Flower Development and Sex Chromosome Evolution in Papaya: Unlike most animal species that produce unisexual individuals, the majority of flowering plants produce flowers that are ‘perfect’ and contain both ‘male’ and ‘female’ organs. Less than 10% of plant species produce flowers, which are unisexual. Papaya is a polygamous plant species producing both dioecious and perfect flowers and provides an opportunity for studying flower development in dioecious and hermaphrodite plant species.

The sex determination system in papaya is particularly intriguing, not only because it has three sex types within the species, also because it shows frequent sex reversal caused by environmental factors. Recent studies showed that sex determination in papaya is controlled by a pair of primitive sex chromosomes. We are cloning the sex determination genes in papaya and performing comparative genomics analysis to understand the origin and evolution of sex chromosomes in Caricaceae.

Genomic Dissection of the complex polyploidy sugarcane genome for energy cane improvement: As a C4 plant, sugarcane (Saccharum spp. Poaceae) 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. However, the large genome size, high ploidy level, interspecific hybridization and aneuploidy make sugarcane one of the most complex genomes and have long hampered genome research in sugarcane. Modern sugarcane cultivars are derived from interspecific hybridization between S. officinarum and S. spontaneum with 80-90% of the genome from S. officinarum and 10-20% of the genome from S. spontaneum. We have constructed bacterial artificial chromosome (BAC) libraries of S. officinarum LA Purple (2n=8x=80) and S. spontaneum haploid clone AP85-441 (2n=4x=32). These two BAC libraries have been used to screen for the major genes involved in Sucrose, Lignin, and Cellulose biosynthesis pathways. We are sequencing selected BAC clones to study allelic variations of major genes affecting biomass yield in sugar cane aiming to understand the complex mechanisms leading to the superior productivity of sugarcane.

Construction of a high density genetic map of pineapple for genome sequencing and marker-assisted selection: Pineapple is the most important economic species among the crassulacean acid metabolism (CAM) plant species and could become the best representative of this under-explored node of the angiosperms. CAM plant species are particularly adapted to arid environments and exhibit a unique water-conserving photosynthetic pathway. Approximately 6% of all vascular plant species in 33 families and 328 genera engage in Crassulacean acid metabolism (CAM), making it the second most common form of photosynthesis. Our long-term goal is to develop pineapple as a model system for CAM plant species to identify, characterize, and clone agronomically important genes, and to elucidate the genome structure and organization of this under-explored node of the angiosperms.

Wang, J.*, J.-K. Na*, Q.Yu*, A.R. Gschwend*, J. Han, F. Zeng, R. Aryal, R. VanBuren, J.E. Murray, W. Zhang, R. Navajas-Pérez, F.A. Feltus, C. Lemke, E.J. Tong, C. Chen, C.M. Wai, R. Singh, M.-L. Wang, X.J. Min, M. Alam, D. Charlesworth, P.H. Moore, J. Jiang, A.H. Paterson, R. Ming. 2012. Sequencing X and Yh chromosomes in papaya revealed the molecular basis of incipient sex chromosome evolution. PNAS (*equal contribution) (in press)

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 (* corresponding authors) (in press)

Na, J.-K., J. Wang, J.E. Murray, A.R. Gschwend, W. Zhang, Q.Yu, R. Navajas-Pérez, A.F. 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

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 DOI: 10.1007/s10681-012-0664-6

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. Molecular Breeding 29: 457-466

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. Micro-collinearity and genome evolution in the vicinity of an ethylene receptor gene of cultivated diploid and allotetraploid coffee species (Coffea). Plant Journal 67: 305-317. (* corresponding author)

Gschwend, A.R., Q. Yu, P.H. Moore, C. Saski, C. Chen, J. Wamg, J.-K. Na, R. Ming. 2011. Construction of papaya male and female BAC libraries and application in physical mapping of sex chromosomes. J. Biomed. Biotechnol. 2011: 929472

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

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.

Wai, C.M., R. Ming, P.H. Moore, R.E. Paull, Q. Yu. 2010. Development of chromosome-specific cytogenetic markers and merging of linkage fragments 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: 261.

Zhang,W., Wai, C.M., Ming, R., Yu, Q., 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.

Damaj, M.D., P.D. Beremand, M.T. Buenrostro-Nava, J. Ivy, S.P. Kumpatla, J. Jifon, G. Beyene, Q. Yu, T.L. Thomas, T.E. Mirkov. 2010. Isolating promoters of multigene family members from polyploidy sugarcane genome by PCR-based walking in BAC DNA. Genome 53: 840-847.

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.

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-Pérez, M.J. Torres, F. Alex 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 story).

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.

Zhang W., X. Wang, Q. Yu, R. Ming, and 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 story).

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.

Yu, Q., S. Hou, F.A. Feltus, M.R. Jones, J.E. 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 linked genes. Plant J. 53:124-132. (cover story)

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 Analyses of Microsatellites in Papaya. Tropical Plant Biology 1: 278-292.

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 paleoAP3 paralogs, CpTM6-1 and CpTM6-2, and a PI ortholog CpPI. Planta 227:741-753. (*equal contribution).

Suzuki J.Y., S. Tripathi, G.A. Fermín, F.-J. Jan, S. Hou, J.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.

Eustice, M., Q. Yu, W. C. 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 Genomes 4:333-341.

Yu, Q., D. Steiger, E.M. 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.