Chifumi Nagai, Ph.D.
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Academic Qualifications
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Current Research
My major research emphasis is to develop new cultivars of tropical plants including coffee, cacao and energy cane for Hawaii and other areas. Biotechnology approaches, such as MAS and genetic transformation, are applied to conventional breeding to accelerate the program. Most of my projects involve international, multidisciplinary research collaboration.
Coffee:
1. Develop new cultivars of coffee with improved beverage quality, and nematode and coffee leaf rust resistance for Hawaii and other areas. The selected promising hybrids are cloned by tissue culture and/or somatic embryos.
2. Identify QTL markers for MAS for arabica coffee. F1 and F2 populations of unique Arabica parents were developed at HARC, and genomic and phenotypic data are collected from segregating populations.
3. Study of lowcaffeine varieties of coffee from Madagascar with good beverage quality in collaboration with FOFIFA and UCC Japan.
Cacao:
1. Select high yielding cacao genotypes for growers in Hawaii. Cacao trees grown in Hawaii were fingerprinted, and we found that major groups of cacao are grown in Hawaii. High yielding trees were identified from phenotypic data collected over multiple years.
2. Identify QTL markers associated with agronomically important traits.
Energycane/ sugarcane:
1. Develop new sugarcane varieties for high biomass using wild species of Saccharum and related species. At HARC's Maunawili Station, we produce progeny of sugarcane for high sugar and biomass yield.
2. Develop molecular markers for high biomass using interspecific mapping populations developed at HARC. Individual plants with extreme phenotype for sugar and biomass yield are identified in interspecific F2 population. We work with Dr. Ray Ming, University of Illinois, for genomics of these individuals.
Selected Publications
Yu, QY, R. Guyot, A.de Kochko, A. Byers, R. Navajas-Perez, B. Langston, C. Dubreuil-Tranchant, A. 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 (Coffea). The Plant Journal doi:10.1111/j.1365-313X.2011.04590.x
Aoki, S., B. S. Sipes, C. Astorga, C. Nagai. 2011. Resistance of Semi-wild Coffea arabica L. from Ethiopia to a root knot nematode, Meloidogyne konaensis. Journal of Nematology (accepted)
R. Y. M. Cabos, B. S. Sipes, C. Nagai, M. Serracin and D. P. Schmitt. 2010. Evaluation of coffee genotypes for root knot-nematode resistance. NEMATROPICA 40(2): 191-202
Wang, M.-L., Uruu, G., Xiong, L., He, X., Nagai, C., Cheah, K. T., Hu, J. S., Nan, G.-L., Sipes, B. S., Atkinson, H. J., Moore, P. M., Rohrbach, K. G., Paull, R. E. (2009) Production of transgenic pineapple plants via adventitious bud regeneration. In Vitro Cellular and Developmental Biology-Plant 45(12):112-121
Nagai,C. J.J. Rakotomalala , R. Katahira, Y. Li , K. Yamagata , H. Ashihara . 2008. Production of new low-caffeine hybrid coffee and biochemical mechanism of low caffeine accumulation. Euphytica 164:133-142
Koshiro, Y., M.C. Jackson, R. Katahira, M.L. Wang, C. Nagai and H. Ashihara. 2007. Biosynthesis of chlorogenic acids in growing and ripening of Coffea Arabica and Coffea canephora plants. Z. Naturforsch. 62c:731-742
Cabos, R., B. Sipes, D. Schmitt, H. Atkinson, C. Nagai. 2006. Transformation of Coffea arabica for Root-knot Nematode Resistance Using Cysteine and Serine Proteinase Inhibitors Proceedings of 21th ASIC International Conference on Coffee Science, 11-15 September, Montpellier, France ( CD-Ram version)
Nagai, C., M. R. Jones, A. E. Byers, D. J. Adamski, R. Ming. 2006. Development and Characterization of a True F2 population for Genetic and QTL Mapping in Arabica. Proceedings of 21th ASIC International Conference on Coffee Science, 11-15 September, Montpellier, France (CD-Ram version)
Koshiro, Y., X.Q.Z. Zheng, M.L. Wang, C. Nagai and H. Ashihara. 2006. Changes in content and biosynthetic activity of caffeine and trigonelline during growth and ripening of Coffea arabica and Coffea canephora fruits. Plant Science. 171. 242-250.
