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                    U.S. DEPARTMENT OF AGRICULTURE
 Sustainable Perennial Crops Laboratory: Beltsville, MD
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ARS Home Northeast Area Beltsville, Maryland (BARC) Beltsville Agricultural Research Center Sustainable Perennial Crops Laboratory People & Locations







Lyndel  Meinhardt
                        Sustainable Perennial Crops Laboratory

                        




                        
                        Research Leader
                        Phone: (301) 504-1995
                        
                        
                        Fax: (301) 504-1998(Employee information on this page comes from the REE Directory. Please contact your front office staff to update the REE Directory.)
                            ProjectsDevelopment of Pathogen- and Plant-Based Genetic Tools and Disease Mitigation Methods for Tropical Perennial Crops
                                                    In-House Appropriated
                                                                    (D)Accession Number: 441868Genotypic Characterization of Genetic Resources for Cacao, Coffee, and Other Tropical Perennial Crops Economically Important to the United States
                                                    In-House Appropriated
                                                                    (D)Accession Number: 444058Identification and Conservation of Fine Flavored Cacao Varieties (Theobroma cacao)
                                                    Non-Funded Cooperative Agreement
                                                                    (N)Accession Number: 436556Molecular Characterization of CATIE International Coffee Collections
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 436780Molecular Characterization of Coffee Germplasm Collection in the Centre National de Recherche Agronomique (CNRA), Cóte d’Ivoire
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 436789Development and Implementation of GBS and SNP Tools for Tropical Plant Genotyping
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 442123Chitin Interactions in Plant Disease Mitigation in Theobroma Cacao and Analysis of Erythroxylum Specie Gene Function
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 442130Evaluate Wild Cacao Germplasm for Tolerance to Biotic and Abiotic Stresses and Develop Genomes and Transcriptomes of Cacao Pathogen Species
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 442174Genomics of Asimini Triloba, the American Pawpaw
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 443004Tropical Plant Genome Sequencing
                                                    Non-Assistance Cooperative Agreement
                                                                    (S)Accession Number: 443785**Publications**
                                                (Clicking on the reprint icon
                                                    Reprint Icon
                                                    will take you to the publication reprint.)Transcriptome profiling identifies gene expression patterns and promoter motifs associated with post-penetration resistance to Phytophthora palmivora in pods of Theobroma cacao genotypes
                                                        

- (Peer Reviewed Journal)Baruah, I., Shao, J.Y., Ali, S., Schmidt, M.E., Meinhardt, L.W., Bailey, B.A., Cohen, S.P. 2024. Transcriptome profiling identifies gene expression patterns and promoter motifs associated with post-penetration resistance to Phytophthora palmivora in pods of Theobroma cacao genotypes. Scientific Reports. 14:4175(2024). https://doi.org/10.1038/s41598-024-54355-8.Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa)
                                                        

- (Peer Reviewed Journal)Park, S., Shi, A., Meinhardt, L.W., Mou, B. 2024. Genome-wide characterization and evolutionary analysis of the AP2/ERF gene family in lettuce (Lactuca sativa). Scientific Reports. 13:21990. https://doi.org/10.1038/s41598-023-49245-4.Genotyping of Jujube (Ziziphus spp.) Germplasm in
New Mexico and Southwestern Texas
                                                        

- (Peer Reviewed Journal)Sapkota, D., Zhang, D., Park, S., Meinhardt, L.W., Yao, S. 2023. Genotyping of Jujube (Ziziphus spp.) Germplasm in New Mexico and Southwestern Texas. Plants. 12:2405. https://doi.org/10.3390/plants12132405.A draft genome resource for Marasmius tenuissimus, an emerging causal agent of thread blight disease in cacao
                                                        

- (Peer Reviewed Journal)Leung, J., Cohen, S.P., Baruah, I., Ali, S., Shao, J.Y., Bukari, Y., Amoako-Attah, I., Meinhardt, L.W., Bailey, B.A. 2023. A draft genome resource for Marasmius tenuissimus, an emerging causal agent of thread blight disease in cacao. PhytoFrontiers. https://doi.org/10.1094/PHYTOFR-03-23-0027-A.Selecting progenies of coffee variety “Mundo Novo” with potential for the specialty coffee market
                                                        

- (Peer Reviewed Journal)Ferraz, G., Lopez, M.E., Zhang, D., Rodrigues-Carvalho, G., Meinhardt, L.W., Chalfun-Junior, A. 2023. Selecting progenies of coffee variety “Mundo Novo” with potential for the specialty coffee market. Beverage Plant Research. 3(1):1-11. https://doi.org/10.48130/BPR-2023-0001.Accurate cultivar authentication of fresh and dry jujube fruits using DNA fingerprints based on a nanofluidic SNP genotyping system
                                                        

- (Peer Reviewed Journal)Song, L., Meinhardt, L.W., Li, Z., Wan, Z., Zhang, D. 2022. Accurate cultivar authentication of fresh and dry jujube fruits using DNA fingerprints based on a nanofluidic SNP genotyping system. Journal of Agricultural and Food Chemistry. 8(9):792. https://doi.org/10.3390/horticulturae8090792.USA Tea: A synopsis of ongoing tea research and USA production issues
                                                        

- (Review Article)D'Auria, J.C., Cohen, S.P., Leung, J., Glockzin, K., Glockzin, K., Gervay-Hague, J., Zhang, D., Meinhardt, L.W. 2022. USA Tea: A synopsis of ongoing tea research and USA production issues. Frontiers in Plant Science. 13:934651. https://doi.org/10.3389/fpls.2022.934651.Genome assemblies of Erythroxylum. coca var. ipadu and Erythroxylum novogranatense var. truxillense
                                                        

