Ray Ming
Associate Professor of Plant Biology
1201 W. Gregory Drive
148 ERML, MC-051
(217) 333-1221
Education
Ph.D. 1995, University of Hawaii
Teaching
IB 204, Genetics
IB 473, Plant Genomics
Research
Sex chromosomes in mammals evolved from a pair of ancestral autosome shared with birds about 310 million years ago (mya). The human Y chromosome is genetically eroded and morphologically distinctive, about one third the size of the X chromosome. Flowering plants appeared about 130-200 million years ago and plant sex chromosomes evolved more recently. The sex chromosomes of Silene latifolia was young with an estimated origin about 10 20 mya. Yet 90% of the Y chromosome in Silene latifolia is degenerated and suppressed for recombination. The recently discovered primitive sex chromosomes in papaya, medaka fish, and stickleback fish are homomorphic and not morphologically distinctive. The ages of the sex chromosomes in these three species were estimated to be 2-3, 10, and 10 million years old for papaya, medaka fish, and stickleback fish, respectively. Papaya has a small male specific region (MSY), about 10-15% of the Y chromosome. The MSY shows suppression of recombination and signs of degeneration. Sequencing and characterization of the recently evolved papaya sex chromosomes will offer insights towards understanding the mechanisms and selection forces leading to the rise of the sex chromosomes. Dissecting the sex determination process in papaya will have direct applications in papaya production in addition to revealing the master switch for gender differentiation.
• Please visit the The Papaya Sex Chromosome Database
The papaya MSY and the corresponding X-specific region are being sequenced and characterized. To estimate the antiquity of the non-recombining region, the extent of divergence of X and Y gene pairs along the region will be calculated, giving special attention to candidate genes for sex determination. Comparing the X and Y DNA sequences and their surroundings will reveal types and extent of chromosomal rearrangements and the role of transposable elements in the degeneration of MSY.
We also study the genome structure and organization of papaya, sugarcane, coffee, and pineapple. The papaya genome has a haploid DNA content of 372 Mb, which is only 86% of the rice genome. We have integrated the genetic and physical maps of the papaya genome and are currently participating in analyzing the papaya whole genome shotgun sequences.
• Download assembled papaya draft genome sequence
We are also sequencing selected bacterial artificial chromosomes (BACs) from sugarcane and Arabica coffee, and mapping quantitative trait loci (QTL) controlling source-sink traits in Arabica coffee and sugarcane.
Publications
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. Agbayani, 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-Perez, 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. Topical Plant Biology doi:10.1007/s12042-007-9000
Paterson, A.H, P. Felker, S. P. Hubbell, R. Ming. 2008. The fruits of tropical plant genomics. Topical Plant Biology 1:3-19.
Yu, Q., R. Navajas-Perez, E. Tong, J. Robertson, P. H. Moore, A. H. Paterson, R. Ming. 2008. Recent origin of dioecious and gynodioecious Y chromosomes in papaya. Topical 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).