Article
Multidisciplinary Sciences
Jheiner Vasquez-Garcia, Julio Cesar Santos-Pelaez, Roiber Malqui-Ramos, Carmen N. Vigo, Wigoberto Alvarado C, Leidy G. Bobadilla
Summary: Agromorphological characterization of cacao accessions in Peru is an important tool for conservation and genetic improvement of cacao germplasm. This study provides a morphological and agronomic characterization of 113 cacao accessions, forming five groups based on similar characteristics. The accessions in certain groups show potential for genetic improvement and advancement in the Peruvian chocolate industry.
Article
Multidisciplinary Sciences
Tuomas Hamala, Eric K. Wafula, Mark J. Guiltinan, Paula E. Ralph, Claude W. dePamphilis, Peter Tiffin
Summary: The study uses 31 chromosome-scale, haplotype-resolved genome assemblies of Theobroma cacao to investigate the fitness consequences of structural variants (SVs) in natural populations. It reveals that the majority of SVs are deleterious, influencing gene expression and likely impairing gene function. Despite the overall detrimental effects, individual SVs bearing signatures of local adaptation are identified, some of which are associated with differentially expressed genes between populations, particularly those involved in pathogen resistance.
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA
(2021)
Article
Virology
Ihsan Ullah, Andrew J. Daymond, Paul Hadley, Michelle J. End, Pathmanathan Umaharan, Jim M. Dunwell
Summary: Cocoa is an important tropical crop, and the exchange of germplasm is crucial for varietal development. Quarantine facilities and screening procedures help minimize the risk of pest and disease transmission. New detection methods for mild virus infections are valuable for early diagnosis.
Article
Biodiversity Conservation
Helmuth Edisson Nieves-Orduna, Markus Mueller, Konstantin V. Krutovsky, Oliver Gailing
Summary: The study revealed a geographic-specific diversity in chloroplast genetics of cacao tree, with the highest haplotype variation observed in western Amazonia. Some haplotypes may have undergone long-distance seed dispersal from west to east in the Amazon basin. The chloroplast haplotypes of cacao populations are associated with the genetic groups identified by previous nuclear SSR analysis.
Article
Agronomy
Paula-Maria Galan, Livia-Ioana Leti, Silvia Strajeru, Denisa-Elena Petrescu, Mirela-Mihaela Cimpeanu, Alina-Carmen Tanasa, Dan-Marius Sandru, Dragos-Lucian Gorgan
Summary: The extreme weather in recent years is the result of climate change, leading to the disappearance of unknown plant species worldwide. The United Nations and FAO have highlighted the urgent need to conserve and study plant germplasm in response to population growth and food insecurity. This study used DNA sequence data for morphological and molecular traits to infer the ancestry of 27 landraces.
Article
Ecology
Danilo E. Bustamante, Lambert A. Motilal, Martha S. Calderon, Amrita Mahabir, Manuel Oliva
Summary: This study explores the genetic structure and ancestry of Fine Aroma cocoa in northern Peru, revealing that it mainly originates from Nacional with some contribution from Criollo. These findings support the development of the fine cocoa industry in Peru.
FRONTIERS IN ECOLOGY AND EVOLUTION
(2022)
Article
Microbiology
Ihsan Ullah, Muhammad Kamran, Jim M. Dunwell
Summary: This study reports the first near-complete genome sequence of cacao polerovirus (CaPV) and develops a multiplex RT-PCR assay for screening and identifying infected cacao clones. Although this virus does not cause severe disease, the new information and diagnostic assay are of strategic importance in developing protocols for the safe international transfer of cacao germplasms.
Article
Horticulture
Ana Henao-Ramirez, Hector Jaime Salazar Duque, Arley Fernando Calle Tobon, Aura Ines Urrea Trujillo
Summary: The study assessed the genetic stability of cocoa plantlets propagated by somatic embryogenesis and conventional grafting for two genotypes using SSR analysis. The results showed that the plant populations were genetically equal and no differences in allelic composition were observed between plantlets propagated by different methods. This indicates that the protocol used is suitable for large-scale propagation of cocoa genotypes for commercial purposes.
INTERNATIONAL JOURNAL OF FRUIT SCIENCE
(2021)
Article
Multidisciplinary Sciences
C. J. Mendoza-Meneses, A. A. Feregrino-Perez, R. G. Guevara-Gonzalez, J. F. Garcia-Trejo
Summary: Cocoa is a vital tropical fruit widely used in the food, cosmetic, and pharmaceutical industries. The implementation of pre-harvest techniques and soil fertilization can significantly increase cocoa yield.
Article
Multidisciplinary Sciences
Frances L. Bekele, Gillian G. Bidaisee, Mathilde Allegre, Xavier Argout, Olivier Fouet, Michel Boccara, Duraisamy Saravanakumar, Isaac Bekele, Claire Lanaud
Summary: This study used genome-wide association studies (GWAS) to identify marker-trait associations (MTAs) in the cacao genome, including traits related to yield. Traits such as seed size, seed length to width ratio, and seed number were found to be associated with markers at different loci, indicating polygenic nature. Approximately 40 candidate genes related to seed development, protein synthesis, carbohydrate transport, and lipid biosynthesis were identified in the regions surrounding the significantly associated markers.