- (Peer Reviewed Journal)Pirro, S., White, D., Bailey, B.A., Meinhardt, L.W. 2022. Genome assemblies of Erythroxylum. coca var. ipadu and Erythroxylum novogranatense var. truxillense. F1000Research. 11:457. https://doi.org/10.12688/f1000research.108549.1.Relationship between genetic distance based on single nucleotide polymorphism markers and hybrid performance in C. canephora
                                                        

- (Peer Reviewed Journal)Akpertey, A., Padi, F., Meinhardt, L.W., Zhang, D. 2022. Relationship between genetic distance based on single nucleotide polymorphism markers and hybrid performance in C. canephora. Plant Breeding. https://doi.org/10.1111/pbr.13005.The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes
                                                        

- (Peer Reviewed Journal)Zheng, J., Meinhardt, L.W., Goenaga, R.J., Matsumoto Brower, T.K., Zhang, D., Yin, Y. 2022. The chromosome-level rambutan genome reveals a significant role of segmental duplication in the expansion of resistance genes. Horticulture Research. 9:uhac014. https://doi.org/10.1093/hr/uhac014.Assessing genetic integrity of Chinese jujube cultivars using Single Nucleotide Polymorphism (SNP) markers
                                                        

- (Peer Reviewed Journal)Song, L., Zhang, H., Li, Z., Meinhardt, L.W., Zhang, D. 2021. Assessing genetic integrity of Chinese jujube cultivars using Single Nucleotide Polymorphism (SNP) markers. Agronomy. 11:2303. https://doi.org/10.3390/agronomy11112303.Impacts of diverse natural products on honey bee viral loads and health
                                                        

- (Peer Reviewed Journal)Boncristiani, D.L., Tauber, J.P., Palmer-Young, E., Cao, L., Chen, Y., Grubbs, K.F., Lopez, J.A., Meinhardt, L.W., Nguyen, V., Oh, S., Peterson, R.J., Zamora, H., Evans, J.D. 2021. Impacts of diverse natural products on honey bee viral loads and health. Journal of Insect Science. 11:10732. https://doi.org/10.3390/app112210732.Mitochondrial genomics of six cacao pathogens from the basidiomycete family Marasmiaceae
                                                        

- (Peer Reviewed Journal)Ali, S., Amoako-Attah, I., Shao, J.Y., Meinhardt, L.W., Bailey, B.A. 2021. Mitochondrial genomics of six cacao pathogens from the basidiomycete family Marasmiaceae. Frontiers in Microbiology. 12:752094. https://doi.org/10.3389/fmicb.2021.752094.Selecting a core set of nuclear SNP markers for molecular characterization of Arabica coffee (Coffea arabica L.) genetic resources
                                                        

- (Peer Reviewed Journal)Zhang, D., Vega, F.E., Solano, W., Fuyuan, S., Infante, F., Meinhardt, L.W. 2021. Selecting a core set of nuclear SNP markers for molecular characterization of Arabica coffee (Coffea arabica L.) genetic resources. Conservation Genetics Resources. https://doi.org/10.1007/s12686-021-01201-y.The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin iosynthetic genes
                                                        

- (Peer Reviewed Journal)Zheng, J., Meinhardt, L.W., Goenaga, R.J., Zhang, D., Yin, Y. 2021. The chromosome-level genome of dragon fruit reveals whole-genome duplication and chromosomal co-localization of betacyanin iosynthetic genes. Horticulture Research. https://doi.org/10.1038/s41438-021-00501-6.Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay
                                                        

- (Peer Reviewed Journal)Akpertey, A., Padi, F., Meinhardt, L.W., Zhang, D. 2021. Effectiveness of Single Nucleotide Polymorphism Markers in Genotyping Germplasm Collections of Coffea canephora Using KASP Assay. Frontiers in Plant Science. https://doi.org/10.3389/fpls.2020.612593.Elevated temperature and drought stress significantly affect fruit quality and activity of anthocyanin-related enzymes in jujube (Ziziphus jujuba mill. cv. ‘Lingwuchangzao’)
                                                        

- (Peer Reviewed Journal)Jiang, W., Li, N., Zhang, D., Meinhardt, L.W., Cao, B., Li, Y., Song, L. 2020. Elevated temperature and drought stress significantly affect fruit quality and activity of anthocyanin-related enzymes in jujube (Ziziphus jujuba mill. cv. ‘Lingwuchangzao’). PLoS ONE. https://doi.org/10.1371/journal.pone.0241491.t003.Molecular characterization of a cacao germplasm collection in Yunnan, China using Single Nucleotide Polymorphism (SNP) markers
                                                        

- (Peer Reviewed Journal)Wang, B., Motilal, L., Meinhardt, L.W., Mischke, B.S., Zhang, D. 2020. Molecular characterization of a cacao germplasm collection in Yunnan, China using Single Nucleotide Polymorphism (SNP) markers. Tropical Plant Biology. https://doi.org/10.1007/s12042-020-09267-y.Genome and transcriptome analysis of the latent pathogen lasiodiplodia Theobromae, an emerging threat to cacao industry

- (Peer Reviewed Journal)Ali, S., Shao, J.Y., Adi, A., Balidion, J., Strem, M., Puig, A.S., Meinhardt, L.W., Bailey, B.A. 2019. Genome and transcriptome analysis of the latent pathogen lasiodiplodia Theobromae, an emerging threat to cacao industry. Genes, Genomes, and Genomics. 63:37–52.Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback (VSD) in Theobroma cacao