Stalmach, A. W. Mullen, C. Nagai, A. Crozier 2006. On-line HPLC analysis of the antioxidant activity of phenolic compounds in brewed, paper filtered coffee. Brazilian Journal of Plant Physiology (for a special edition on coffee). 18(1):253-262.
Peterson, S.W., F.E. Vega, F. Posada and C. Nagai. 2005. Penicillium coffeae, a new endophytic species isolated from a coffee plant and its phylogenetic relationship to P. fellutanum,P. thiersii and P. brocae based on parsimony analysis of multilocus DNA sequences. Mycologia 97(3) 659-666.
Ashihara, H., X.Q. Zheng and C. Nagai. 2004. Pyridine nucleotide cycle and trigonelline synthesis in developing leaves and fruits of Coffea Arabica. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Rakotomalala, J.J.R., T. Kumamoto, T. Aburatani, A. Rabeniafara, C. Nagai, K. Sanbongi, Y. Kawashima and Y. Rabenantoandro. 2004. Caffeine content distribution among mascarocoffea species in Madagascar. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Jackson, M., S. Steiman, C. Nagai, C. Cavaletto. 2004. Green coffee chemistry and its possible application for group discrimination and correlation of cupping quality. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Nagai, C., R.V. Osgood, C. Cavaletto, H.C. Bittenbender, K. Weaver, J. Clayton, M. Jackson, R. Loero and R. Ming. 2004. Breeding and selection of coffee cultivars for Hawaii with high cupping quality using Mokka hybrids. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Schnell, R.J., C.T. Olano, J.S. Brown, A.W. Meerow, C. Cervantes-Martinez, C. Nagai, and J.C. Motamayor. 2005. Retrospective determination of the parental population of superior cacao (Theobroma cacao L ) seedlings and association of microsatellite alleles with productivity. J. Amer. Soc. Hort. Sci 130(2) 181-190. 2005.
Zheng, X.Q., C. Nagai and H. Ashihara. 2004. Pyridine nucleotide cycle and trigonelline (N-methylnicotinic acid) synthesis in developing leaves and fruits of Coffea arabica. Physiologia Plantarum 122: 404-411.
Zheng X.Q., Y. Koyama, C. Nagai, H. Ashihara. 2004. Biosynthesis, accumulation and degradation of the obromine in developing Theobroma cacao fruits. J. Plant Physiol.161. 363-369.
Pearl, H.M, C. Nagai, P.H. Moore, D.L. Steiger, R.V. Osgood, R. Ming. 2004. Construction of a genetic map for arabica coffee. Thoer. Appl. Genet. 108:829-835.
Kato, C.Y., C. Nagai, P.H. Moore, F. Zee, M.S. Kim, D.L. Steiger, R. Ming. 2004. Intra-specific DNA polymorphism in pineapple (Ananas comosus L.) assessed by AFLP markers. Genetic Resources and Crop Evolution. Genetic Resources and Crop Evolution 51:815-825.
Steiger, D.L., C. Nagai, P.H. Moore, P.H. Morden, R.V. Osgood, and R. Ming. 2002. AFLP analysis of genetic diversity within and among coffea arabica cultivars. Thoer. Appl. Genet. 108:209-215.
Nagai, C., W.G. Sun, H.C. Bittenbender, F.C. Meinzer, C.G. Cavaletto, M. Jackson, R. Ming and R.V. Osgood. Coffee Breeding and Selection in Hawaii. 2001. Proceedings, 19th ASIC International Conference on Coffee Science, Trieste, Italy.
