Research Project: Characterizing and Evaluating the Genetic Diversity and Horticultural Value of Genetic Resources for Cacao and Other Tropical tree crops Economically important to the United States

Location: Sustainable Perennial Crops Laboratory

Publications (Clicking on the reprint icon will take you to the publication reprint.)

The American Cherimoya Genome reveals insights into the intra-specific divergence, the evolution of magnoliales, and a putative gene cluster for acetogenin biosynthesis - (Peer Reviewed Journal)
Li, T., Nousias, O., Zheng, J., Meinhardt, L.W., Goenaga, R.J., Zhang, D., Yin, Y. 2024. The American Cherimoya Genome reveals insights into the intra-specific divergence, the evolution of magnoliales, and a putative gene cluster for acetogenin biosynthesis. Plants. 13(5):636. https://doi.org/10.3390/plants13050636.

Cross-pollination with native genotypes improves fruit set and yield quality of Peruvian cacao varieties - (Peer Reviewed Journal)
Vansynghel, J., Thomas, E., Ocampo-Ariza, C., Maas, B., Zhang, D., Ulloque-Dewenter, C., Steffan-Dewenter, I. 2023. Cross-pollination with native genotypes improves fruit set and yield quality of Peruvian cacao varieties. Agriculture, Ecosystems and Environment. https://doi.org/10.1016/j.agee.2023.108671.

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.

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.

Growth and nutritional responses of juvenile wild and domesticated cacao genotypes to soil acidity - (Peer Reviewed Journal)
Ahnert, D., Paiva, A., Almeida, A.F., De Araujo, Q.R., Zhang, D., Baligar, V.C. 2022. Growth and nutritional responses of juvenile wild and domesticated cacao genotypes to soil acidity. Agronomy. https://doi.org/10.3390/agronomy12123124.

Sources, indicators, and assessment of soil contamination by potentially toxic metals - (Peer Reviewed Journal)
Shentu, J., He, Z., Xin, X., Zhang, T., Yang, X., Baligar, V.C. 2022. Sources, indicators, and assessment of soil contamination by potentially toxic metals. Sustainability. 14:15878. https://doi.org/10.3390/su142315878.

Edaphic and physiographic attributes and their impact on death of cacao trees in drought years - (Peer Reviewed Journal)
Souza, J.J., Silveira, F.E., Silva Pereira, B., Mateus-Rodriguez, J., Ahnert, D., Baligar, V.C. 2022. Edaphic and physiographic attributes and their impact on death of cacao trees in drought years. Agronomy Journal. 115(3):1069-1084. https://doi.org/10.1002/agj2.21215.

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.

Growth and nutritional responses of juvenile wild and domesticated cacao genotypes to soil acidity - (Peer Reviewed Journal)
Arevalo-Hernandez, C., Arevalo-Ardini, E., Farfana, A., Amaringo-Gomez, M., Daymond, A., Zhang, D., Baligar, V. 2022. Growth and nutritional responses of juvenile wild and domesticated cacao genotypes to soil acidity. Agronomy. 12(12):3124. https://doi.org/10.3390/agronomy12123124.

Physiological, biochemical and molecular responses of young cacao plants grown in compacted and phosphorus-limited coastal plain soil - (Peer Reviewed Journal)
Tosto, T., Almeida, A., Paiva, A., Ahnert, D., Baligar, V.C. 2022. Physiological, biochemical and molecular responses of young cacao plants grown in compacted and phosphorus-limited coastal plain soil. Journal of Plant Growth Regulation. 42:2389–2407. https://doi.org/10.1007/s00344-022-10712-3.

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.

Is the genetic integrity of wild coffea canephora from ivory coast threatened by hybridization with introduced coffee trees from central africa? - (Peer Reviewed Journal)
Gnapi, E.D., Pokou, D., Legnate, H., Zhang, D., Montagnon, C., Bertrand, B., N'Guetta, S. 2022. Is the genetic integrity of wild coffea canephora from ivory coast threatened by hybridization with introduced coffee trees from central africa? Euphytica. 218:62. https://doi.org/10.1007/s10681-022-03004-0.

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.

Effect of different edaphic crop conditions on the free amino acid profile of the PH-16 dry cacao beans - (Peer Reviewed Journal)
Araujo, Q.R., Loureiro, G.A., Povoas, C., Steinmacher, S., Santos, S.S., Ahnert, D., Baligar, V.C. 2021. Effect of different edaphic crop conditions on the free amino acid profile of the PH-16 dry cacao beans. Agronomy. 11(8):1637. https://doi.org/10.3390/agronomy11081637.

