, T. Gayraud, V. Guignon, K. Jahn, V. Jamilloux, T. Jo&ueml;t, K. Labadie, T. Lan, J. Leclercq, M. Lepelley, T. Leroy, LT. Li, P. Librado, L. Lopez, A. Muñoz, B. Noel, A. Pallavicini, G. Perrotta, V. Poncet, D. Pot, Priyono, M. Rigoreau, M. Rouard, J. Rozas, C. Tranchant-Dubreuil, R. VanBuren, Q. Zhang, AC. Andrade, X. Argout, B. Bertrand, A. de Kochko, G. Graziosi, RJ. Henry, Jayarama, R. Ming, C. Nagai, S. Rounsley, D. Sankoff, G. Giuliano, VA. Albert, P. Wincker, P. Lashermes. 2014. The coffee genome provides insight into the convergent evolution of caffeine biosynthesis.  Science 345, 1181-1184 (2014). 

  104. The Tree of Sex Consortium. 2014. Sex determination: Why so many ways of doing it? PLoS Biology, 12(7): e100189912(7): e1001899.

  103. Zhang, Q., L. Li, R. VanBuren, Y. Liu, M. Yang, L. Xu, J. E. Bowers, C. Zhong, Y. Han, S. Li, R. Ming. 2014 Optimization of linkage mapping strategy and construction of a high-density American lotus linkage map. BMC Genomics 15: 372.

  102. Berdan, E.L., Kozak, G.M., Ming, R. Rayburn, A.L., Kiehart, R., and Fuller, R.C.  2014. Insight into genomic changes accompanying divergence: genetic linkage maps and synteny of Lucania goodei and L. parva reveal a Robertsonian fusion.  G3: Genes, Genomes, and Genetics. doi: 10.1534/g3.114.012096. 

  101. The Tree of Sex Consortium. 2014. Tree of Sex: A database of sexual systems. Scientific Data 1.

  100. Zhang, J. J. Liu, R. Ming. 2014. Genomic analysis of pineapple. Journal of Experimental Botany 65:3395-3404.

  99. Zhang, J. A. Boualem, A. Bendahmane, R. Ming. 2014. Genomics of sex determination. Current Opinion in Plant Biology 18:110-116. 

  99. Na, J.K., J. Wang,R. Ming.2014. Accumulation of interspersed and sex-specific repeats in the non-recombining region of papaya sex chromosomes. BMC Genomics. 15:335.

  97. Aryal, R., G. Jagadeeswaran, Y. Zheng, Q. Yu, R. Sunkar, R. Ming. 2014. Sex specific expression and distribution of small RNAs in papaya. BMC Genomics. 15:20.. BMC Genomics. 15:20.

  96. Han, J., J.E. Murray1, Q. Yu, P.H. Moore, R. Ming. 2014. The effects of gibberellic acid on sex expression and secondary sexual characteristics in papaya. HortScience 49:378-383.

  95. Aryal, R., R. Ming 2014. Sex determination in flowering plants: Papaya as a model system. Plant Sci. 218:56-62.

  94. Wang, J., S. Nayak, K. Koch, R. Ming. 2013.  Carbon partitioning in sugarcane (Saccharum species).   Frontiers in Plant Biotechnology. 4:201 

  93. Xin, H., J. Zhang, W. Zhu, N. Wang, P. Fang, Y. Han, R. Ming, S. Li. 2013. The effects of artificial selection on sugar metabolism and transporter genes in grape. Tree Genetics & Genomes. 9:1343-1349.

  92. Zhang, J., J. Arro, Y. Chen, R. Ming. 2013. Haplotype analysis of sucrose synthase gene family in three Saccharum species. BMC Genomics. 14:314.

  91. VanBuren, R., B. Walters, R. Ming, X.J. Min. 2013. Analysis of expressed sequence tags and alternative splicing genes in sacred lotus (Nelumbo nucifera Gaertn.). Plant Omics Journal. 6:311-317.

  90. Lum, G., R. VanBuren, R. Ming, X.J. Min. 2013. Secretome Prediction and Analysis in Sacred Lotus (Nelumbo nucifera Gaertn.).Tropical Plant Biology. 6:131-137.