Moore, P.H., H. Albert, M. Fitch, C. Nagai, G-L.Nan, J. Zhu, D. Christopher, S. Ferreira, J. Hu, R. Mannshaldt, R. Paull, K. Rohrbach, B. Sipes and D. Gonsalves. 1997. Alternatives to pesticide use for controlling pests of tropical crops. USDA/ARS Workshop. Reducing Pesticide Risk: Approaches to Sustainable Pest Management. December 2-4 1997, Riverside, CA. p. 20.
Nagai C. and R. Ibraham. 1997. Clonal propagation of A. koa. Koa: Decade of Growth. proceedings of the Symposium. Hawaii Forest Industry Association 1996 Annual Symposium November 18, 19. Honolulu, Hawaii,1996. pp. 30-32.
Tang,W.D. S.S. Sun, C. Nagai and P.H. Moore. 1996. Regulation of expression of glucuronidase in transgenic sugarcane by promoters of RUBISCO small sub unit genes. Sugarcane. Research towards Efficient and Sustainable Production. Willson JR, Hogarth DM, Cambell JA and Garside AL (eds.) CSIRO Division of Tropical Crops and Pastures, Brisbane. pp.117-119.
Sun, S.S., A. Maretzki, C. Nagai, K. Houchens, and D. Bidney. 1993. Development of a transformation system for sugarcane. Sugar Cane 5:1-7.
Brewbaker, J.L. and C. Nagai. 1992. Breeding of tropical sweetcorn. Hort.Sci.27(6):645.
Schnell, R.J. and C. Nagai. 1992. Variation in agronomic characters among maternal half-sib families of Saccharum officinarum and elite Hawaiian commercial clones. Trop. Agric. 69:203-206.
Nagai, C., B.S. Ahoowalia, and T.L. Tew. 1991. Somaclonal variants from an intergeneric hybrid: Saccharum spp. hybrid x Erianthus arundinaceum. Euphytica 53:193-199.
Moore, P.H., C. Nagai, and M. Fitch. 1989. Production and evaluation of sugarcane haploids. International Society of Sugarcane Technologists XX Congress, Proceedings. Sao Paulo, Brazil, October 19-20. 2:599-607.
Tew, T.L., K.K. Wu, R.J. Schnell and C. Nagai. 1988. Registration of 'H74-1715' sugarcane. Crop Science 28:197.
Nagai, C., B.S. Ahloowalia, D.J Heinz, and T.L. Tew. 1986. Colchicine-induced aneuploids from cell culture of sugarcane. Euphytica 35(3):1029-1038.
Brewbaker, J.L., C. Nagai and E.H. Liu. 1985. Genetic polymorphisms of 13 maize peroxidases. J. Heredity 76:159-167.
Nagai, C. and J.L. Brewbaker. 1983. Chromosomal location of peroxidase isozyme: Px3. Maize Genetics Coop. News Letter. 57:49- 51.
Liu, E.H., C. Nagai and J.L. Brewbaker. 1981. Peroxidase isozymes in maize: characterization of locus Px7. Maize Genetics Coop. News Letter. 55:43-44.
Reports Fingerprinting of Cacao Germplasm in Hawaii
by C. Nagai, R. Heinig, C. T. Olano, J. C. Motamayor, and R. J. Schnell (September 2009)
Selection of Potentially Elite Individual Coffee Trees on Coffee Farms on Five Hawaiian Islands
by Chifumi Nagai, Weiguo Sun, Robert V. Osgood, Frederick Meinzer and H. C. Bittenbender (June 1998)
Vegetative Propagation of Coffea arabica L. Using Softwood Cuttings
by Weiguo Sun, Chifumi Nagai and Robert V. Osgood (June 1998)
Selection of Potentially Elite Individual Coffee Trees in Five Coffee Growing Areas in Hawaii
by C. Nagai, W. G. Sun, R. V. Osgood, F. C. Meinzer and H. C. Bittenbender (May 1998)
My major research emphasis is to develop new cultivars of tropical plants including coffee, cacao and energy cane for Hawaii and other areas. Biotechnology approaches, such as MAS and genetic transformation, are applied to conventional breeding to accelerate the program. Most of my projects involve international, multidisciplinary research collaboration.
