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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #424482

Research Project: Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources

Location: Sustainable Perennial Crops Laboratory

2018 Annual Report


Objectives
The goal of this project is to improve the management efficiency of and facilitate the use of germplasm of tropical tree crops, primarily Theobroma cacao. The specific objectives are: Objective 1: Elucidate geospatial patterns of genetic diversity in cacao and other tropical tree crops, and incorporate that information into the project website, cacao and other tropical crop databases, and/or GRIN-Global. Sub-objective 1.A. Identify traditional varieties in farmers’ fields and characterize wild populations in non-U.S. national cacao collections. Sub-objective 1.B. Assess geospatial distribution of genetic diversity in the primary gene pool of T. cacao. Objective 2: Apply the preceding genetic information to strategically acquire new accessions of cacao and other tropical tree crops to fill gaps in genebank collections, and to support in situ, dynamic conservation of selected taxa. Objective 3: Evaluate cacao genetic resources for host-plant resistance to priority diseases, in conjunction with domestic and international collaborators. The first two objectives function together to identify and analyze the existing diversity within the primary cacao gene pool. This identifies diversity gaps that need to be filled by collecting from the remaining wild populations. This permits in-depth analysis of origin, dispersal, and population dynamics to be conducted. The third objective, to initiate evaluations of key agronomic traits, is based on the information about genetic diversity and germplasm revealed in the other two objectives, as well as in previous projects. Germplasm accessions harboring favorable genes/alleles that can contribute to new genetic variation of agronomic traits will be identified. These same objectives are applicable to other tropical tree crops. These priority crops are in the process of being identified in conjunction with ARS tropical tree crop curators and similar research goals will be initiated as necessary.


Approach
The project will first elucidate geospatial patterns of genetic diversity in the primary gene pool of T. cacao using research tools of genomics, spatial genetics and bioinformatics. Cacao germplasm that have been collected and maintained in various ex-situ genebanks will be characterized using single nucleotide polymorphism (SNP) markers. The generated SNP data, together with those previously obtained from the two international genebanks and other non-U.S. national collections, will be compiled and used for assessment of genetic diversity within and among collections. Completion of this work will allow ARS to have a clear understanding about the scope of existing wild germplasm and traditional varieties maintained in the non-U.S. national collections. It will also enable mapping of the geographical distribution of traditional varieties of T. cacao in the Americas using tools of spatial genetics. Second, diversity gaps in ex situ collections will be identified and filled through new collection expeditions, with emphasis on increasing representation from the geographical center of diversity. Based on the existing information, ARS collecting expeditions will focus on the Peruvian Amazon bordered by Brazil and Colombia, including Ríos Ucayali, Putumayo, Yavari, and their tributaries. In addition, landraces and traditional varieties which have a distinct genetic profile, specific regional distribution, and fine flavor, will be identified to support in situ/on-farm conservation. Resulting information will serve as a scientific baseline to support rational decision-making for future germplasm conservation and utilization. Finally, in collaboration with the curators of international and national collections, cacao germplasm will be evaluated for key agronomic traits, primarily disease resistance. Quantitative trait loci mapping, based on field evaluation, SNP genotyping, and genome-wide association mapping will be applied to discover new sources of resistance to major diseases. Approaches established and utilized in cacao will be applied to other tropical tree crops of major economic importance as they are identified and as conservation procedures are established.