  89. Zheng, Y., G. Jagadeeswaran, K. Gowdu, N. Wang,S. Li, R. Ming, R. Sunkar. 2013. Genome-Wide Analysis of MicroRNAs in Sacred Lotus, Nelumbo nucifera (Gaertn). Tropical Plant Biology. 6:117-130.

  88. Jia, R.Z., R. Ming, Y.J. Zhu. 2013. Genome-Wide Analysis of Nucleotide-Binding Site (NBS) Disease Resistance (R) Genes in Sacred Lotus (Nelumbo nucifera Gaertn.) Reveals Their Transition Role During Early Evolution of Land Plants. Tropical Plant Biology. 6:98-116.

  87..Singh,R., R. Ming, Q. Yu. 2013. Nucleotide Composition of the Nelumbo nucifera Genome. Tropical Plant Biology. 6:85-97.

  86. Ming R, VanBuren R, Liu Y, Yang M, Han Y, Li LT, Zhang Q, Kim MJ, Schatz MC, Campbell M, Li J, Bowers JE, Tang H, Lyons E, Ferguson AA, Narzisi G, Nelson DR, Blaby-Haas CE, Gschwend AR, Jiao Y, Der JP, Zeng F, Han J, Min X, Hudson KA, Singh R, Grennan AK, Karpowicz SJ, Watling JR, Ito K, Robinson SA, Hudson ME, Yu Q, Mockler TC, Carroll A, Zheng Y, Sunkar R,1 Jia R, Chen N, Arro J, Wai CM, Wafula E, Spence A, Han Y, Xu L, Zhang J, Peery R, Haus MJ, Xiong W, Walsh JA, Wu J, Wang ML, Zhu YJ, Paull RE, Britt AB, Du C, Downie SR, Schuler, MA, Michael TP, Long SP, Ort DR, Schopf JW, Gang DR, Jiang N, Yandell M, dePamphilis CW, Merchant SS, Paterson AH, Buchanan BB, Li S, J. Shen-Miller. 2013. Genome of the long-living sacred lotus (Nelumbo nucifera Gaertn.). Genome Biology. doi:10.1186/gb-2013-14-5-r41

  85. VanBuren, R., R. Ming. 2013. Dynamic transposable element accumulation in the nascent sex chromosomes of papaya. Mobile Genetic Elements (accepted).

  84. Aryal, R., X. Yang, Q. Yu, R. Sunkar, L. Li, R. Ming. 2013. Asymmetric purine-pyrimidine distribution in cellular small RNA population of papaya. BMC Genomics. 13:682

  83. Gschwend, A.R., C.M.Wai, F.Zee • A.K. Arumuganathan, R. Ming. 2013. Genome size variation among sex types in dioecious and trioecious Caricaceae species. Euphytica. DOI 10.1007/s10681-012-0815-9

  82. Zhu, L., J. Zhang, Y. Chen, H. Pan, R. Ming. 2013. Identification and genes expression analysis of  ATP-dependent phosphofructokinase family members among three Saccharum species. Functional Plant Biology. DOI:10.1071/FP12182.

  81. Wu J, Wang Z, Shi Z, Zhang S, Ming R, Zhu S, Khan MA, Tao S, Korban SS, Wang H, Chen NJ, Nishio T, Xu X, Cong L, Qi K, Huang X, Wang Y, Zhao X, Wu J, Deng C, Gou C, Zhou W, Yin H, Qin G, Sha Y, Tao Y, Chen H, Yang Y, Song Y, Zhan D, Wang J, Li L, Dai M, Gu C, Wang Y, Shi D, Wang X, Zhang H, Zeng L, Zheng D, Wang C, Chen M, Wang G, Xie L, Sovero V, Sha S, Huang W, Zhang S, Zhang M, Sun J, Xu L, Li Y, Liu X, Li Q, Shen J, Wang J, Paull RE, Bennetzen JL, Wang J, Zhang S. 2013. The genome of the pear (Pyrus bretschneideri Rehd.). Genomo Res. doi:10.1101/gr.144311.112

  80. Wai, C.M., P. H. Moore, R. E. Paull, R. Ming, Q. Yu. 2013. An integrated cytogenetic and physical map reveals unevenly distributed recombination spots along the papaya sex chromosomes. Chromosome Res. DOI 10.1007/s10577-012-9312-1. 