Coffee:
1. Develop new cultivars of coffee with improved beverage quality, and nematode and coffee leaf rust resistance for Hawaii and other areas. The selected promising hybrids are cloned by tissue culture and/or somatic embryos.
2. Identify QTL markers for MAS for arabica coffee. F1 and F2 populations of unique Arabica parents were developed at HARC, and genomic and phenotypic data are collected from segregating populations.
3. Study of lowcaffeine varieties of coffee from Madagascar with good beverage quality in collaboration with FOFIFA and UCC Japan.
Cacao:
1. Select high yielding cacao genotypes for growers in Hawaii. Cacao trees grown in Hawaii were fingerprinted, and we found that major groups of cacao are grown in Hawaii. High yielding trees were identified from phenotypic data collected over multiple years.
2. Identify QTL markers associated with agronomically important traits.
Energycane/ sugarcane:
1. Develop new sugarcane varieties for high biomass using wild species of Saccharum and related species. At HARC's Maunawili Station, we produce progeny of sugarcane for high sugar and biomass yield.
2. Develop molecular markers for high biomass using interspecific mapping populations developed at HARC. Individual plants with extreme phenotype for sugar and biomass yield are identified in interspecific F2 population. We work with Dr. Ray Ming, University of Illinois, for genomics of these individuals.
Selected Publications
Yu, QY, R. Guyot, A.de Kochko, A. Byers, R. Navajas-Perez, B. Langston, C. Dubreuil-Tranchant, A. 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 (Coffea). The Plant Journal doi:10.1111/j.1365-313X.2011.04590.x
Aoki, S., B. S. Sipes, C. Astorga, C. Nagai. 2011. Resistance of Semi-wild Coffea arabica L. from Ethiopia to a root knot nematode, Meloidogyne konaensis. Journal of Nematology (accepted)
R. Y. M. Cabos, B. S. Sipes, C. Nagai, M. Serracin and D. P. Schmitt. 2010. Evaluation of coffee genotypes for root knot-nematode resistance. NEMATROPICA 40(2): 191-202
Wang, M.-L., Uruu, G., Xiong, L., He, X., Nagai, C., Cheah, K. T., Hu, J. S., Nan, G.-L., Sipes, B. S., Atkinson, H. J., Moore, P. M., Rohrbach, K. G., Paull, R. E. (2009) Production of transgenic pineapple plants via adventitious bud regeneration. In Vitro Cellular and Developmental Biology-Plant 45(12):112-121
Nagai,C. J.J. Rakotomalala , R. Katahira, Y. Li , K. Yamagata , H. Ashihara . 2008. Production of new low-caffeine hybrid coffee and biochemical mechanism of low caffeine accumulation. Euphytica 164:133-142
Koshiro, Y., M.C. Jackson, R. Katahira, M.L. Wang, C. Nagai and H. Ashihara. 2007. Biosynthesis of chlorogenic acids in growing and ripening of Coffea Arabica and Coffea canephora plants. Z. Naturforsch. 62c:731-742
Cabos, R., B. Sipes, D. Schmitt, H. Atkinson, C. Nagai. 2006. Transformation of Coffea arabica for Root-knot Nematode Resistance Using Cysteine and Serine Proteinase Inhibitors Proceedings of 21th ASIC International Conference on Coffee Science, 11-15 September, Montpellier, France ( CD-Ram version)
Nagai, C., M. R. Jones, A. E. Byers, D. J. Adamski, R. Ming. 2006. Development and Characterization of a True F2 population for Genetic and QTL Mapping in Arabica. Proceedings of 21th ASIC International Conference on Coffee Science, 11-15 September, Montpellier, France (CD-Ram version)
Koshiro, Y., X.Q.Z. Zheng, M.L. Wang, C. Nagai and H. Ashihara. 2006. Changes in content and biosynthetic activity of caffeine and trigonelline during growth and ripening of Coffea arabica and Coffea canephora fruits. Plant Science. 171. 242-250.