- (Peer Reviewed Journal)Ali, S., Asman, A., Shao, J.Y., Firmansyah, A., Susilo, A., Rosamana, A., Mcmahon, P., Junaid, M., Guest, D., Kheng, T., Meinhardt, L.W., Bailey, B.A. 2019. Draft genome sequence of fastidious pathogen Ceratobasidium theobromae, which causes vascular-streak dieback (VSD) in Theobroma cacao. Fungal Biology and Biotechnology. 6:14.Genetic improvement of Chinese jujube for disease resistances: current status, knowledge gaps and research needs
                                                        

- (Peer Reviewed Journal)Song, L., Cao, B., Meinhardt, L.W., Bailey, B.A., Zhang, D. 2019. Genetic improvement of Chinese jujube for disease resistances: current status, knowledge gaps and research needs. Crop Breeding, Genetics and Genomics. 2019;1:e190015. https://doi.org/10.20900/cbgg20190015.Accurate differentiation of green beans of Arabica and Robusta coffee using nanofluidic array of single nucleotide polymorphism (SNP) markers

- (Peer Reviewed Journal)Zhang, D., Vega, F.E., Huawei, T., Johnson, E., Solano, W., Meinhardt, L.W. 2020. Accurate differentiation of green beans of Arabica and Robusta coffee using nanofluidic array of single nucleotide polymorphism (SNP) markers. Journal of AOAC International. 103:315–324.HPLC Quantification and MS/NMR confirmation of Javamide-I/-II in Arabica and Robusta coffee beans from different regions for finding better bean sources for Javamide-I/-II
                                                        

- (Peer Reviewed Journal)Park, J.B., Wang, T.T., Zhang, D., Vega, F.E., Meinhardt, L.W. 2019. HPLC Quantification and MS/NMR confirmation of Javamide-I/-II in Arabica and Robusta coffee beans from different regions for finding better bean sources for Javamide-I/-II. Austin Chromatography. 6(1):1051. https://doi.org/10.26420/austinchromatogrl.2019.1051.Genetic identity and origin of ‘Piura Porcelana’ – a fine-flavored traditional variety of cacao (Theobroma cacao) from the Peruvian Amazon

- (Peer Reviewed Journal)Arevalo, E., Zhou, L., Meinhardt, L.W., Motilal, L., Mischke, B.S., Zhang, D. 2019. Genetic identity and origin of ‘Piura Porcelana’ – a fine-flavored traditional variety of cacao (Theobroma cacao) from the Peruvian Amazon. Tree Genetics and Genomes. 15:11.Assessing hidden parentage and genetic integrity of the “United Fruit Clones” of cacao (Theobroma cacao) from Costa Rica using SNP markers

- (Peer Reviewed Journal)Mata, A., Arciniegas, A.L., Phillips, W.M., Meinhardt, L.W., Mischke, B.S., Zhang, D. 2018. Assessing hidden parentage and genetic integrity of the “United Fruit Clones” of cacao (Theobroma cacao) from Costa Rica using SNP markers. Breeding Science. 68:545-553.Candidate SSR tags for fruit and seed traits of Theobroma cacao L. in the International Cocoa Genebank Trinidad

- (Proceedings)Motilal, L., Zhang, D., Mischke, B.S., Meinhardt, L.W., Umaharan, P. 2018. Candidate SSR tags for fruit and seed traits of Theobroma cacao L. in the International Cocoa Genebank Trinidad. Proceedings of the International Symposium on Cocoa Research. p.13-17.Understanding the genetic structure and parentage of the clonal series of cacao UF, CC, PMCT and ARF preserved in the international cacao collection at CATIE (IC3)

- (Proceedings)Arciniegas-Leal, A., Mata-Quiros, A., Phillips-Mora, W., Meinhardt, L.W., Zhang, D. 2018. Understanding the genetic structure and parentage of the clonal series of cacao UF, CC, PMCT and ARF preserved in the international cacao collection at CATIE (IC3). Proceedings of the International Symposium on Cocoa Research. November 13-17, 2017, Lima, Peru. 26:1-11.Genetic Diversity and Genetic Structure of Wild Cacao Collected in the Oriente using Single Nucleotide Polymorphisms

- (Proceedings)Motilal, L., Zhang, D., Mischke, B.S., Meinhardt, L.W., Umaharan, P. 2018. Genetic Diversity and Genetic Structure of Wild Cacao Collected in the Oriente using Single Nucleotide Polymorphisms. Proceedings of the International Symposium on Cocoa Research. November 13-17, 2018, Lima, Peru. 12:1-8.Molecular characterization of farmer selections of cacao (Theobroma cacao) from Jamaica using Single Nucleotide Polymorphism (SNP) markers
                                                        

- (Peer Reviewed Journal)Lindo, A.A., Robinson, D.E., Tennant, P.F., Meinhardt, L.W., Zhang, D. 2018. Molecular characterization of farmer selections of cacao (Theobroma cacao) from Jamaica using Single Nucleotide Polymorphism (SNP) markers. Tropical Plant Biology. https://doi.org/10.1007/s12042-018-9203-5.Morphological variants of Moniliophthora roreri on artificial media and the biotroph/necrotroph shift

- (Peer Reviewed Journal)Bailey, B.A., Ali, S., Strem, M.D., Meinhardt, L.W. 2018. Morphological variants of Moniliophthora roreri on artificial media and the biotroph/necrotroph shift. Fungal Biology. 122(7):701-716.Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms

- (Peer Reviewed Journal)Ali, S., Shao, J.Y., Strem, M.D., Amoako-Attah, I., Melnick, R., Yaw Akrofi, A., Coulibaly, K., Ismael Kebe, K., Guiltinan, Begoude, B., Ten Hoopen, G., Shen, D., Lary, D.J., Kronmiller, B., Tyler, B., Meinhardt, L.W., Bailey, B.A. 2017. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod rot, underwent increases in genome sizes and gene numbers by different mechanisms. Genome Biology and Evolution. 9:536-557.Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod induce similar reactions when infecting pods of a susceptible cacao genotype

