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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

2017 Annual Report

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.

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
In FY 2017, progress was made in understanding spatial distribution of genetic diversity in the Upper Amazon. In collaboration with the Tropical Crop Institute (ICT), Peru and other collaborators in the chocolate industry, we analyzed newly collected leaf samples from the Yavari river and bean samples from the Jurua river, Brazil. The single nucleotide polymorphism (SNP) analytical result revealed a new germplasm group, which positioned in between the reported groups of Iquitos and Purus. This result suggests that future collecting expeditions in this area will be needed in order to fill a gap of genetic diversity in current international cacao genebanks, as well as in national collections in Peru. This information will be used by cacao researchers to improve their understanding about distribution of genetic diversity in the primary gene pool and facilitate conservation and use of cacao genetic resources. Progress was made in molecular and phenotypic characterization of traditional variety of cacao from Cusco, Peru. In collaboration with San Antonio Abad del Cusco National University, National Agriculture Research Institute of Peru and Bioversity International, we genotyped a germplasm collection of Chuncho cacao from the Apurimac, Ene, and Urubamba valleys and analyzed organoleptic variation in this collection. The result confirmed that Chuncho cacao is native to Southern Peru and most of the Chuncho trees were genetically related to the germplasm groups of Madre de Dios and Ucayali, but the variety has its own distinguished genetic identity. Large diversity was found in this collection in terms of pulp flavors and aromas, which is associated with fine flavor bean quality of Chuncho cacao. The result demonstrates its potential to be used to produce fine flavor cocoa for premium chocolate in international market. This information will be used by cacao researchers to improve their understanding about distribution of genetic diversity in the primary gene pool and facilitate conservation and use of cacao genetic resources. Progress was made in assessing genetic diversity of cacao in Jamaica. In collaboration with the University of West Indies at Mona, Jamaica, we analyzed cacao germplasm maintained at the Orange River Agricultural Research Station in St. Mary and Montpelier Agricultural Research Station in St. James as well as from farmer’s fields in St. Thomas. Based on SNP genotyping data, pedigree analysis showed that the cacao germplasm in Jamaica are composed of Trinitario and various hybrids derived between Trinitario and Upper Amazon Forasteros groups including Parinari, Iquitos Mixed Calabacillo (IMC) and Scavina (SCA). However, these hybrids were derived from a very small number of parental clones. Moreover, ‘United Fruit’ (UF) clones, the important source of resistance for Frosty pod disease, was not found in the Jamaica germplasm. Frosty pod disease has been recently found in Jamaica. The present study, however, suggests that better host resistance needs to be incorporated into the Jamaica cacao germplasm. Progress was made in molecular characterization of the ‘United Fruit’ (UF) clones, which were developed by the United Fruit Company in Costa Rica, and they represent one of the earliest groups of improved cacao germplasm in the world. Some of these UF clones have been used as key progenitors for breeding resistance/tolerance to Frosty Pod and Black Pod diseases in the Americas. However their utilization in Asia and Africa has been minimal, partially due to the lack of information about their genetic background. Accurate information on the identity and background of these clones is important for their effective use in breeding. We analyzed their deoxyribonucleic acid (DNA) fingerprints based on SNPs and verified their integrity. Our result showed that approximately one third of the UF clones are duplicates and can be eliminated from the collection. Pedigree analysis showed that the UF clones were mainly composed of Trinitario, ancient Nacional clones and hybrids between ancient Nacional and Amelonado. This result filled the information gap about the UF clones and will be used by scientists and extension specialists to improve their efficiency in management of cacao genetic resources. Progress was made in cross-specific amplification of SNP markers in for the identification of abaca (Musa textilis Nee) germplasm. Abaca is a diploid Musa species native to the Philippines, where it is cultivated as an important fiber crop. In the present study, we evaluated 192 putative SNP markers developed for banana and plantain, using 180 abaca germplasm accessions maintained in the Philippine Fiber Industry Development Authority, Philippines. A high level of genetic redundancy was found in the national collection of Abaca germplasm. Only 60% of the analyzed accessions have unique SNP genotypes. However, some duplicate groups have clearly different phenotypic/morphological characters (e.g. pigments), in spite of their identical SNP profiles. This result suggests that somaclonal mutation played significant role in the genome evolution and clone stability of Abaca. Our result demonstrated that the germplasm collection of Abaca can be significantly reduced based on the SNP profiles and morphological characteristics. The selected SNP markers also showed a high level of polymorphism in Musa acuminata and Musa balbisiana, demonstrating their potential usefulness in genotype identification for other related Musa species, including banana and plantain. Progress was made in analyzing genetic diversity in tea germplasm from India. Assam is part of the primary gene pool of tea. Assam is also a major tea producing state in India, which contributes more than 53% of Indian’s annual production of tea. In 2017, we collaborated with scientists from Tocklai Tea Research Institute (TTRI) at Assam and characterized their tea germplasm collection. Using SNP markers developed in Beltsville, Maryland, we revealed the population structure in the Assam tea germplasm and clarified the relationship between Indian Assam population and Chinese Assam population. Our result also demonstrated the hybrid feature of Dajering tea, which was derived from crosses between introduced Chinese small leaf tea and Indian Assam tea. This information will be used by tea researchers to improve their understanding about genetic diversity in the primary gene pool and facilitate conservation and use of tea genetic resources. The information will also be used by the US tea industry for marketing premium tea products.


Review Publications
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.
Cosme-Reyes, S.M., Cuevas, H.E., Zhang, D., Oleksyk, T.K., Irish, B.M. 2016. Genetic diversity of naturalized cacao (Theobroma cacao L.) in Puerto Rico. Tree Genetics and Genomes. doi: 10.1007/s11295-016-1045-4.