Progress Report
2018 is the last year of the project “Genetic Diversity Assessment of Cacao and Other Tropical Tree Crop Genetic Resources” (8042-21000-267-00D), which started in March 2013. Any remaining research activities in this project have been incorporated into the new in-house 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 (Project No. 8042-21000-281-00D), which started March, 2018. Technologies developed for cacao are being applied to other tropical perennial crops that are important to the U.S., including tea, coffee, pineapple, longan, ornamental and oil Camellia, as well as Musa species. For these species, Single nucleotide polymorphic (SNP) markers have been developed through data mining of genomic data available in public databases, and array based genotyping was performed for germplasm collections maintained at USDA ARS and in collaborating institutions. The project made significant progress in the molecular characterization of cacao genetic resources maintained in international and national genebanks, in Trinidad, Costa Rica, Ecuador, Peru, Jamaica, Nigeria, Ghana, Indonesia, as well as in the International Germplasm Quarantine Center (ICGC) in Reading, UK. A total of 8,640 cacao accessions were analyzed using SNP markers adapted by this project. High levels of mislabeling were identified in most the ex situ collections, which proved the effectiveness of SNP markers for reducing off-types and genetic redundancies; thereby providing a strong basis for improving the accuracy and efficiency in cacao genebank management and breeding, as well as for mobilizing improved varieties to cacao farmers. In collaboration with the International Cacao Quarantine Center (ICQC), University of Reading, UK and Mars, Inc., an online tool to compare single nucleotide polymorphism (SNP) profiles of individual trees was developed. The verification status of accessions in a collection will be included in the International Cocoa Germplasm Database (ICGD) and made widely available to the cacao community, with web pages created to highlight reference genotypes and compare other genetic fingerprints to these. New collecting expeditions conducted in Peru have led to the establishment of a large collection of wild cacao germplasm, comprising 550 wild cacao accessions, in Tarapoto, Peru. A combined analysis of the newly collected trees and the existing germplasm in the two international genebanks was conducted using SNP markers. The analysis led to the identification of three new populations in the Amazon, including the populations of Beni/Madre del Dios, Yavari/Jurua and Putumayo/Caquetá. These findings significantly increased our understanding about the scope of existing wild germplasm and traditional varieties maintained in non-U.S. national collections. It also enables mapping of the geographical distribution of natural populations of T. cacao in the Americas. Based on the new information, diversity gaps in ex situ collections were identified and will be filled through new collection expeditions. In collaboration with the Cacao Research Center, University of West Indies, the London Cocoa Trade Amazon project (LCT EEN) collection was analyzed using SNP markers. The results identified intra-plot mislabeling, enabled reconstruction of pedigrees and provided valuable insight into the genetic structure of this wild cacao population and revealed a new germplasm group, adjacent to the reported Curaray cacao groups in Ecuador. These finding suggest that future collecting expeditions in this area are needed to fill this gap in the current international cacao genebanks, as well as in national collections in Ecuador and Colombia. Landraces and traditional varieties which have a distinct genetic profile, specific regional distribution, and fine flavor, were identified. These include “Chuncho cacao” and “Piura Porcelana” from Peru, Ancient Nacional from Ecuador, Ancient Criollo and Amelonado from Honduras, Nicaragua and Puerto Rico. These findings provide scientific baseline information to support rational decision making for in situ/on-farm conservation in these regions, as well as for production of fine-flavored cacao beans for premium chocolate markets. Frosty pod disease resistant clones developed by the Center for Tropical Agricultural Research and Education (CATIE), Costa Rica were analyzed using SNP markers. Our result showed that the resistant progenitors includes a wide array of wild germplasm groups from the Upper Amazon, indicating a high diversity in terms of different genes/alleles underling the resistance. In collaboration with the Cacao Research Centre in University of West Indies, the cacao germplasm group “Refractario” (Nacional hybrids) were evaluated for key agronomic traits, primarily disease resistance. SNP genotyping, and genome-wide association mapping were applied to identify markers associated with resistance to Witches’ broom disease and yield components. Yunnan Province is potentially a new cacao production region in China. Using SNP markers, the genetic diversity in the cacao collection maintained in the Xishuangbanna Tropical Botanical Garden in Yunnan China was evaluated. This collection has a narrow genetic background and were mostly comprised of Amelonado hybrids. These results revealed a large gap in the genetic diversity of this collection suggesting that new introductions are needed to increase the genetic diversity of the collection. Tea is an important commodity, representing a $40 billion-a-year global market ($12 billion in the U.S.). The SNP fingerprinting technology developed by this project can accurately identify tea genotypes as well as their processed products of loose-leaf tea, so that the products can be traced back to the original varieties. This technology is robust and cost-effective, showing high potential for practical application in the value chain of this industry. Through collaborative research with Tea scientists in Asian countries, we analyzed 760 tea accessions that originated from China, India, Vietnam, Laos, Myanmar, Thailand, Korea and Japan, to establish a framework for tea cultivar classification. Analysis of genetic diversity in the primary gene pool of C. sinensis revealed that there are four major genetic lineages of tea germplasm, corresponding to small leaf China types and three broad leaf Assam type viz. Indian Assam, Chinese Assam, and Cambodian Assam. Each lineage has its independent origin and site of domestication. This finding provides novel base line information for improving the efficiency in conservation and utilization of tea plant genetic resources. This method has been applied to assist tea researchers in California and Mississippi for tea cultivar identification. It can also be used by U.S. tea growers and U.S. industry for marketing premium tea products. Camellia oleifera is a member of the Theaceae family and is cultivated in Asia to produce tea oil. In the U.S., C. oleifera has been used as an ornamental plant but it has potential as a commercial oil seed crop for the southeast. Understanding the genetic diversity and relatedness among germplasm resources is useful for accurate varietal identification and efficient management of C. oleifera genetic resources. A set of single nucleotide polymorphism (SNP) markers was developed and tested in oil tea samples collected from U.S. and China. The validation led to the designation of 96 SNP markers that unambiguously identified all tested C. oleifera varieties. The SNP based genotyping also led to the differentiation of C. oleifera populations from different geographic origin. Plantain is giant perennial rhizomatous herb native to Southeast Asia and Western Pacific. Accurate identification of plantain germplasms is essential for efficient management, exchange, and use of plantain genetic resources. In collaboration with TARS, USDA and the national agricultural research institute of Côte-d’Ivoire, 294 SNPs from the International Banana Genomic database were evaluated and tested for plantain cultivar identification. The validation led to the designation of genotyping panel of SNP markers that unambiguously identified all tested plantain accessions and led to the differentiation of plantain populations. Coffee is an economically important perennial crop represents a $100+ billion-a-year global market. Globally over 20,000 coffee accessions have been collected and maintained in various repositories in different countries. The accessions have not always been properly maintained and accessions often arrive bearing limited information about their correct identity. A set of SNP markers was developed and tested for their ability to identify and separate coffee germplasm, including both Coffea canephora (robusta) and C. arabica cultivars. This method provides a powerful tool for the management of coffee genetic resources and breeding, where accurate and efficient cultivar identification is essential. Robusta coffee accounts for 40.0% of the global coffee production. However, Robusta coffee has been treated as bulk coffee and there is no method for cultivar classification. In collaboration with the National Agricultural Research Institute of Côte-d’Ivoire (CNRA), the genetic diversity in the primary genepool of C. canephora was analyzed. Results of this study clarified the genetic structure of C. canephora germplasm, which provides baseline information for the classification of Robusta coffee. In the last five years, this project has hosted 10 visiting scientists and Cacao Borlaug Fellows from major cacao and tea producing countries in Asia and the Americas. These achievements have led to the publication of 20 scientific papers in peer-reviewed international journals.


