Ray Ming

rayming@illinois.edu

148 ERML
Office: 217-333-1221

Mail: 1201 W. Gregory Dr. Urbana, IL. 61801
Lab Page

Ray Ming
Professor

Education

Ph.D. 1995, University of Hawaii

Teaching Interests

IB 364, Human Genome and Bioinformatics
IB 472, Plant Molecular Biology
IB 473, Plant Genomics

Evolution of primitive sex chromosomes, genome structure of papaya, sugarcane, coffee and pineapple

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.

Representative Publications

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. Genome 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 (in press)

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. (in press).

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. DOI :10.1007/s10681-016-1672-8.

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. Zhang,R. 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.