Defining Thresholds for Identifying Genetically Redundant Accessions within CIAT's Global Cassava Collection
Monica Carvajal, Gustavo Cardona, Peter Wenzl
International Center for Tropical Agriculture (CIAT), Genetic Resource Progr., Colombia
Crop diversity is critical for food security, climate adaptation, dietary quality and poverty reduction. Cassava is a critical source of carbohydrates for ~500 million people in Africa and elsewhere. The International Center for Tropical Agriculture conserves the globally largest collection of cassava (Manihot esculenta) and its wild relatives (6,155 accessions). The collection, currently conserved in vitro under slow-growth conditions, will be cryopreserved once genetically redundant accessions have been removed. We conducted an experiment to determine thresholds for identifying genetically redundant accessions by genotyping technical and biological replicates from a group of accessions. Twenty-five cassava accessions were selected for DNA extraction. Three types of replicates were analysed to quantify genetic distances (Gd): (i) different individuals from the same accession “Individual-Reps”, (ii) different DNA samples extracted from the same individual “Extract-Reps”, and (iii) the same DNA sample analysed twice “DNA-Reps”. In addition, 17 accessions were randomly selected from a core collection to compare Gd between replicate pairs using a more diverse group of accessions. DNA samples were analysed using the DArTseq genotyping platform (DArT-PL) to generate dense profiles of SNP and ‘in-silicoDArT' markers (the latter being the presence/absence of sequence-tags in the genome representation). Marker identification and allele-calling were performed using DS14 software (KDCompute plug-in system). A total of 188 samples and 114,545 markers were obtained (59,519 SNP/55,026 ‘in-silicoDArT). SNP markers were used to compute distance matrices after applying additional marker-specific quality filters, such as sequencing depth, call rate and polymorphism content. The variation in the average Gd between replicate pairs (Individual-Reps, Extract-Reps and DNA-Reps) was used as a criterion to adjust marker-quality thresholds to retain a maximum number of markers while producing close-to-zero genetic-distance estimates for replicate pairs. The thresholds values determined in this study will be used to identify a genetically non-redundant subset of DArTseq-characterised accessions for cryopreservation to reduce long-term conservation costs.
Keywords: Cassava, genetic diversity, genotyping
Contact Address: Monica Carvajal, Intern. Center for Tropical Agriculture (CIAT), Genetic Resource Program, Km 17 recta Cali Palmira, Cali, Colombia, e-mail: m.carvajalcgiar.org