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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Sustainable Perennial Crops Laboratory » Research » Research Project #436780

Research Project: Molecular Characterization of CATIE International Coffee Collections

Location: Sustainable Perennial Crops Laboratory

Project Number: 8042-21000-303-004-S
Project Type: Non-Assistance Cooperative Agreement

Start Date: Jun 15, 2019
End Date: Jun 15, 2024

This collaboration will assist CATIE to improve the genetic integrity, reduce genetic redundancy, analyze genetic diversity, evaluate horticultural traits and enhance the use of the coffee germplasm, which are housed in CATIE’s living germplasm collections. Results of this project will contribute to more efficient management of coffee germplasms, sharing of accurate information among users, better use of germplasm for varietal development through the identification of horticultural traits, such as new sources of resistance and tolerance to biotic and abiotic stresses and quality attributes. The result of molecular characterization and germplasm evaluation of the CATIE coffee collection will be utilized by other USDA ARS units to develop an ARS coffee collection through the strategic acquisition of specific genetically diverse coffee accessions from the CATIE collection.

Verify genotype identity of CATIE clones. Leaves of the coffee accessions in the CATIE living germplasm bank will be sampled following the guidelines established by SPCL and used for DNA extraction. The samples will be sent to USDA/ARS, Beltsville Agricultural Research Center (BARC)/Sustainable Perennial Crops Laboratory (SPCL) or a designated third party for DNA extraction. The DNA samples will be fingerprinted using Single-Nucleotide Polymorphism (SNP) markers. Off-types in the germplasm bank will be identified based on the DNA profiles. Parentage analysis will be applied to confirm the pedigree relationship in case the parental combinations are known. Standard SNP profiles will be established for each of these clones. Once the standard SNP profiles are established, the SNP-based genotype verification can be used as a routine procedure in CATIE to improve and monitor the accuracy of varietal dissemination. Develop methods for marker-assisted evaluation of coffee germplasm. Based on the genetic diversity and population structure in the CATIE coffee genebank, a subset of samples will be selected and fingerprinted using Genotyping by Sequencing or coffee SNP chip. Genome-wide association studies (GWAS) will be performed to detect quantitative trait loci (QTLs), and genomic selection (GS) will be performed to establish associations between SNPs and phenotypes to incorporate genome-wide markers to assist germplasm evaluation.