- (Peer Reviewed Journal)Ali, S., Shao, J.Y., Strem, M.D., Lary, D.J., Meinhardt, L.W., Bailey, B.A. 2017. Phytophthora megakarya and P. palmivora, closely related causal agents of cacao black pod induce similar reactions when infecting pods of a susceptible cacao genotype. Frontiers in Plant Science. 8:169.Association mapping of fruit, seed and disease resistance traits in Theobroma cacao L

- (Peer Reviewed Journal)Motilal, L., Zhang, D., Mischke, B.S., Meinhardt, L.W., Boccara, M., Lanaud, C., Umaharan, P. 2016. Association mapping of fruit, seed and disease resistance traits in Theobroma cacao L. Planta. 244(6):1265-1276.Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm

- (Peer Reviewed Journal)Zhou, L., Vega, F.E., Tan, H., Ramirez Lluch, A., Meinhardt, L.W., Fang, W., Mischke, B.S., Irish, B.M., Zhang, D. 2016. Developing Single Nucleotide Polymorphism markers for the identification of Coffee germplasm. Tropical Plant Biology. 9:82-95.Moniliophthora roreri Genome and Transcriptome

- (Book / Chapter)Meinhardt, L.W., Bailey, B.A. 2016. Moniliophthora roreri Genome and Transcriptome. In: Bailey, B.A., Meinhardt, L.W., editors. Cacao diseases: A history of old enemies and new encounters, Switzerland: Springer. p. 97-135.Cacao diseases: A history of old enemies and new encounters

- (Book / Chapter)Bailey, B.A., Meinhardt, L.W. 2016. Cacao diseases: A history of old enemies and new encounters. Switzerland: Springer. 633 pages.Phytophthora megakarya, a causal agent of black pod rot in Africa

- (Book / Chapter)Bailey, B.A., Ali, S., Akrofi, A., Meinhardt, L.W. 2016. Phytophthora megakarya, a causal agent of black pod rot in Africa. In: Bailey, B.A., Meinhardt, L.W., editors. Cacao diseases: A history of old enemies and new encounters. Switzerland: Springer. p. 267-303.PCR-based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa

- (Peer Reviewed Journal)Ali, S., Amoako-Attah, I., Bailey, R., Strem, M.D., Schmidt, M.E., Yaw Akrofi, A., Kolawole, O.O., Surendra, S.J., Goss, E., Didier Begoude, B.A., Martijin Ten, H., Phillips, W., Tyler, B., Meinhardt, L.W., Bailey, B.A. 2016. PCR-based identification of cacao black pod causal agents and identification of biological factors possibly contributing to Phytophthora megakarya's field dominance in West Africa. Plant Pathology. doi: 10.1111/ppa.12496.Developing Single Nucleotide Polymorphism (SNP) markers for the identification of pineapple (Ananas comosus) germplasm

- (Peer Reviewed Journal)Zhou, L., Matsumoto Brower, T.K., Tan, H., Meinhardt, L.W., Mischke, B.S., Wang, B., Zhang, D. 2015. Developing Single Nucleotide Polymorphism (SNP) markers for the identification of pineapple (Ananas comosus) germplasm. Horticulture Research. 2:15056.Genetic identity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by molecular markers

- (Peer Reviewed Journal)Dinarti, D., Susilo, A.W., Meinhardt, L.W., Ji, K., Motilal, L., Mischke, B.S., Zhang, D. 2015. Genetic identity and parentage in farmer selections of cacao from Southern Sulawesi, Indonesia revealed by molecular markers. Journal of Breeding Science. 65:438-446.Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality

- (Peer Reviewed Journal)Ali, S., Shao, J.Y., Strem, M.D., Phillips-Mora, W., Zhang, D., Meinhardt, L.W., Bailey, B.A. 2015. Combination of RNAseq and SNP nanofluidic array reveals the center of genetic diversity of cacao pathogen Moniliophthora roreri in the upper Magdalena Valley of Colombia and its clonality. Frontiers in Microbiology. doi: 10.3389/fmicb.2015.00850.Identification of the varietal origin of loose leaf tea based on analysis of a single leaf by SNP nanofluidic array

- (Peer Reviewed Journal)Fang, W., Meinhardt, L.W., Tan, H., Zhou, L., Wang, X., Mischke, B.S., Zhang, D. 2016. Identification of the varietal origin of loose leaf tea based on analysis of a single leaf by SNP nanofluidic array. Journal of Agricultural and Food Chemistry. doi: 10.1016/j.cj.2016.02.001.Developing Single Nucleotide Polymorphism (SNP) markers from transcriptome sequences for the identification of longan (Dimocarpus longan) germplasm

- (Peer Reviewed Journal)Wang, B., Tan, H., Fang, W., Meinhardt, L.W., Mischke, B.S., Matsumoto Brower, T.K., Zhang, D. 2015. Developing Single Nucleotide Polymorphism (SNP) markers from transcriptome sequences for the identification of longan (Dimocarpus longan) germplasm. Horticulture Research. DOI:10.1038/hortres.2014.65.Cacao Flavor through Genetics – Anatomy of Fine Flavor

- (Popular Publication)Sequine, E., Meinhardt, L.W. 2014. Cacao Flavor through Genetics – Anatomy of Fine Flavor. The Manufacturing Confectioner. 94:25-30.Genetic identity, ancestry and parentage in farmer selections of cacao from Aceh, Indonesia revealed by single nucleotide polymorphism (SNP) markers