Growth, physiological, nutrient uptake efficiency and shade tolerance responses of cacao genotypes under different shades - (Peer Reviewed Journal)
Arevalo-Gardini, E., Farfan, A., Barraza, F., Arevalo-Hernandez, C.0., Alegre, J., Baligar, V.C. 2021. Growth, physiological, nutrient uptake efficiency and shade tolerance responses of cacao genotypes under different shades. Agronomy. 11:1536. https://doi.org/10.3390/agronomy11081536.

Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome - (Peer Reviewed Journal)
Galvez, L.C., Koh, R.B., Barbosa, C.C., Asunto, J.C., Catalla, J.L., Atienza, R.G., Costalesa, K.T., Aquino, V.M., Zhang, D. 2021. Sequencing and de Novo Assembly of Abaca (Musa textilis Née) var. Abuab Genome. Genes. 12:1202. https://doi.org/10.3390/genes12081202.

Carbon dioxide concentration and light levels on growth and mineral nutrition of juvenile cacao genotypes - (Peer Reviewed Journal)
Baligar, V.C., Elson, M.K., Almeida, A., Araujo, D., Ahnert, D., He, Z. 2021. Carbon dioxide concentration and light levels on growth and mineral nutrition of juvenile cacao genotypes. American Journal of Plant Sciences. 12:818-839.

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 impact of ambient and elevated [CO2] and low to adequate photosynthetic photon flux density on growth, physiology and nutrient use efficiency of juvenile cacao genotypes - (Peer Reviewed Journal)
Baligar, V.C., Elson, M.K., Almeida, A., Araujo, Q.R., Ahnert, D., He, Z. 2021. The impact of ambient and elevated [CO2] and low to adequate photosynthetic photon flux density on growth, physiology and nutrient use efficiency of juvenile cacao genotypes. Agronomy. https://doi.org/10.3390/agronomy11020397.

Fruit morphology measurements of Jujube Cultivar ‘Lingwu Changzao’ (Ziziphus jujuba Mill. cv. Lingwuchangzao) during fruit development - (Peer Reviewed Journal)
Ma, Y., Song, L., Wang, Z., Zhang, D., Cao, B. 2021. Fruit morphology measurements of Jujube Cultivar ‘Lingwu Changzao’ (Ziziphus jujuba Mill. cv. Lingwuchangzao) during fruit development. Horticulturae. https://doi.org/10.3390/horticulturae7020026.

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.

Impact of ambient and elevated [co2] in low light levels on growth, physiology and nutrient uptake of tropical perennial legume cover crops - (Peer Reviewed Journal)
Baligar, V.C., Elson, M.K., He, Z., Li, Y., Paiva, A.D., Almeida, A.A., Ahnert, D. 2021. Impact of ambient and elevated [co2] in low light levels on growth, physiology and nutrient uptake of tropical perennial legume cover crops. Plants. https://doi.org/10.3390/plants10020193.

Mitigation of Pb toxicity by Mn in seedling of the cacao clonal CCN 51 genotype grown in soil: physiological, biochemical, nutritional and molecular responses - (Peer Reviewed Journal)
Muñoz, J.A., Almeida, A.F., Pirovani, C.P., Ahnert, D., Baligar, V.C. 2021. Mitigation of Pb toxicity by Mn in seedling of the cacao clonal CCN 51 genotype grown in soil: physiological, biochemical, nutritional and molecular responses. Ecotoxicology. https://doi.org/10.1007/s10646-021-02348-y.

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.

Comparative effectiveness of activated dolomite phosphate rock and biochar for immobilizing cadmium and lead in soils - (Peer Reviewed Journal)
Liu, B., He, Z., Liu, R., Montenegro, A.C., Ellis, M., Li, Q., Baligar, V.C. 2020. Comparative effectiveness of activated dolomite phosphate rock and biochar for immobilizing cadmium and lead in soils. Chemosphere. https://doi.org/10.1016/j.chemosphere.2020.129202.

Growth and nutritional responses of wild and domesticated cacao genotypes to soil Cd stress - (Peer Reviewed Journal)
Gardini, G.E., Arevalo-Hernandez, C.C., Barraza, F., Farfan, A., He, Z.L., Baligar, V.C. 2020. Growth and nutritional responses of wild and domesticated cacao genotypes to soil Cd stress. Science of the Total Environment. https://doi.org/10.1016/j.scitotenv.2020.144021.

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.

Light intensity effects on growth, physiological and nutritional parameters of tropical perennial legume cover crops - (Peer Reviewed Journal)
Baligar, V.C., Elson, M.K., He, Z., Li, Y., Paiva, A.D., Ahnert, D., Almeida, A.F. 2020. Light intensity effects on growth, physiological and nutritional parameters of tropical perennial legume cover crops. Agronomy. https://doi.org/10.3390/agronomy10101515.

