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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

2015 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 2015, progress was made in analyzing the mating system and outcrossing rate in natural populations of cacao in the Amazon rainforest. Wild cacao trees typically occur in low population densities and rely on insects for cross-pollination. It is of conservation interest to understand the role of the mating system in the formation of the current distribution of cacao genetic diversity in its primary gene pool. Using Single Nucleotide Polmorphism (SNP) markers, we comparatively analyzed cacao samples from Ecuador and French Guiana, both of which were collected from natural populations. A significant level of spatial structure and selfing (>10%) was observed in both populations, in spite of the fact that the mating occurred mainly via outcrossing. This information will be used by researchers and policy makers to design conservation strategy for wild cacao. It can also be used by breeders and agronomists for cacao cultivar deployment, as well as for production of cacao planting material in bi-parental seed gardens in Asia and Africa. NP301 C2 PS2B Progress was made in the collecting expedition from the Putumayo River along the border area of Brazil and Peru. Putumayo river is the last major river system in our sampling plan for Peru, and no previous expedition has covered it geographically. In collaboration with the Tropical Research Institute, Peru, a total of 71 wild trees were sampled from the north, central and southern parts of the river. This new collecting expedition fills a major geographical gap for the diversity survey of wild cacao in the Amazon. This information will be used by researchers to reduce diversity gap in ex situ national and international cacao collections. NP301 C2 PS2B Progress was made in using single nucleotide polymorphism (SNP) genotyping method for genotyping of West African cacao germplasm. In collaboration with the Ghana Cacao Research Institute, International Institute of Tropical Agriculture and World Cocoa Foundation, a total of 2,551 trees maintained in six seed gardens, breeders' clonal collections and farmers’ fields in Ghana were genotyped. The results provide an overall assessment regarding the effect of clone mislabeling on the efficiency of variety recommendations in cacao and reinforces the need to accurately identify contamination in hybrid progenies. The results provide a strong basis for improving the efficiency in cacao germplasm management and variety development process, as well as mobilizing available certified, improved varieties to cacao farmers in West Africa. Scientists, plant breeders and farmers across West Africa will use this information. Through the same collaborative framework, we used SNP markers to assist the quality control in seeds garden in Nigeria. A total of 450 seedlings from four government seed gardens in Nigeria were analyzed. False hybrids, either due to the unwanted cross pollination or selfing were identified. These results provide scientific baseline information for monitoring the quality of cacao seeds production in Nigeria. NP301 C2 PS2B In collaboration with USDA ARS Tropical Diseases and Germplasm Station in Hilo, Hawaii, we developed SNP markers for pineapple (Ananas comosus) germplasm management. Pineapple is a tropical perennial herbaceous fruit crop with great economic importance. The crop is cultivated in all tropical and subtropical countries and ranks third in production among tropical fruits, following banana and mango. Accurate cultivar identification is essential for germplasm management and breeding. We developed a set of single nucleotide polymorphism (SNP) markers and tested their efficacy in one of the USDA pineapple collections, which is one of the largest pineapple collections in the world. The validation led to the designation of 40 SNP markers that unambiguously identified all tested pineapple varieties. The SNP based genotyping led to the identification of a significant amount of genetic redundancy maintained in this collection. This information will be used by researchers, pineapple producers and industry to improve the accuracy in germplasm management, breeding, and plant material propagation. NP301 C2 PS2B Progress was also made in the development of SNP markers for accurate identification of coffee cultivars. Coffee is a popular beverage and the world’s most traded commodity apart from oil with a current global retail value of US $75 billion. We designed a set of single nucleotide polymorphism (SNP) markers based on the expressed sequence tag (EST) found in coffee genomic databases, and validated these SNP markers in a diverse group of coffee varieties, including both arabica (Coffea arabica) and robusta (Coffea canephora). This method can also accurately differentiate green beans of arabica and robusta coffee based on a single coffee bean. It can also accurately identify each cultivars of Robusta coffee. This tool is highly useful for the management of coffee genetic resources and breeding, where accurate and efficient genotype identification is essential. This method also provides a robust tool for quality control of raw material for the coffee industry.

1. SNP fingerprinting cacao germplasm collections from Ghana. The cacao germplasm collections in Ghana houses most of the cacao germplasm utilized by all of the cacao improvement programs in West Africa but this collection has significant amount of mislabeling that prevents efficient use of these genetic materials. In collaboration with the Ghana Cacao Research Institute, International Institute of Tropical Agriculture, and the World Cocoa Foundation, a total of 2,551 trees maintained in seed gardens, clonal collections and from farmers’ fields in Ghana were genotyped using SNP markers developed by ARS Scientists in Beltsville, Maryland. The results provided an overall assessment of mislabeling on the efficiency in cacao and reinforced the need to accurately identify hybrid progenies. The results provide a strong basis for improving the efficiency of cacao germplasm management and varietal development processes in West Africa. These findings will help rectify germplasm collection identification problems that have hampered cacao improvement programs in West Africa since the introduction of cacao in the late 1800s and will be used by scientists, plant breeders and farmers.

Review Publications
Padi, F.K., Ofori, A., Takrama, J., Djan, E., Opoku, S.Y., Bhattacharjee, R., Motamayor, J., Zhang, D. 2015. The impact of SNP fingerprinting and parentage analysis on the effectiveness of variety recommendations in cacao. Tree Genetics and Genomes. DOI:10.1007/s11295-015-0875-9.
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.
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.
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.