  79. Bradley, C. A., A. Wood, G. R. Zhang, J. E. Murray, D. V. Phillips, R. Ming. 2012. Genetic diversity of Cercospora sojina revealed by amplified fragment length polymorphism markers. Canadian Journal of Plant Pathology. 34:410–416. 

  78. Yang M, Han Y, VanBuren R, Ming R, Xu L, Han Y, Liu Y. 2012 Genetic linkage maps for Asian and American lotus constructed using novel SSP markers derived from the genome of sequenced cultivar. BMC genomics 13(1) 653

  77. Wang, J., J.-K. Na, Q. Yu, A. R. Gschwend, J. Han, F. Zeng, R. Aryal, R. VanBuren, J.E. Murray1, W. Zhang, R.N. Pérez, F.A. Feltus, C. Lemke, E. J. Tong, C. Chen, C.M. Wai, R. Singh, M.-L. Wang, X. Min, M. Alam, D. Charlesworth, P.H. Moore, J. Jiang, A. H. Paterson, R. Ming. 2012. Sequencing papaya X and Yh chromosomes revealed molecular basis of incipient sex chromosome evolution. PNAS. 109:13710-13715.

  76. Gschwend, A.R., Q. Yu, E.J. Tong, F. Zeng, J. Han, R. VanBuren, R. Aryal, D. Charlesworth, P.H. Moore, A.H. Paterson, R. Ming. 2012. Rapid divergence and expansion of the X chromosome in papaya. PNAS. 109:13716-13721.

  75. Zhang, J., C. Nagai, Q. Yu, Y.-B. Pan, T. Ayala-Silva, R. J. Schnell, J. C. Comstock, A. K. Arumuganathan, R. Ming. 2012. Genome size variation in three Saccharum species. Euphytica.  185:511–519.

  74. Ming, R., Q. Yu, P. H. Moore, R. E. Paull, N. J. Chen, M.-Li Wang, Y. J. Zhu, M. A. Schuler, J. Jiang, A. H. Paterson. 2012. Genome of papaya, a fast growing tropical fruit tree. Tree Genet. Genomics. 8:445–462.

  73. Swaminathan, K., W. B. Chae, T. Mitros, K. Varala, L. Xie, A. Barling, K Glowacka, M. Hall, S. Jezowski, R. Ming, M. Hudson, J. A. Juvik, S. P. Moose, D. S. Rokhsar. 2012. Deep sequencing identifies markers for a framework genetic map and reveals recent allotetraploidy in Miscanthus. BMC Genomics. 13:142.

  72. Gschwend, A.R., L.A. Weingartner, R.C. Moore, R. Ming. 2012. The sex-specific region of sex chromosomes in animals and plants. Chromosome Research 20:57–69.

  71. James, B., C. Chen, A. Rudolph, K. Swaminathan, J. Murray, J.-K. Na, A. Spence, B. Smith, M. Hudson, S. Moose, R. Ming. 2012 Development of microsatellite markers in autopolyploid sugarcane and comparative analysis of conserved microsatellites in sorghum and sugarcane. Mol Breeding 30:661-119.

  70. Na, J.-K., J, Wang, J. E. Murray, A. R. Gschwend, W. Zhang, Q. Yu, R. N. Pérez, F. A. Feltus, C. Chen, Z.Kubat, P. H. Moore, J. Jiang, A. H. Paterson, R. Ming 2012 Construction of physical maps for the sex-specific regions of papaya sex chromosomes. BMC Genomics. 13:176.