Mitigation of cadmium toxicity by zinc in young cacao plants - (Peer Reviewed Journal)
Santos, M.L., Almeida, A., Silva, N.M., Silva, J.V., Barroso, J.P., Souza, J.O., Ahnert, D., Baligar, V.C. 2020. Mitigation of cadmium toxicity by zinc in young cacao plants. Environmental and Experimental Botany. https://doi.org/10.1016/j.envexpbot.2020.104201.

Mitigation of Cd toxicity by Mn in young plants of cacao, evaluated by the proteomic profiles of laves and roots - (Peer Reviewed Journal)
Oliveira, B.R., Almeida, A.A., Pirovani, C.P., Barroso, J.P., Neo, C.H., Santos, N.A., Ahnert, D., Mangabeira, P.A., Baligar, V.C. 2020. Mitigation of Cd toxicity by Mn in young plants of cacao, evaluated by the proteomic profiles of laves and roots. Ecotoxicology and Environmental Safety. 29:340–358. https://doi.org/10.1007/s10646-020-02178-4.

Interactions between soil, leaves and beans nutrient status and dry biomass of beans and pod husk of forastero cacao: An exploratory study - (Peer Reviewed Journal)
Araujo, Q., Loureiro, G.A., Ahnert, D., Valdez, R., Baligar, V.C. 2020. Interactions between soil, leaves and beans nutrient status and dry biomass of beans and pod husk of forastero cacao: An exploratory study. Communications in Soil Science and Plant Analysis. https://doi.org/10.1080/00103624.2020.1729369.

Foliar applied cuprous oxide fungicide induces physiological, biochemical and molecular changes in cacao leaves - (Peer Reviewed Journal)
Santos, S.J., Almeida, A.F., Ahnert, D., Silva, N.M., Santo, M.L., Santos, N.A., Baligar, V.C. 2020. Foliar applied cuprous oxide fungicide induces physiological, biochemical and molecular changes in cacao leaves. Scientia Horticulturae. 265:109224.

Mineral nutrition of cacao (Theobroma cacao L.): Relationships between foliar concentrations of mineral nutrients and crop productivity - (Peer Reviewed Journal)
Marrocos, P.C., Araujo, Q.R., Loureiro, G.A., Sodre, G.A., Ahnert, D., Baligar, V.C. 2020. Mineral nutrition of cacao (Theobroma cacao L.): Relationships between foliar concentrations of mineral nutrients and crop productivity. Journal of Plant Nutrition. 15 (11):2369–79.

Quality green tea (camellia sinensis l.) Clones marked through novel traits - (Peer Reviewed Journal)
Patel, P., Zhang, D., Borthakur, D., Hazarika, M., Boruah, P., Barooah, R., Sabbapondit, S., Neog, N., Gogoi, R. 2019. Quality green tea (camellia sinensis l.) Clones marked through novel traits. Beverages. 5(4):63.

Wide ranging differences in tolerance to Phytopthora palmivora in four genetic groups of cacao - (Peer Reviewed Journal)
Fister, A., Leamdro, M., Zhang, D., Marden, J., Tiffin, P., Depamphilis, C., Maximova, S., Guiltinan, M. 2019. Wide ranging differences in tolerance to Phytopthora palmivora in four genetic groups of cacao. Tree Genetics and Genomes. 16:1. https://doi.org/10.1007/s11295-019-1396-8.

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.

Growth, physiological and nutrient uptake traits of Crotalaria cover crops influenced by levels of carbon dioxide under low light Intensities - (Peer Reviewed Journal)
Baligar, V.C., Elson, M.K., He, Z.L., Li, Y.C., Paiva, A.D., Ahnert, D. 2018. Growth, physiological and nutrient uptake traits of Crotalaria cover crops influenced by levels of carbon dioxide under low light Intensities. International Journal of Plant Sciences. 23(1):1-14.

Physiological, ultrastructural, biochemical and molecular responses of young cocoa plants to the toxicity of cr (iii) in soil - (Peer Reviewed Journal)
Nascimento, J.L., Almeida, A.F., Barroso, J.P., Mangabeira, P.O., Ahnert, D., Souza, A.G., Silva, J.V., Baligar, V.C. 2018. Physiological, ultrastructural, biochemical and molecular responses of young cocoa plants to the toxicity of cr (iii) in soil. Ecotoxicology and Environmental Safety. 159:272-283.

Conserving and exploiting cocoa genetic resources: the key challenges - (Book / Chapter)
Laliberte, B., End, M., Cryer, N., Daymond, A., Engels, J., Esks, A., Gilmour, M., Lachenaud, P., Phillips-Mora, W., Turnbull, C., Umaharan, P., Zhang, D., Weise, S. 2018. Conserving and exploiting cocoa genetic resources: the key challenges. In: Umaharan, P., Achieving sustainable cultivation of cocoa, Cambridge, UK: Burleigh Dodds Science Publishing. 25 p.