Stalmach, A. W. Mullen, C. Nagai, A. Crozier 2006. On-line HPLC analysis of the antioxidant activity of phenolic compounds in brewed, paper filtered coffee. Brazilian Journal of Plant Physiology (for a special edition on coffee). 18(1):253-262.
Peterson, S.W., F.E. Vega, F. Posada and C. Nagai. 2005. Penicillium coffeae, a new endophytic species isolated from a coffee plant and its phylogenetic relationship to P. fellutanum,P. thiersii and P. brocae based on parsimony analysis of multilocus DNA sequences. Mycologia 97(3) 659-666.
Ashihara, H., X.Q. Zheng and C. Nagai. 2004. Pyridine nucleotide cycle and trigonelline synthesis in developing leaves and fruits of Coffea Arabica. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Rakotomalala, J.J.R., T. Kumamoto, T. Aburatani, A. Rabeniafara, C. Nagai, K. Sanbongi, Y. Kawashima and Y. Rabenantoandro. 2004. Caffeine content distribution among mascarocoffea species in Madagascar. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Jackson, M., S. Steiman, C. Nagai, C. Cavaletto. 2004. Green coffee chemistry and its possible application for group discrimination and correlation of cupping quality. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Nagai, C., R.V. Osgood, C. Cavaletto, H.C. Bittenbender, K. Weaver, J. Clayton, M. Jackson, R. Loero and R. Ming. 2004. Breeding and selection of coffee cultivars for Hawaii with high cupping quality using Mokka hybrids. Proceedings (CD-RAM). 20th ASIC International Conference on Coffee Science, Bangalore, India.
Schnell, R.J., C.T. Olano, J.S. Brown, A.W. Meerow, C. Cervantes-Martinez, C. Nagai, and J.C. Motamayor. 2005. Retrospective determination of the parental population of superior cacao (Theobroma cacao L ) seedlings and association of microsatellite alleles with productivity. J. Amer. Soc. Hort. Sci 130(2) 181-190. 2005.
Zheng, X.Q., C. Nagai and H. Ashihara. 2004. Pyridine nucleotide cycle and trigonelline (N-methylnicotinic acid) synthesis in developing leaves and fruits of Coffea arabica. Physiologia Plantarum 122: 404-411.
Zheng X.Q., Y. Koyama, C. Nagai, H. Ashihara. 2004. Biosynthesis, accumulation and degradation of the obromine in developing Theobroma cacao fruits. J. Plant Physiol.161. 363-369.
Pearl, H.M, C. Nagai, P.H. Moore, D.L. Steiger, R.V. Osgood, R. Ming. 2004. Construction of a genetic map for arabica coffee. Thoer. Appl. Genet. 108:829-835.
Kato, C.Y., C. Nagai, P.H. Moore, F. Zee, M.S. Kim, D.L. Steiger, R. Ming. 2004. Intra-specific DNA polymorphism in pineapple (Ananas comosus L.) assessed by AFLP markers. Genetic Resources and Crop Evolution. Genetic Resources and Crop Evolution 51:815-825.
Steiger, D.L., C. Nagai, P.H. Moore, P.H. Morden, R.V. Osgood, and R. Ming. 2002. AFLP analysis of genetic diversity within and among coffea arabica cultivars. Thoer. Appl. Genet. 108:209-215.
Nagai, C., W.G. Sun, H.C. Bittenbender, F.C. Meinzer, C.G. Cavaletto, M. Jackson, R. Ming and R.V. Osgood. Coffee Breeding and Selection in Hawaii. 2001. Proceedings, 19th ASIC International Conference on Coffee Science, Trieste, Italy.