- (Peer Reviewed Journal)Lukman, Zhang, D., Susilo, A., Dinarti, D., Bailey, B.A., Mischke, B.S., Meinhardt, L.W. 2014. Genetic identity, ancestry and parentage in farmer selections of cacao from Aceh, Indonesia revealed by single nucleotide polymorphism (SNP) markers. Tropical Plant Biology. 7:133-143.Varietal identification of tea (Camellia sinensis [L.] Kuntze) using nanofluidic array of Single Nucleotide Polymorphism (SNP) markers

- (Peer Reviewed Journal)Fang, W., Meinhardt, L.W., Tan, H., Zhou, L., Mischke, B.S., Zhang, D. 2014. Varietal identification of tea (Camellia sinensis [L.] Kuntze) using nanofluidic array of Single Nucleotide Polymorphism (SNP) markers. Horticulture Research. DOI:10.1038/hortres.2014.35.Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers

- (Peer Reviewed Journal)Ji, K., Takrama, J., Meinhardt, L.W., Mischke, B.S., Opoku, S., Padi, F., Zhang, D. 2014. Verification of genetic identity of introduced cacao germplasm in Ghana using single nucleotide polymorphism (SNP) markers. African Journal of Biotechnology. 13(21):2127-2136.Exogenous abscisic acid significantly affects proteome in tea plant (Camellia sinensis) exposed to drought stress

- (Peer Reviewed Journal)Zhou, L., Xu, H., Mischke, B.S., Meinhardt, L.W., Zhang, D., Fang, W. 2014. Exogenous abscisic acid significantly affects proteome in tea plant (Camellia sinensis) exposed to drought stress. Horticulture Research. doi:10.1038/hortres.2014.29.Differential gene expression by Moniliophthora roreri while overcoming cacao tolerance in the field

- (Peer Reviewed Journal)Bailey, B.A., Melnick, R.L., Strem, M.D., Crozier, J., Shao, J.Y., Sicher, Jr., R.C., Ali, S.S., Zhang, D., Philips-Mora, W., Meinhardt, L.W. 2014. Differential gene expression by Moniliophthora roreri while overcoming cacao tolerance in the field. Molecular Plant Pathology. DOI:10.1111/mpp.12134.Successful pod infections by Moniliophthora roreri result in differential Theobroma cacao gene expression depending on the clone’s level of tolerance

- (Peer Reviewed Journal)Ali, S., Melnick, R., Strem, M.D., Crozier, J., Shao, J.Y., Sicher  Jr, R.C., Zhang, D., Philips-Mora, W., Meinhardt, L.W., Bailey, B.A. 2014. Successful pod infections by Moniliophthora roreri result in differential Theobroma cacao gene expression depending on the clone’s level of tolerance. Molecular Plant Pathology. DOI:10.1111/mpp.12126.Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases

- (Peer Reviewed Journal)Meinhardt, L.W., Thomazella, D.P., Teixeira, P.J., Costa, G.G., Carazzolle, M., Schuster, S., Carlson, J.E., Guiltinan, M.J., Mieczkowski, P., Crow, J., Farmer, A., Ramaraj, T., Crosier, J., Davis, R.E., Shao, J.Y., Pereira, G.A., Bailey, B.A. 2014. Genome and secretome analysis of the hemibiotrophic fungal pathogen, Moniliophthora roreri, which causes frosty pod rot disease of cacao: mechanisms of the biotrophic and necrotrophic phases. Biomed Central (BMC) Genomics. 15:164.Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers

- (Peer Reviewed Journal)Sitther, V., Zhang, D., Harris, D., Zee, F.T., Yadav, A., Meinhardt, L.W., Dhekney, S. 2014. Genetic characterization of guava (psidium guajava l.) Germplasm in the United States using microsatellite markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-014-0078-5.Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authenticity and traceability

- (Peer Reviewed Journal)Fang, W., Meinhardt, L.W., Mischke, B.S., Bellato, C., Motilal, L., Zhang, D. 2013. Accurate determination of genetic identity for a single cacao bean, using molecular markers with a nanofluidic system, ensures cocoa authenticity and traceability. Journal of Agricultural and Food Chemistry. 62:481-487.Microsatellite-aided detection of genetic redundancy improves management of the International Cocoa Genebank, Trinidad

- (Peer Reviewed Journal)Motilal, L., Zhang, D., Mischke, B.S., Meinhardt, L.W., Umaharan, P. 2013. Microsatellite-aided detection of genetic redundancy improves management of the International Cocoa Genebank, Trinidad. Tree Genetics and Genomes. 9:1395-1411.Physiological traits and metabolites of cacao seedlings influenced by potassium in growth medium
                                                        

- (Peer Reviewed Journal)Li, Y., Elson, M.K., Zhang, D., Sicher, Jr., R.C., Hang, L., Meinhardt, L.W., Baligar, V.C. 2013. Physiological traits and metabolites of cacao seedlings influenced by potassium in growth medium. American Journal of Plant Sciences. 4:1074-1080.Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome

- (Peer Reviewed Journal)Pereira, G.A., Ambrosio, A.B., Nascimento, L.C., Oliveira, B.V., Teixeira, P.J., Tiburcio, R.A., Thomazella, D.P., Leme, A.F., Carazzolle, M.F., Vidal, R.O., Mieczkowski, P., Meinhardt, L.W., Garcia, O. 2013. Global analyses of Ceratocystis cacaofunesta mitochondria: from genome to proteome. Biomed Central (BMC) Genomics. 2013(14):91.Dynamic changes in pod and fungal physiology associated with the shift from biotrophy to necrotrophy during the infection of Theobroma cacao by Moniliophthora roreri

