Email RayRay Ming
Professor of Plant Biology
1201 W. Gregory Drive
148 ERML, MC-051
(217) 333-1221
Education
Ph.D. 1995, University of Hawaii
Teaching
IB 472, Plant Molecular Biology
IB 473, Plant Genomics
Research
The basic biology of tropical plants is under-explored, despite their importance in agriculture and conservation of biodiversity. The lack of information about the reproductive biology of these plants is particularly significant as therein lies the determinants controlling fruit and seed production and quality. The goal of our research program is to understand the genetic and genomic basis of reproduction in selected tropical plant species. Our current research focus is on understanding the evolution of sex chromosomes in the family Caricaceae and the molecular basis of sex determination in papaya, as well as exploring the genome structure and the dynamics of genome evolution in polyploid crop plants with the long term goal of applying this knowledge and genomic resources to tropical crop improvement.
Sex chromosome evolution in papaya
Papaya (Carica papaya L.) is a major fruit crops in the tropics. It is primarily a fresh-market fruit and is also used in drinks, jams, and as a dried and crystallized fruit candy. Green fruit, leaves, and flowers can be cooked as a vegetable. Papaya fruit is rich in vitamins A and C and is a good source for the minerals K, Mg, and B. Papaya fruit is ranked number one in terms of potential health benefits among 34 common fruits based on the percentage of the United States Recommended Daily Allowance (USRDA) for vitamin A, vitamin C, potassium, folate, niacin, thiamine, riboflavin, iron, and calcium plus fiber. Papain, obtained from papaya latex, is the most widely studied and utilized member of a large family of cysteine proteases. Papain has direct medical applications for wound debridement, the removal of necrotic tissue; external treatment of hard tissues, wart and scar tissue removal, acne treatment, depilation, skin cleansing treatment, and inclusion in toothpaste. It is used for treatment of Parkinsonism and for tetanus vaccines and immunoglobulin samples for intravenous injection. Besides its nutritional and medicinal properties, papaya has a number of characteristics that contribute to its being used as an experimental model for tree crops. Papaya has small genome of 372 Mb, a short juvenile phase of 3 to 8 months, and a short generation time of 9 to 15 months.
The genetics of sex determination in trioecious papaya (plants having male, female, and hermaphrodite flowers on different individuals) have fascinated generations of geneticists and papaya breeders. It had been debated for nearly 70 years whether papaya contained sex chromosomes, in the absence of convincing cytological evidence of their existence. We conducted high density genetic mapping of the papaya genome and demonstrated strong suppression of recombination at the sex determination loci. With evidence from fine mapping, physical mapping, and survey sequencing of the sex determination locus, we concluded that sex determination in papaya is controlled by a pair of incipient sex chromosomes. Since then, we have estimated the age of these papaya sex chromosomes at about 6-7 million years, and the divergence time of the Y (controlling male) and Yh (controlling hermaphrodite) chromosomes at about 73,000 years. We have now completed the 8.1 Mb hermaphrodite specific region of the Yh chromosome (HSY) and its 3.5 Mb X counterpart. Degeneration of the Yh chromosome is evident with the loss of 46% of the genes in its X chromosome counterpart. The expansion of the HSY is caused by accumulation of retrotransposons. We are now focusing on identification of sex determination genes and engineering a true breeding hermaphrodite variety without the Yh chromosome to improve papaya production.
• Please visit the The Papaya Sex Chromosome Database: MSY region, X-chromosome
The agricultural importance, unique biological features, and the incipient sex chromosomes justified the sequencing of the papaya genome. The transgenic variety SunUp female genomic DNA was sequenced for its impact on the papaya industry and to avoid complications of genome assembly in the heterozygous sex-specific region of the sex chromosomes. SunUp was developed through transformation of Sunset, which has undergone more than 25 generations of inbreeding, an ideal homozygous genotype for a genome sequencing project. Papaya is the 5th angiosperm genome to be sequenced and the first transgenic crop to be characterized at the whole genome level.