Moore, P.H., H. Albert, M. Fitch, C. Nagai, G-L.Nan, J. Zhu, D. Christopher, S. Ferreira, J. Hu, R. Mannshaldt, R. Paull, K. Rohrbach, B. Sipes and D. Gonsalves. 1997. Alternatives to pesticide use for controlling pests of tropical crops. USDA/ARS Workshop. Reducing Pesticide Risk: Approaches to Sustainable Pest Management. December 2-4 1997, Riverside, CA. p. 20.
Nagai C. and R. Ibraham. 1997. Clonal propagation of A. koa. Koa: Decade of Growth. proceedings of the Symposium. Hawaii Forest Industry Association 1996 Annual Symposium November 18, 19. Honolulu, Hawaii,1996. pp. 30-32.
Tang,W.D. S.S. Sun, C. Nagai and P.H. Moore. 1996. Regulation of expression of glucuronidase in transgenic sugarcane by promoters of RUBISCO small sub unit genes. Sugarcane. Research towards Efficient and Sustainable Production. Willson JR, Hogarth DM, Cambell JA and Garside AL (eds.) CSIRO Division of Tropical Crops and Pastures, Brisbane. pp.117-119.
Sun, S.S., A. Maretzki, C. Nagai, K. Houchens, and D. Bidney. 1993. Development of a transformation system for sugarcane. Sugar Cane 5:1-7.
Brewbaker, J.L. and C. Nagai. 1992. Breeding of tropical sweetcorn. Hort.Sci.27(6):645.
Schnell, R.J. and C. Nagai. 1992. Variation in agronomic characters among maternal half-sib families of Saccharum officinarum and elite Hawaiian commercial clones. Trop. Agric. 69:203-206.
Nagai, C., B.S. Ahoowalia, and T.L. Tew. 1991. Somaclonal variants from an intergeneric hybrid: Saccharum spp. hybrid x Erianthus arundinaceum. Euphytica 53:193-199.
Moore, P.H., C. Nagai, and M. Fitch. 1989. Production and evaluation of sugarcane haploids. International Society of Sugarcane Technologists XX Congress, Proceedings. Sao Paulo, Brazil, October 19-20. 2:599-607.
Tew, T.L., K.K. Wu, R.J. Schnell and C. Nagai. 1988. Registration of 'H74-1715' sugarcane. Crop Science 28:197.
Nagai, C., B.S. Ahloowalia, D.J Heinz, and T.L. Tew. 1986. Colchicine-induced aneuploids from cell culture of sugarcane. Euphytica 35(3):1029-1038.
Brewbaker, J.L., C. Nagai and E.H. Liu. 1985. Genetic polymorphisms of 13 maize peroxidases. J. Heredity 76:159-167.
Nagai, C. and J.L. Brewbaker. 1983. Chromosomal location of peroxidase isozyme: Px3. Maize Genetics Coop. News Letter. 57:49- 51.
Liu, E.H., C. Nagai and J.L. Brewbaker. 1981. Peroxidase isozymes in maize: characterization of locus Px7. Maize Genetics Coop. News Letter. 55:43-44.
Reports Fingerprinting of Cacao Germplasm in Hawaii
by C. Nagai, R. Heinig, C. T. Olano, J. C. Motamayor, and R. J. Schnell (September 2009)
Selection of Potentially Elite Individual Coffee Trees on Coffee Farms on Five Hawaiian Islands
by Chifumi Nagai, Weiguo Sun, Robert V. Osgood, Frederick Meinzer and H. C. Bittenbender (June 1998)
Vegetative Propagation of Coffea arabica L. Using Softwood Cuttings
by Weiguo Sun, Chifumi Nagai and Robert V. Osgood (June 1998)
Selection of Potentially Elite Individual Coffee Trees in Five Coffee Growing Areas in Hawaii
by C. Nagai, W. G. Sun, R. V. Osgood, F. C. Meinzer and H. C. Bittenbender (May 1998)