  69. Blas, A.L., Q. Yu, O.J. Veatch, R.E. Paull, P.H. Moore, R. Ming. 2012 Genetic mapping of quantitative trait loci controlling fruit size and shape in papaya. Mol Breeding 29:457–466

  68. VanBuren, R., J. Li, F. Zee, J. Zhu, C. Liu, A. K. Arumuganathan, R. Ming. 2011. Longli is not a Hybrid of Longan and Lychee as Revealed by Genome Size Analysis and Trichome Morphology. Tropical Plant Biology 4:228-236.

  67. Souza G. M., A. D’Hont, B. Potier, H. Berges, J. E. Ferreira, M. Vincentz, R. Ming, R. Henry, R. Casu, M.-A. Van Sluys, A. Paterson. 2011. The Sugarcane Genome Sequencing Initiative: Strategies for Sequencing a Highly Complex Genome. Tropical Plant Biology 4:145-156.

  66. Brewbaker, J. L., S. K. Kim, Y. S. So, M. Logrono, H. G. Moon, R. Ming, X. Lu, A. D. Josue. 2011. General Resistance in Maize to Souther Rust (Puccinia polysora Undeerw.).  Crop Sci. 51:1393-1409.

  65. Yu, Q., R, Guyot, A. de Kochko, A. Byers, R. Navajas-Pérez, B. J. Langston, C. Dubreuil-Tranchant, A. H. Paterson, V. Poncet, C. Nagai, R. Ming. 2011. Microcolinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species. The Plant Journal 67:305-317.

  64. Ming, R., A. Bendahmane, S. S. Renner  2011. Sex chromosomes in land plants.  Annual Review of Plant Biology 62:485-514.

  63. Gschwend, A.R., P. Moore, Q. Yu, C. Saski, C. Chen, J. Wang, J.-K. Na, R. Ming. 2011.  Construction of papaya male and female BAC libraries and application in physical mapping of the sex chromosomes. Journal of Biomedicine and Biotechnology doi:10.1155/2011/929472.

  62. Wu, X., J. Wang, J.-K. Na, Q. Yu, R. C. Moore, F. Zee, S. C. Huber, R. Ming. 2010. The Origin of the non-recombining  region of sex chromosomes in Carica and Vasconcellea. The Plant Journal 63:801-810.

  61. Zhang, W., Wai, C.M., Ming, R., Yu, Q., and  Jiang, J. 2010. Integration of genetic and cytological maps and development of a pachytene chromosome-based karyotype in papaya. Tropical Plant Biology 3:166-170.

  60. Wai, C.M., Ming. R., Moore, P.H., Paull, R.E., Yu, Q. 2010. Development of chromosome-specific cytogenetic markers and merging of broken linkage groups in papaya. Tropical Plant Biology 3:171-181. 

  59. Wang, J., B. Roe, S. Macmil, Q. Yu, J. E. Murray, H. Tang, C. Chen, F. Najar, G. Wiley, J. Bowers, M.-A. Van Sluys, D. S. Rokhsar, M. E. Hudson, S. P. Moose, A. H. Paterson, R. Ming. 2010. Microcollinearity between autopolyploid sugarcane and diploid sorghum genomes. BMC Genomics 11(1):261.

  58. Blas, A. L., R. Ming, Z. Liu, O. J. Veatch, R. E. Paull, P. H. Moore, Q. Yu. 2010. Cloning of papaya chromoplast specific lycopene β-cyclase, CpCYC-b, controlling fruit flesh color reveals conserved microsynteny and a recombination hotspot. Plant Physiology 152:2013-2022.

  57. de Kochko, A,  S. Akaffou, A. Andrade, C. Campa, D. Crouzillat, R. Guyot, P. Hamon, R. Ming, L. A. Mueller, V. Poncet, C. Tranchant-Dubreuil, S. Hamon. 2010. Advances in Coffea Genomics. Advances in Botanical Research 53:24-63. 

  56. Swaminathan, K., M. Alabady, K. Varala, E. De Paoli, I. Ho,  D. Rokhsar, A. K. Arumuganathan, R. Ming , P. J. Green, B. C. Meyers, S. P. Moose, M. E. Hudson. 2010. Genomic and small RNA sequencing of Miscanthus x giganteus shows the utility of sorghum as a reference genome sequence for Andropogoneae grasses. Genome Biology 11(2):R12.