Accomplishments
1. Sorting teas by its DNA. Tea (Camellia sinensis) is an important commodity, representing a $40 billion-a-year global market (12 billion in the U.S.). Despite the economic importance, there is no easy means of classifying cultivated tea plants. Through collaborative research with tea scientists in Asian countries, ARS scientists in Beltsville, Maryland analyzed 760 tea types that originated from China, India, Vietnam, Laos, Myanmar, Thailand, Korea and Japan by cultivar. The genetics of the tea germplasm lined up into four groups, corresponding to small leaved China type, and three broad leaved Assam types: Indian, Chinese, and Cambodian. Each of the four genetic groups has its independent origin and site of domestication, and all can freely inter-bred, resulting in a wide array of hybrids in teas. This DNA grouping method was used to assist tea researchers in California and Mississippi to identify tea cultivars. The genetic grouping will also be used by U.S. tea growers and the U.S. tea industry for quality sourcing and for the marketing of premium tea products.


Review Publications
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.
Olasupo, F., Adewale, D., Aikpokpodion, P., Muyiwa, A., Bhattacharjee, R., Gutierrez, O.A., Motamayor, J., Schnell, R., Ebai, S., Zhang, D. 2018. Genetic identity and diversity of Nigerian cacao genebank collections verified by Single Nucleotide polymorphisms (SNPs): A guide to field genebank management and utilization. Tree Genetics and Genomes. https://doi.org/10.1007/s11295-018-1244-2.