- (Peer Reviewed Journal)Bailey, B.A., Crozier, J., Strem, M.D., Melnick, R.L., Zhang, D., Maximova, S., Guiltinan, M., Meinhardt, L.W. 2013. Dynamic changes in pod and fungal physiology associated with the shift from biotrophy to necrotrophy during the infection of Theobroma cacao by Moniliophthora roreri. Physiological and Molecular Plant Pathology. 81:84-96.A potential role for an extracellular methanol oxidase secreted by Moniliophthora perniciosa in Witches' broom disease in cacao

- (Peer Reviewed Journal)Oliveira, B., Teixeira, G., Reis, O., Barau, J., Teixeira, P.J., Rio, M.S., Domingues, R.R., Meinhardt, L.W., Leme, A.F., Rincones, J., Pereira, G.A. 2012. A potential role for an extracellular methanol oxidase secreted by Moniliophthora perniciosa in Witches' broom disease in cacao. Fungal Genetics and Biology. 49:922-932.Elucidating genetic identities of cacao germplam in an international cacao collection using molecular markers

- (Peer Reviewed Journal)Motilal, L., Zhang, D., Umaharanl, P., Boccara, M., Mischke, B.S., Sankar, A., Meinhardt, L.W. 2012. Elucidating genetic identities of cacao germplam in an international cacao collection using molecular markers. Plant Genetic Resources: Characterization and Utilization. 10(3):232-241.Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by Single Nucleotide Polymorphism (SNP) markers

- (Peer Reviewed Journal)Ji, K., Zhang, D., Motilal, L., Boccara, M., Lachenaud, P., Meinhardt, L.W. 2012. Genetic diversity and parentage in farmer varieties of cacao (Theobroma cacao L.) from Honduras and Nicaragua as revealed by Single Nucleotide Polymorphism (SNP) markers. Genetic Resources and Crop Evolution. DOI: 10.1007/s10722-012-9847-1.Theobroma

- (Book / Chapter)Zhang, D., Figueira, A., Motilal, L., Lachenaud, P., Meinhardt, L.W. 2011. Theobroma. In: Kole, C., editor. Wild Crop Relatives: Genomic and Breeding Resources, Plantation and Ornamental Crops. New York, NY: Springer-Verlag Berlin Heidelberg. p. 277-296.The hemibiotrophic cacao pathogen Moniliophthora perniciosa depends on a mitochondrial alternative oxidase for biotrophic development

- (Peer Reviewed Journal)Thomazella, D.P., Teixeira, P., De Oliveira, H., Saviani, E., Rincones, J., Toni, I., Osvaldo, R., Garcia, O., Meinhardt, L.W., Salgado, I., Pereira, G.A. 2012. The hemibiotrophic cacao pathogen Moniliophthora perniciosa depends on a mitochondrial alternative oxidase for biotrophic development. New Phytologist. 194(4):1025-1034.The Mitochondrial Genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao

- (Peer Reviewed Journal)Costa, G.G., Cabrera, O., Tiburico, R.A., Medrano, F., Carazzolle, M., Thomazella, D., Schuster, S., Carlson, J.E., Guiltinan, M.J., Bailey, B.A., Mieckowski, P., Pereira, G.A., Meinhardt, L.W. 2012. The Mitochondrial Genome of Moniliophthora roreri, the frosty pod rot pathogen of cacao. Fungal Biology. 116(5):551-562.Dissecting genetic structure in farmer selections of Theobroma cacao in the Peruvian Amazon:  implications for on-farm conservation and rehabilitation

- (Peer Reviewed Journal)Zhang, D., Gardini, E.A., Baligar, V.C., Bailey, B.A., Meinhardt, L.W. 2011. Dissecting genetic structure in farmer selections of Theobroma cacao in the Peruvian Amazon:  implications for on-farm conservation and rehabilitation. Tropical Plant Biology. 4:106-116.Assessing genetic diversity in java fine-flavor cocoa (theobroma cacao l.) Germplasm by simple sequence repeat (ssr) markers

- (Peer Reviewed Journal)Susilo, A., Zhang, D., Motalal, L., Meinhardt, L.W. 2011. Assessing genetic diversity in java fine-flavor cocoa (theobroma cacao l.) Germplasm by simple sequence repeat (ssr) markers. Tropical Agriculture (Trinidad). 55:84-92.Genetic diversity and spatial structure in cacao (Theobroma cacao L.) germplasm from Bolivia

- (Peer Reviewed Journal)Zhang, D., July, W., Johnson, E., Somarriba, E., Philips-Mora, W., Astorga, C., Mischke, B.S., Meinhardt, L.W. 2011. Genetic diversity and spatial structure in cacao (Theobroma cacao L.) germplasm from Bolivia. Genetic Resources and Crop Evolution. DOI: dx.doi.org/10.1007/s10722-011-9680-y.Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: Accession and plot homogeneity information for germplasm management

- (Peer Reviewed Journal)Motilal, L., Zhang, D., Pathmanathan, U., Mischke, B.S., Pinney, S.M., Meinhardt, L.W. 2011. Microsatellite fingerprinting in the International Cocoa Genebank, Trinidad: Accession and plot homogeneity information for germplasm management. Plant Genetic Resources. 9:430-438.AFLP Phylogeny of 36 Erythroxylum species- genetic relationships among Erythroxylum species inferred by AFLP analysis

- (Peer Reviewed Journal)Emche, S.D., Zhang, D., Islam, M.B., Bailey, B.A., Meinhardt, L.W. 2011. AFLP Phylogeny of 36 Erythroxylum species- genetic relationships among Erythroxylum species inferred by AFLP analysis. Tropical Plant Biology. 4(2):126-133.Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm

- (Abstract Only)Zhang, D., Livingstone, D., Irish, B.M., Kuhn, D.N., Schnell II, R.J., Meinhardt, L.W. 2011. Comparison of single nucleotide polymorphisms and simple sequence repeats in genotype identification and diversity assessment of cacao germplasm. Annual International Plant & Animal Genome Conference. 2011.Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao

