Location: Sustainable Perennial Crops Laboratory
Project Number: 8042-21000-303-005-S
Project Type: Non-Assistance Cooperative Agreement
Start Date: Jun 30, 2019
End Date: Jun 29, 2024
This collaboration will assist CNRA in improving the genetic integrity, reduce genetic redundancy, analyze genetic diversity, evaluate horticultural traits and enhance the use of the coffee germplasm, which are housed in CNRA’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. This project will generate information about genetic diversity in the CNRA coffee collection, which will be utilized by other USDA ARS units to strategically introduce diverse coffee accessions from CNRA for the development of an ARS coffee collection.
Assess genetic integrity and genetic diversity in coffee germplasm: Leaves of the coffee clones in the CNRA living germplasm bank will be sampled following the guidelines established by the ARS Sustainable Perennial Crops Laboratory (SPCL) and used for DNA extraction. DNA extraction will be carried out at CNRA Central Biotechnology laboratory. The DNA samples will be sent to ARS and fingerprinted using SNP markers. Mislabeled accessions in the germplasm bank will be identified and pedigree relationships will be verified based on SNP profiles. Standard SNP profiles will be established for each of these coffee accessions. The SNP-based genotype verification will be used as a routine procedure in CNRA to improve and monitor the accuracy of varietal propagation and dissemination. The SNP data will also be used to analyze genetic diversity in the genebank holdings. Develop methods for marker-assisted evaluation of coffee germplasm: Based on the genetic diversity in the CNRA coffee genebank, a subset of samples will be selected and fingerprinted using Genotyping-by-Sequencing (GBS) or coffee SNP chip. Genome-wide association studies (GWAS) will be performed to detect quantitative trait loci (QTLs) of phenotypic traits. Genomic selection (GS) will be performed to establish associations between SNP markers and phenotypes to incorporate genome-wide markers to assist germplasm evaluation. The result of marker-trait relationship will then be validated in different germplasm groups and at different locations in CNRA.