Article
Agronomy
Pietro Della Sala, Christian Cilas, Teresa E. Gimeno, Steven Wohl, Stephen Yaw Opoku, Alina Gainusa-Bogdan, Fabienne Ribeyre
Summary: In West Africa, Harmattan-induced atmospheric and soil droughts pose recurring hazards for cacao cultivation. The study in Ghana's Eastern region during one Harmattan season found that atmospheric drought caused a similar decline in Leaf Area Index (LAI) as soil water stress, indicating the importance of both types of drought on cacao trees. However, atmospheric and soil water stresses did not have a synergistic effect on transpiration, and the interactive effect of both types of drought influenced sap velocity. This suggests that not only reduced precipitation but also increasing atmospheric drought may negatively impact cacao production in West Africa under the influence of the Harmattan winds.
AGRICULTURAL AND FOREST METEOROLOGY
(2021)
Article
Plant Sciences
Abraham Akpertey, Francis K. Padi, Lyndel Meinhardt, Dapeng Zhang
Summary: Accurate genotype identification is crucial for breeding new varieties of Coffea canephora L. with tolerance to biotic and abiotic stresses. This study validated SNP markers, uncovering mislabeling in genetic material and parentage errors. Analysis revealed significant genetic divergence among different populations of C. canephora genotypes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Forestry
Julian Fernando Mateus-Rodriguez, Fiona Lahive, Paul Hadley, Andrew J. Daymond
Summary: This study investigated the combined effects of increased temperature and atmospheric carbon dioxide concentration on the growth and photosynthesis of cacao seedlings. The results showed that elevated carbon dioxide concentration increased dry weight, leaf area, and photosynthesis rate, while decreasing transpiration and stomatal conductance. Increasing temperature had a positive effect on photosynthesis but led to a decrease in dry weight and leaf area. Elevated carbon dioxide concentration and temperature improvements were observed in high temperature-tolerant genotypes.
Article
Plant Sciences
Carlos E. Gonzalez-Orozco, Jaime A. Osorio-Guarin, Roxana Yockteng
Summary: This study calculates the phylogenetic diversity of cocoa genotypes and identifies biodiversity priority areas in Colombia for conservation and breeding programmes. The Caribbean and North Andes regions show the highest phylogenetic diversity, while the Amazonia genotypes have a more ancient origin. It is recommended to prioritize conservation in areas where wild cocoa is found and prioritize breeding programmes for recently diverged lineages with low relative phylogenetic diversity.
PLANT GENETIC RESOURCES-CHARACTERIZATION AND UTILIZATION
(2023)
Article
Biodiversity Conservation
Mathieu Rouard, Julie Sardos, Guilhem Sempere, Catherine Breton, Valentin Guignon, Ines van den Houwe, Sebastien C. Carpentier, Nicolas Roux
Summary: This research introduces a digital catalog of high-density markers for banana germplasm to facilitate access to genetic diversity information, aim at maximizing conservation and use of climate-ready varieties.
PLANTS PEOPLE PLANET
(2022)
Article
Plant Sciences
Boyi Wang, Lambert A. Motilal, Lyndel W. Meinhardt, Jiantao Yin, Dapeng Zhang
TROPICAL PLANT BIOLOGY
(2020)
Article
Plant Sciences
Abraham Akpertey, Francis K. Padi, Lyndel Meinhardt, Dapeng Zhang
Summary: Accurate genotype identification is crucial for breeding new varieties of Coffea canephora L. with tolerance to biotic and abiotic stresses. This study validated SNP markers, uncovering mislabeling in genetic material and parentage errors. Analysis revealed significant genetic divergence among different populations of C. canephora genotypes.
FRONTIERS IN PLANT SCIENCE
(2021)
Article
Biodiversity Conservation
Dapeng Zhang, Fernando E. Vega, William Solano, Fuyuan Su, Francisco Infante, Lyndel W. Meinhardt
Summary: The study screened 672 candidate SNPs using Nano-Fluidic Array genotyping and selected a panel of 96 SNPs for genotyping Coffea arabica based on call rate, Minor Allele Frequency, and Linkage Disequilibrium. This validated panel is suitable for coffee germplasm conservation, crop improvement, varietal identification, seed and nursery accreditation, and coffee bean authentication.
CONSERVATION GENETICS RESOURCES
(2021)
Article
Plant Sciences
Jinfang Zheng, Lyndel W. Meinhardt, Ricardo Goenaga, Dapeng Zhang, Yanbin Yin
Summary: Dragon fruits, economically important tropical fruits, belong to the family of Cactaceae and have evolved to adapt to arid environments. The draft genome of Hylocereus undatus was reported, revealing similarities in protein-coding genes with other Cactaceae plants and a whole-genome duplication event in their common ancestor. The genome also enabled the discovery of functional enrichment related to drought resistance and fruit flavor in dragon fruits.