- (Peer Reviewed Journal)Tiburcio, R.A., Costa, G.G., Carazzolle, M.F., Schuster, S.C., Carlson, J.E., Guiltinan, M.J., Bailey, B.A., Argueso, J.L., Mieckowski, P., Meinhardt, L.W., Pereira, G.A. 2009. Genes acquired by horizontal transfer are potentially involved in the evolution of phytopathogenicity in Moniliophthora perniciosa and Moniliophthora roreri, two of the major pathogens of cacao. Journal of Molecular Evolution. 70:85-97.The relic Criollo cacao in Belize- genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad

- (Peer Reviewed Journal)Motilal, L., Zhang, D., Umaharan, P., Mischke, B.S., Mooleedhar, V., Meinhardt, L.W. 2010. The relic Criollo cacao in Belize- genetic diversity and relationship with Trinitario and other cacao clones held in the International Cocoa Genebank, Trinidad. Plant Genetic Resources: Characterization and Utilization. Available at http://dx.doi.org/10.1017/S1479262109990232.Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Peruvian Amazon using microsatllite DNA markers

- (Peer Reviewed Journal)Zhang, D., Boccara, M., Motilal, L., Mischke, B.S., Johnson, E.S., Butler, D., Bailey, B.A., Meinhardt, L.W. 2009. Molecular characterization of an earliest cacao (Theobroma cacao L.) collection from Peruvian Amazon using microsatllite DNA markers. Tree Genetics and Genomes. http://dx.doi.org/10.1007/s11295-009-0212-2.A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao

- (Peer Reviewed Journal)Mondego, J.M., Carazolle, M.F., Costa, G., Formighieri, L.P., Parizzi, L.P., Rincones, J., Cotomacci, C., Vidal, R.O., Estrela, R.C., Garcia, O., Castro, L.A., Gramacho, K.P., Goncalves, M.S., Neto-Goes, A., Barbosa, L.V., Guiltinan, M.J., Bailey, B.A., Meinhardt, L.W., Cascardo, J.C., Pereira, G.A. 2008. A genome survey of Moniliophthora perniciosa gives new insights into Witches’ Broom Disease of cacao. Biomed Central (BMC) Genomics. 9:548.The occurrence and frequency of Witches’ Broom Disease associated with Wild Cacao from the Upper Amazon of Peru

- (Abstract Only)Arevalo, E.G., Marquez, D.K., Samuels, G.J., Zhang, D., Robles, R., Arevalo, J., Barreto, A., Alvardo, C., Baligar, V.C., Meinhardt, L.W. 2008. The occurrence and frequency of Witches’ Broom Disease associated with Wild Cacao from the Upper Amazon of Peru. XX Congress Peruano de Fitopatologia 2008. Meeting Abstract. #58.COMPARATIVE GENOME ANALYSES OF MONILIOPHTHORA PERNICIOSA AND MONILIOPHTHORA RORERI: TWO CLOSELY RELATED PHYTOPATHOGENIC BASIDIOMYCETES THAT CAUSE DISTINCTLY DIFFERENT DISEASES OF THEOBROMA CACAO

- (Abstract Only)Meinhardt, L.W., Bailey, B.A., Guiltinan, M., Carazzolle, M.F., Lacerda, G., Mondego, J., Formigheri, E., Periera, G.A. 2008. Comparative genome analyses of moniliophthora perniciosa and moniliophthora roreri: two closely related phytopathogenic basidiomycetes that cause distinctly different diseases of theobroma cacao. Mid Atlantic Plant Molecular Biology Society Conference. .Moniliophthora perniciosa, the causal agent of witches’ broom disease of cacao: What’s new from this old foe?

- (Review Article)Meinhardt, L.W., Rincones, J., Bailey, B.A., Aime, M.C., Griffith, C., Zhang, D., Pereira, G. 2008. Moniliophthora perniciosa, the causal agent of witches’ broom disease of cacao: What’s new from this old foe. Molecular Plant Pathology. 9(5):577-588.Population Structure and Genetic Diversity of the Trinitario Cacao (Theobroma Cacao L.) from Trinidad and Tobago

- (Peer Reviewed Journal)Johnson, E.S., Bekele, F., Brown, J.S., Song, J.H., Motamayor, J., Zhang, D., Schnell II, R.J., Meinhardt, L.W. 2009. Population Structure and Genetic Diversity of the Trinitario Cacao (Theobroma Cacao L.) from Trinidad and Tobago. Crop Science. 49:564-572.The phytopathogenic basidiomycete Moniliophthora perniciosa senesces and contains a kalilo-like plasmid stably integrated in its large mitochondrial genome

- (Peer Reviewed Journal)Formighieri, E.F., Tiburcio, R.A., Armas, E.D., Shimo, H.M., Carels, N., Goes-Neto, A., Araujo, M.R., Cotomacci, C., Carazzolle, M.F., Thomazella, D.P., Sardinha-Pinto, N., Rincones, J., Digiampietri, L.A., Carraro, D.M., Azeredo-Espin, A., Reis, S.F., Deckman, A.C., Gramacho, K., Goncalves, M.S., Moura-Neto, J.P., Luciana, V.B., Meinhardt, L.W., Cascardo, J.C., Pereira, G.A. 2008. The phytopathogenic basidiomycete Moniliophthora perniciosa senesces and contains a kalilo-like plasmid stably integrated in its large mitochondrial genome. Mycological Research. http://apsjournals.apsnet.org/doi/pdf/10.1094/MPMI-21-7-0891.Molecular characterization of an International cocoa collection using microsallte markers

