Ray Ming


Professor of Plant Biology
1201 W. Gregory Drive

148 ERML, MC-051
(217) 333-1221



Ph.D. 1995, University of Hawaii




IB 364, Human Genome and Bioinformatics

IB 472, Plant Molecular Biology

IB 473, Plant Genomics




Sex expression in papaya (Carica papaya L.; Family Caricaceae) is controlled by loci in the male specific region of the Y chromosome (MSY) and slightly modified hermaphrodite specific region of the Yh chromosome (HSY). Unlike other ancient sex chromosomes, the MSY of papaya is about 7 million years old and restricted to a small region about 8 Mb. Due to the enforced heterozygosity provided by YY lethality, there is no true breeding hermaphrodite variety, causing the problem of planting multiple seedlings per hill that delays fruit production.  Identification and characterization of the sex determination and YY lethality genes will lead to the first sex change operation in plants that have direct benefit on papaya improvement. Our long-term goal is to understand the molecular basis of sex determination and the evolutionary mechanisms governing the formation and divergence of sex chromosomes. Complete sequencing of the HSY, MSY, and their X counterpart coupled with analysis of sex reversal mutants revealed candidate genes for sex determination.  We are actively working on identification and validation of the sex determination genes controlling stamen and carpel development and designing strategies to engineer true breeding hermaphrodite papaya varieties. This work will enhance our understanding of reproductive biology in flowering plants and demonstrate the application of basic research on crop improvement.


 • Please visit the The Papaya Sex Chromosome Database: MSY region, X-chromosome

 • Download assembled papaya draft genome sequence


Energy cane and sugarcane cultivars are generally derived from interspecific hybridization between high sugar content and biomass yield Saccharum officinarum and wild Saccharum species, primarily S. spontaneum. Commercial energy cane and sugarcane cultivars are subsequently developed through additional rounds of backcrossing to S. officinarum or hybrids to recover the high biomass yield and high sugar content while retaining biotic and abiotic stress resistance provided by S. spontaneum. This scheme has been practiced for a century due to the need to recover high sugar content.  We propose a new paradigm for energy cane breeding to utilize the transgressive segregation in true F2 populations from interspecific crosses, because sugar content is not a limiting factor for selecting high biomass energy cane cultivars.  Our initial field trial yielded clones with 3 folds increase of biomass yield compared toits high yielding  S. officinarum parent.  Such extraordinary yield performance is due to pyramiding genes/alleles for biomass yield in autopolyploid genome, an advantage of 8 potential alleles for each gene in autooctoploid. Our long term goal is to establish a new paradigm to accelerate energy cane breeding programs and maximize the biomass yield for biofuel production. Understanding the mechanisms of the extraordinary transgressive segregation in autopolyploid sugarcane will accelerate the application of this new paradigm in energy cane breeding programs, and may have implication in crop improvement programs of other autopopyploid crops.


Recent Publications


Han, J., J.E. Murray, Q. Yu, P.H. Moore, R. Ming. 2014. The effects of gibberellic acid on sex expression and secondary sexual characteristics in papaya. HortScience (in press).


Aryal, R., R. Ming 2014. Sex determination in flowering plants: Papaya as a model system. Plant Sci. (in press).


Wang, J., S. Nayak, K. Koch, R. Ming. 2013.  Carbon partitioning in sugarcane (Saccharum species).   Frontiers in Plant Biotechnology. doi: 10.3389/fpls.2013.00201


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.


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.


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.


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.


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


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


VanBuren, R., R. Ming. 2013. Dynamic transposable element accumulation in the nascent sex chromosomes of papaya. Mobile Genetic Elements 3:1-5.


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


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


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.


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. 23: 396-408.


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.


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.


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


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.


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.


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.


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.


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.


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.


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 and application of microsatellite markers in polyploid Sugarcane. Mol Breeding 30:661-119.


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.


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


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.


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.


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.


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.


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


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.


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.


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.


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.


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.


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.


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. 


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.