HORTICULTURE RESEARCH
(2021)
Article
Genetics & Heredity
Leny Calano Galvez, Rhosener Bhea Lu Koh, Cris Francis Cortez Barbosa, Jayson Calundre Asunto, Jose Leonido Catalla, Robert Gomez Atienza, Kennedy Trinidad Costales, Vermando Masinsin Aquino, Dapeng Zhang
Summary: The study sequenced and assembled the genome of a Philippine indigenous crop, abaca, revealing genomic features, repetitive elements, and predicted gene structures, which will facilitate gene discovery for crop improvement and genetic diversity studies.
Article
Agronomy
Abraham Akpertey, Francis Kwame Padi, Lyndel Meinhardt, Dapeng Zhang
Summary: The study analyzed the genetic distances between parental clones of Robusta coffee hybrids and found a significant correlation between genetic distances and hybrid yield performance. Selecting hybrids with higher genetic distances can increase yield gain, and inter-group hybrids outperformed intra-group hybrids in cumulative yield.
Letter
Plant Sciences
Jinfang Zheng, Lyndel W. Meinhardt, Ricardo Goenaga, Tracie Matsumoto, Dapeng Zhang, Yanbin Yin
HORTICULTURE RESEARCH
(2022)
Article
Agronomy
Lihua Song, Bing Cao, Yue Zhang, Lyndel W. Meinhardt, Dapeng Zhang
Summary: Chinese jujube germplasm has a high rate of mislabeling, but the development of SNP markers can aid in variety identification and parentage analysis.
Article
Agronomy
Diane Estelle Gnapi, Desire N'Da Pokou, Hyacinthe Legnate, Zhang Dapeng, Christophe Montagnon, Benoit Bertrand, Assonvo Simon-Pierre N'guetta
Summary: Robusta coffee is an important source of income and employment for many developing countries. However, genetic erosion from the introduction of Congolese accessions threatens the genetic integrity of wild populations from the Guinean gene pool. Pollen from the Congolese gene pool shows greater ability to pollinate the Guinean group, necessitating conservation measures for wild populations.
Review
Plant Sciences
John C. C. D'Auria, Stephen P. P. Cohen, Jason Leung, Kayla Glockzin, Kyle Mark Glockzin, Jacquelyn Gervay-Hague, Dapeng Zhang, Lyndel W. W. Meinhardt
Summary: The article discusses information related to tea production, genetics, and chemistry, as well as production issues that may impact emerging tea production and research in the United States.
FRONTIERS IN PLANT SCIENCE
(2022)
Article
Agronomy
Cesar O. Arevalo-Hernandez, Enrique Arevalo-Gardini, Abel Farfan, Martin Amaringo-Gomez, Andrew Daymond, Dapeng Zhang, Virupax C. Baligar
Summary: Cacao is an important tropical crop, but the soils it grows in are often acidic and low in fertility. This study evaluated 60 cacao genotypes and found that early growth predictors of acid soil tolerance are the number of leaves and root area. Nutrient uptake, particularly for N, Ca, Mg, and K, may play a role in soil acidity tolerance. Ten genotypes were identified as potentially tolerant to soil acidity and could be used for breeding acid soil-tolerant cacao varieties.
Article
Agronomy
Diane Estelle Gnapi, Desire N'Da Pokou, Hyacinthe Legnate, Dapeng Zhang, Doffou Selastique Akaffou, Kouame Cyrille Koffi, Benoit Bertrand, Christophe Montagnon, Assanvo Simon-Pierre N'Guetta
Summary: This study focuses on the genetic structuring of Coffea canephora populations in Côte d'Ivoire using SNP markers. The results reveal the presence of two main genetic groups, Guinean and Congolese, and four subgroups within the Congolese group. Among the agronomic traits analyzed, the SG1 and SG2 subgroups displayed the highest performance. The findings highlight the importance of selecting the best progenitors within the Guinean group. This research provides valuable insights for future coffee breeding programs.
BIOTECHNOLOGIE AGRONOMIE SOCIETE ET ENVIRONNEMENT
(2022)
Article
Horticulture
Yue Zhang, Yaping Ma, Lyndel W. Meinhardt, Dapeng Zhang, Bing Cao, Lihua Song
Summary: Chinese jujube is an economically important fruit tree with high adaptability to various climate conditions. Traditional jujube cultivars in Ningxia, China are highly valued for their unique flavor and quality. This study developed a multi-locus SNP barcoding method for cultivar authentication of jujube fruits, which showed high reliability and practicality. The method has the potential to be applied for the authentication of other stone fruits as well.
Article
Horticulture
Yaping Ma, Dapeng Zhang, Zhuangji Wang, Lihua Song, Bing Cao
Summary: The research on the growing patterns of 'Lingwu Changzao' jujube shows that fruit traits follow double 'S' growth curves, while stone traits stop increasing early in fruit growth period. This indicates a high fruit-stone ratio as a desirable quality attribute for 'Lingwu Changzao' as fresh-eating fruits.