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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #444058

Research Project: Genotypic Characterization of Genetic Resources for Cacao, Coffee, and Other Tropical Perennial Crops Economically Important to the United States

Location: Sustainable Perennial Crops Laboratory

Project Number: 8042-21000-303-000-D
Project Type: In-House Appropriated

Start Date: Mar 14, 2023
End Date: Mar 13, 2028

Objective: Objective 1. In collaboration with domestic and international cooperators, characterize genotypically and evaluate phenotypically priority cacao and coffee genetic resources, breeding stocks, and cultivars, and disseminate data via the project’s website, genetic resource, or genomic databases, and GRIN-Global. Sub-Objective 1A: With NPGS and international cooperators, assess genetic integrity, diversity, and population structure of coffee germplasm collections in Hawaii, Puerto Rico, Costa Rica, Ivory Coast, and other major coffee collections in Africa and the Central America national Institutions. Sub-Objective 1B: Evaluate cacao genetic resources for drought tolerance to identify promising clones for breeding drought-tolerant varieties. Sub-Objective 1C: Analyze candidate genes conferring core stress response to assess adaptive genetic variation in cacao genetic resources. Objective 2: Conduct research to develop genomic tools and approaches and then apply them to improving the efficacy of genetic resource management of other tropical perennial crops, such as sugarcane, tea, Annona, Garcinia, peach palm, pitaya, sapodilla, and sapote. Sub-Objective 2A: Develop draft genomes for other priority tropical crops, including mangosteen (Garcinia mangostana), sapodilla (Manilkara zapota), Mamey sapote (Pouteria sapota), egg fruit (Pouteria campechiana) and Spanish lime (Melicoccus bijugatus). Sub-Objective 2B: SNP marker characterization of genetic resources of other priority tropical crops maintained in US national germplasm collections, including sugarcane (Saccharum spp), tea (Camellia sinensis), longan (Dimocarpus longan), rambutan (Nephelium spp.), peach palm (Bactris gasipaes), Pouteria spp., pitaya (Hylocereus spp.), Garcinia spp and Annona spp.

Firstly, the project will evaluate and characterize priority genetic resources of coffee and cacao in collaboration with US and international genebank curators and breeders. The primary focus will be on enhancing the genetic integrity of C. arabica and C. canephora resources held in ex situ collections in various locations worldwide, including Hilo (Hawaii), Mayaguez (Puerto Rico), CATIE (Costa Rica), CNRA (Ivory Coast), as well as other African, Asian, and Latin American countries where Arabica and Robusta coffee genetic resources originated and developed. To achieve this, SNP genotyping will be used to identify and eliminate off-types and genetic redundancy in the collections. Subsequently, a global analysis of genetic diversity and population structure will be performed. The aim of cacao germplasm evaluation is to assess drought tolerance in diverse agroecology across tropical America. Research will be conducted with collaborating institutions in Peru and Brazil. Newly collected wild cacao accessions, traditional varieties, and international clones, will be evaluated to identify promising genotypes that can withstand drought stress. Superior parental genotypes with better drought tolerance will be integrated into breeding programs. Adaptive genetic variation in wild cacao populations will be analyzed using candidate genes that confer core stress response. Genotyping-By-Sequencing (GBS) will be conducted on the evaluated wild cacao populations. SNPs that are adaptive or maladaptive in response to climate change will be identified. Secondly, the project will address the lack of genomic resources and genetic diversity information of priority tropical perennial crops that have been under-investigated. In collaboration with the University of Nebraska-Lincoln (UNL), the project will develop high-quality genome for five under-studied species, including mangosteen, sapodilla, sapote, egg fruit, and Spanish lime. Once the genome assemblies are developed, gene prediction and genome annotation will be performed. RNA-Seq data will be generated and used as transcribed gene evidence to further improve the accuracy and reliability of the annotations. Based on the draft genomes of these tropical specialty crops, the project will develop SNP markers for these species through whole-genome resequencing. The SNPs then will be evaluated for their and applied for germplasm identification and genetic diversity analysis. Additional species for SNP discovery and diversity analysis include tea, peach palm, pitaya, and Musa spp. The resulting information will provide tropical crop researchers with valuable tools for future conservation and crop improvement programs. All sequences, genome assemblies, annotation data, genotyping data, and analytic results are free to the public after the publication of relevant research. Public awareness of the resources will be through relevant publications, conference, and seminar presentations, NCBI, and USDA GRIN-Global database.