  55. Yu, Q., E. Tong, R. L. Skelton, J. E. Bowers, M. R. Jones, J. E. Murray, S. Hou, P. Guan, R. A. Acob, M.-C. Luo, P. H. Moore, M. Alam, A. H. Paterson, R. Ming. 2009. A physical map of the papaya genome with integrated genetic map and genome sequence. BMC Genomics 10:371.

  54. Blas, A.L., Q. Yu, C. Chen, O. Veatch, P. H. Moore, R. E. Paull, R. Ming. 2009. Enrichment of a papaya high-density genetic map with AFLP markers. Genome 52:716-725.

  53. Lam, E., J. Shine Jr, J. da Silva, M. Lawton, S. Bonos, M. Calvino, H. Carrer, M. C. Silva-Filho, N. Glynn, Z. Helsel, J. Ma, E. Richard Jr., G. Souza, R. Ming. 2009. Improving Sugarcane for Biofuel: Engineering for an even better feedstock. Global Change Biology Bioenergy 1:251-255.

  52. Porter, B.W., M. Paidi, R. Ming, M. Alam, W.T. Nishijima, Y.J. Zhu. 2009. Genome-wide analysis of Carica papaya reveals a small NBS resistance gene family. Mol. Genet. Genomics 281:609-626. 

  51. Paterson, A.H. J.E. Bowers, R. Bruggmann, I. Dubchak, J. Grimwood, H. Gundlach, G. Haberer, U. Hellsten, T. Mitros, A. Poliakov, J. Schmutz, M. Spannagl, H. Tang, X. Wang, T. Wicker, A.K. Bharti, J. Chapman, F.A. Feltus, U. Gowik, I.V. Grigoriev, E. Lyons, C.A. Maher, M. Martis, A. Narechania, R.P. Otillar, B.W. Penning, A.A. Salamov, Y. Wang, L. Zhang, N.C. Carpita, M. Freeling, A.R. Gingle, C.T. Hash, B. Keller, P. Klein, S. Kresovich, M.C. McCann, R. Ming, D.G. Peterson, Mehboob-ur-Rahman, D. Ware, P. Westhoff, K. F. X. Mayer, J. Messing, D. S. Rokhsar. 2009. The Sorghum bicolor genome and the diversification of grasses. Nature 457:551-556.

  50. Lyons, E., B. Pedersen, J. Kane, M. Alam, R. Ming, H. Tang, X. Wang, J. Bowers, A. Paterson, D. Lisch, M. Freeling. 2008. Finding and Comparing Syntenic Regions among Arabidopsis and the Outgroups Papaya, Poplar, and Grape: CoGe with Rosids. Plant Physiology 148:1772-1781.

  49. Nelson, D. R., R. Ming, M. Alam, M. A. Schuler. 2008. Comparison of cytochrome P450 genes from six plant genomes. Tropical Plant Biology 1:216-235.

  48. Paull, R. E., B. Irikura, P. Wu, H. Turano, N. J. Chen, A. Blas, J. K. Fellman, A. R. Gschwend, C. M. Wai, Q. Yu, G. Presting, M. Alam, R. Ming. 2008. Fruit development, ripening and quality related genes in the papaya genome. Tropical Plant Biology 1:246-277 (Cover article).

  47. Wang, J., C. Chen, J.-K. Na, Q. Yu, S. Hou, R. E. Paull, P. H. Moore, M. Alam, R. Ming.  2008. Genome-wide comparative analysis of microsatellites in papaya. Tropical Plant Biology 1:278-292.

  46. Suzuki, J. Y., S. Tripathi, G. A. Fermín, F.-J. Jan, S. Hou, H. Saw, C. M. Ackerman, Q. Yu, M. C. Schatz, K. Y. Pitz, M. Yépes, M. M. M. Fitch, R. M. Manshardt, J. L. Slightom, S. A. Ferreira, S. L. Salzberg, M. Alam, R. Ming, P. H. Moore, D. Gonsalves. 2008. Characterization of insertion sites in Rainbow papaya, the first commercialized transgenic fruit crop. Tropical Plant Biology 1:293-309.