• Download assembled papaya draft genome sequence
Genomics of biofuel feedstocks sugarcane and energy cane
Sugarcane (Saccharum spp., Poaceae) is a large, perennial, tropical or subtropical crop grown worldwide in a zone within 30o of the equator. It is vegetatively propagated from axillary buds on stem cuttings for production and sexually propagated for breeding. The first crop is harvested from 12 to 24 months after planting, and "ratoon" crops may be harvested at shorter to equal time periods. Traditionally, the main products of sugarcane were sugar, molasses, and fiber for fuel. Sugars can be easily converted to ethanol and carbon dioxide by simple bacteria through fermentation. As a C4 plant, sugarcane/energy cane has been recognized as one of the world's most efficient crops in converting solar energy into chemical energy. Sugarcane is also among the crops having the most favorable input/output ratios of 1:3 in the US and 1:8 in Brazil. Sugarcane was domesticated in New Guinea about 10,000 years ago. Sugarcane improvement started in prehistoric times with selection on natural variations and continuing to the current techniques of hybridization and genetic engineering. Enormous yield increase has been achieved in the last century by breeding for sugar content, cane yield, ratooning ability, disease and insect resistance, and abiotic stress tolerance. However, sugar content has reached a plateau and increasing cane yield has been slow in the past few decades. Recently developed genomic resources and acquired molecular tools in sugarcane have the potential to further improve sugar and biomass production. One of our goals is to explore the molecular basis of sucrose accumulation in sugarcane. We have annotated gene families in the sucrose, lignin, cellulose, and starch biosynthesis pathways, as well as families of sugar transporters. All these gene families are involved in sucrose metabolism directly or indirectly. We will use high throughput sequencing technology to genotype segregating population by sequencing, and dissect the complex traits of sugar content, fiber content, and biomass yield by sequencing transcriptomes of extreme segregants.
Like all domesticated crops, genetic diversity was reduced for those genes controlling favorable traits, and for sugarcane, high sugar content would be the most intensively selected trait. Modern breeding via interspecific hybridization further reduced the genetic diversity for high sucrose content. Another goal of our research program is to identify the domestication genes in S. officinarum accessions that have greater genetic diversity than that of commercial cultivars but reduced diversity than those of the wild species S. robustum and S. spontaneum.
Traditional sugarcane and energy cane breeding programs use the same strategy via interspecific hybridization and backcrossing to S. officinarum with sugarcane emphasizing sugar yield and energy cane on biomass yield. We are currently exploring a new paradigm utilizing transgressive segregation to maximize biomass yield of energy cane.
Publications
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 DOI 10.1007/s10577-011-9255-y
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 DOI 10.1007/s11032-011-9651-1.
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 DOI: 10.1007/s11032-011-9562-1
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.
Wai, C.M., J. Han, R. Singh, R. Aryal, M.-L. Wang, R. Ming. 2011. Analyzing the papaya genome. In: Karen Nelson (ed.): Genomics and the Developing World. Springer, Heidelberg, Germany.
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. 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.
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.
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.
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.
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.
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.
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.
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.
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).
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.
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.
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.
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).
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.
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.
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.
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).
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.
Paterson, A.H, P. Felker, S. P. Hubbell, R. Ming. 2008. The fruits of tropical plant genomics. Tropical Plant Biology 1:3-19.
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.
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.
Vega, F.E., A.W. Ebert, R. Ming. 2008. Coffee germplasm resources, genomics, and breeding. Plant Breeding Review 30:415-447.
Ackerman, C.M., Q. Yu, S. Kim, R.E. Paull, P.H. Moore, R. Ming. 2008. B-class MADS-box genes in trioecious papaya: Two TM6 paralogs, CpTM6-1 and CpTM6-2, and a PI ortholog CpPI. Planta 227:741-753.
Yu, Q., S. Hou, F.A. Feltus, M. R. Jones, J. Murray, O. Veatch, C. Lemke, J.H. Saw, R.C. Moore, J. Thimmapuram, L. Liu, P.H. Moore, M. Alam, J. Jiang, A. H. Paterson, R. Ming. 2008. Low X/Y divergence in four pairs of papaya sex-liked genes. Plant J. 53:124-132 (Cover article).
Chen, C., Q. Yu, S. Hou, Y. Li, M. Eustice, R. L. Skelton, O. Veatch, R. Herdes, L. Diebold, J. Saw, Y. Feng, L. Bynum, L. Wang, P. H. Moore, R. E. Paull, M. Alam, R. Ming. 2007. Construction of a sequence-tagged high density genetic map of papaya for comparative structural and evolutionary genomics in Brassicales. Genetics 177:2481-2491.
Yu, Q., S. Hou, R. Hobza, F.A. Feltus, X. Wang, W. Jin, R.L. Skelton, A. Blas, C. Lemke, J. H. Saw, P. H. Moore, M. Alam, J. Jiang, A. H. Paterson, B. Vyskot, R. Ming. 2007. Chromosomal location and gene paucity of the male specific region on papaya Y chromosome. Mol. Genet. Genomics 278:177-185.
Ming, R., Q. Yu, P.H. Moore. 2007. Sex determination in papaya. Seminars in Cell and Developmental Biology 18:401-408.
Ming, R., P.H. Moore. 2007. Genomics of sex chromosomes. Current Opinion in Plant Biology. 10:123-130.
Ming, R., J. Wang, P.H. Moore, A.H. Paterson. 2007. Sex chromosomes in flowering plants. American Journal of Botany. 94:141-150 (Cover article).