- (Peer Reviewed Journal)Zhang, D., Mischke, B.S., Johnson, E.S., Mora, A., Phillips-Mora, W., Meinhardt, L.W. 2008. Molecular characterization of an International cocoa collection using microsallte markers. Tree Genetics & Genomics. doi:  http://dx.doi.org/10.1007/s11295-008-0163-z.Differential gene expression between the biotrophic-like and saprotrophic mycelia of the Witches’ broom pathogen Moniliophthora perniciosa

- (Peer Reviewed Journal)Rincones, J., Scarpari, L.M., Mondego, J.M., Carazzolle, M.F., Formighieri, E.F., Costa, G.G., Barau, J.G., Vilas-Boas, L.A., Sabha, M., Azevedo, R.A., Dias, R., Cascardo, J.M., Meinhardt, L.W., Periera, G.A. 2008. Differential gene expression between the biotrophic-like and saprotrophic mycelia of the Witches’ broom pathogen Moniliophthora perniciosa. Molecular Microbiology. 21:891-908.Differential gene expression between the biotrophic-like and saprotrophic mycelia of the Witches’ broom pathogen Moniliophthora perniciosa.

- (Abstract Only)Rincones, J., Scarpari, L.M., Mondego, J.M., Formighieri, E.F., Sabha, M., Carazzolle, M.F., Barau, J.G., Meinhardt, L.W., Pereira, G.A. Differential gene expression between the biotrophic-like and saprotrophic mycelia of the Witches’ broom pathogen Moniliophthora perniciosa. Fungal Genetics Conference Proceedings. www.fgsc.net/asil2007/xxivfgcposterabs.htmON THE ANCESTRY OF THE ICS CLONES OF TRINIDAD AND TOBAGO

- (Abstract Only)Johnson, E.S., Bekele, F.L., Zhang, D., Schnell Ii, R.J., Meinhardt, L.W. 2008. On the ancestry of the ics clones of trinidad and tobago. Plant and Animal Genome VX Conference Abstracts.Poster Presentation at the PAG XVI Conference, San Diego, CA. January 12-16, Abstr. P121, p. 149.Genetic comparison of two related fungal pathogens of Theobroma cacao

- (Proceedings)Meinhardt, L.W., Bailey, B.A., Guiltinan, M., Pereira, G.A. 2007. Genetic comparison of two related fungal pathogens of Theobroma cacao. International Conference on Microbial Genomes.Genetic diversity and population structure of cacao landraces in Northern and Central coastal Ecuador

- (Peer Reviewed Journal)Zhang, D., Amores, F., Cedeno, A., Hermann, M., Meinhardt, L.W. 2008. Genetic diversity and population structure of cacao landraces in Northern and Central coastal Ecuador. Conservation Genetics. 9(2) 327-337.Involvement of calcium oxalate degradation during programmed cell death in Theobroma cacao tissues triggered by the hemibiotrophic fungus Moniliophthora perniciosa

- (Peer Reviewed Journal)Ceita, G.D., Macedo, J.N., Santos, T.B., Alemanno, L., Gesteira, A.D., Micheli, F., Mariano, A.C., Gramacho, K.P., Silva, D.D., Meinhardt, L.W., Mazzafera, P., Pereira, G.A., Cascardo, J.D. Involvement of calcium oxalate degradation during programmed cell death in Theobroma cacao tissues triggered by the hemibiotrophic fungus Moniliophthora perniciosa. Plant Science. 173 (2007) 106-117Characterization of Necrosis and Ethylene inducing Proteins (NEP) in the Basidiomycete Moniliophthora perniciosa, the Causal Agent of Witches’ Broom in Theobroma cacao

- (Peer Reviewed Journal)Garcia, O., Macedo, J., Tiburcio, R., Zaparoli, G., Bittencourt, L.M., Ceita, G., Rincones, J., Micheli, F., Gesteira, A., Mariano, A., Schiavinato, M.A., Medrano, F., Meinhardt, L.W., Pereira, G.A., Cascardo, J.C. 2007. Characterization of Necrosis and Ethylene inducing Proteins (NEP) in the Basidiomycete Moniliophthora perniciosa, the Causal Agent of Witches’ Broom in Theobroma cacao. Mycological Research. 111:443-455.CONCENTRATION AND UPTAKE OF P,ZN AND FE AS INFLUENCED BY SOIL ACIDITY, AND LEVELS AND FORMS OF N,P AND FE IN CACAO

- (Abstract Only)Baligar, V.C., Fageria, N.K., Machado, R.C., Meinhardt, L.W. 2006. Concentration and uptake of p,zn and fe as influenced by soil acidity, and levels and forms of n,p and fe in cacao. Proceedings of the International Cocoa Producer's Conference. 10.09.06“Refractario” cocoa – genetic identity and genetic structure assessed using microsallite markers

- (Peer Reviewed Journal)Zhang, D., Boccara, M., Motilal, L., Butler, D.R., Umaharan, P., Mischke, B.S., Meinhardt, L.W. 2006. “Refractario” cocoa – genetic identity and genetic structure assessed using microsallite markers. Conservation Genetics. 9(2):327-337.GENETIC VARIABILITY AND CHROMOSOME-LENGTH POLYMORPHISMS OF THE WITCHES’ BROOM PATHOGEN CRINIPELLIS PERNICIOSA FROM VARIOUS PLANT HOSTS IN SOUTH AMERICA

- (Peer Reviewed Journal)Rincones, J., Mazotti, G.D., Griffith, G.W., Pomela, A.W., Figueira, A., Queiroz, M.V., Pereira, J.F., Azevedo, R.A., Pereira, G.A., Meinhardt, L.W. 2006. Genetic variability and chromosome-length polymorphisms of the witches’ broom pathogen crinipellis perniciosa from various plant hosts in south america. Mycological Research. 110:821-832.
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