  45. Freeling, M., E. Lyon, B. Pedersen, M. Alam, R. Ming, D. Lisch. 2008. Many or most genes in Arabidopsis transposed after the origin of the order Brassicales. Genome Research 18:1924-1937.

  44. Zhang, W., X. Wang, Q. Yu, R. Ming, J. Jiang. 2008. DNA methylation and heterochromatinization in the male-specific region of the primitive Y chromosome of papaya. Genome Research 18:1938-1943 (Cover article).

  43. Tang, H., X. Wang, J. E. Bowers, R. Ming, M. Alam, A. H. Paterson. 2008. Unraveling ancient hexaploidy through multiply aligned angiosperm gene maps. Genome Research 18:1944-1954.

  42. Nagarajan, N., R. Navajas-Pérez, M. Pop, M. Alam, R. Ming, A. H. Paterson, S. L. Salzberg. 2008. Genome-wide analysis of repetitive elements in papaya. Tropical Plant Biology 1:191-201.

  41. Tang, H., J. E. Bowers, X. Wang, R. Ming, M. Alam, A. H. Paterson. 2008. Synteny and colinearity in plant genomes. Science 320:486-488. 

  40. Ming, R.*, S. Hou*, Y. Feng*, Q. Yu*, A. Dionne-Laporte, J. H. Saw, P. Senin, W. Wang, B. V. Ly, K. L. T. Lewis, S. L. Salzberg, L. Feng, M. R. Jones, R. L. Skelton, J. E. Murray, C. Chen, W. Qian, J. Shen, P. Du, M. Eustice, E. Tong, H. Tang, E. Lyons, R. E. Paull, T. P. Michael, K. Wall, D. Rice, H. Albert, M.-L. Wang, Y. J. Zhu, M. Schatz, N. Nagarajan, R. Acob, P. Guan, A. Blas, C. M. Wai, C. M. Ackerman, Y. Ren, C. Liu, J. Wang, J. Wang, J.-K. Na, E. V. Shakirov, B. Haas, J. Thimmapuram, D. Nelson, X. Wang, J. E. Bowers, A. R. Gschwend, A. L. Delcher, R. Singh, J. Y. Suzuki, S. Tripathi, K. Neupane, H. Wei, B. Irikura, M. Paidi, N. Jiang, W. Zhang, G. Presting, A. Windsor, R. Navajas-Pérez, M. J. Torres, F. A. Feltus, B. Porter, Y. Li, A. M. Burroughs, M.-C. Luo, L. Liu, D. A. Christopher, S. M. Mount, P. H. Moore, T. Sugimura, J. Jiang, M. A. Schuler, V. Friedman, T. Mitchell-Olds, D. E. Shippen, C. W. dePamphilis, J. D. Palmer, M. Freeling, A. H. Paterson, D. Gonsalves, L. Wang, M. Alam. 2008.  The draft genome of the transgenic tropical fruit tree papaya (Carica papaya Linnaeus). Nature 452:991-996. (*Equal contribution) (Cover article).

  39. Yu, Q., D. Steiger, E. Kramer, P.H. Moore, R. Ming. 2008. Floral MADS-Box genes in trioecious papaya: Characterization of AG and AP1 subfamily genes revealed a sex-type-specific gene. Tropical Plant Biology 1:97-107.

  38. Paterson, A.H, P. Felker, S. P. Hubbell, R. Ming. 2008.  The fruits of tropical plant genomics. Tropical Plant Biology 1:3-19.

  37. Yu, Q., R. Navajas-Pérez, E. Tong, J. Robertson, P. H. Moore, A. H. Paterson, R. Ming. 2008. Recent origin of dioecious and gynodioecious Y chromosomes in papaya. Tropical Plant Biology 1:49-57.

  36. Eustice, M., Q. Yu, C.W. Lai, S. Hou, J. Thimmapuram, L. Liu, M. Alam, P.H. Moore, G.G. Presting, R. Ming. 2008. Development and application of microsatellite markers for genomic analysis of papaya. Tree Genetics and Genomics 4:333-341.

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