1 / 30

SSR Analysis of the USDA-ARS Cacao collection

SSR Analysis of the USDA-ARS Cacao collection. Brian M. Irish USDA-ARS Tropical Agriculture Research Station Mayaguez, Puerto Rico. Management of Tropical/Subtropical Genetic Resources and Associated Information. Horticulturist/Plant pathologist

kyros
Download Presentation

SSR Analysis of the USDA-ARS Cacao collection

An Image/Link below is provided (as is) to download presentation Download Policy: Content on the Website is provided to you AS IS for your information and personal use and may not be sold / licensed / shared on other websites without getting consent from its author. Content is provided to you AS IS for your information and personal use only. Download presentation by click this link. While downloading, if for some reason you are not able to download a presentation, the publisher may have deleted the file from their server. During download, if you can't get a presentation, the file might be deleted by the publisher.

E N D

Presentation Transcript

  1. SSR Analysis of the USDA-ARS Cacao collection Brian M. Irish USDA-ARS Tropical Agriculture Research Station Mayaguez, Puerto Rico

  2. Management of Tropical/Subtropical Genetic Resources and Associated Information • Horticulturist/Plant pathologist • Bananas, plantains, cacao, sapote, nispero, Annona spp., Garcinia spp., bamboo, mango, quenepa (Spanish lime) • Acquire, propagate (disease-free), maintain, characterize and distribute • Genetic diversity • Characterize • Phenotypic, Molecular • All information is incorporated in our GRIN database • All accessions are propagated clonally by means of divisions, cuttings, air-layers or grafting • 2 field/1 lab technicians, 1 Information technologist, 1 gardener, 3 part time lab/field technicians, 1 graduate/1 undergraduate students

  3. Cacao or Cocoa • Industry (billion dollar industry in the U.S.) • Cosmetics, soaps • Chocolate (bars, powder) • Large food processors: ADM/Barry Callebaut • Confectionary industry • Mars, Hershey's, Cadbury, Nestle and many others • Other industries that are directly related in chocolate making • Sugar, dairy, nuts • Replicated and characterized collection with freely available germplasm

  4. Cacao collection at TARS • Theobroma cacao • 154 accessions/clones (924) • In the process of introducing ~50-100 accessions • Breeding/selection programs at CATIE, EET-Pichilingue, CRU, U. Reading, Brazil and USDA • Evaluation • Number, weight, color, size of pods, number and weight of seed, chocolate quality, disease and insect resistance • Due to the nature of how the crop is propagated and the length of time it has been maintained, errors in propagation have accumulated (world) • A set of 15 microsatellite markers have been used to fingerprint cacao worldwide.

  5. Accession -AC T 1/1. From 9/6/07-9/14/07 Day 1 Day 2 Day 3 Day 4 Day 5 Day 6 Day 7 Day 8 Day 9

  6. April 8th, 2008 6 1 2 5 3 4

  7. Microsatellites (SSRs) • Short repetitive sequences in Eukaryotes in non coding regions of the genome • Highly variable and inherited in Mendelian fashion • Developed at CIRAD and USDA • On different chromosomes (10) and separate linkage groups • High allelic diversity in cacao genotypes • mTcCIR – Microsatellite Theobroma cacao CIRAD

  8. Table 3.Characteristics and summary statistics for the 15 International set of microsatellite primers utilized for fingerprinting the USDA-ARS Tropical Agriculture Research Station cacao (Theobroma cacao) collection.

  9. Clone #101-TARS 23Heterozygous and consistent for all 6 plants

  10. Clone #42-EET 53Heterozygous/homozygous and inconsistent across the 6 plants

  11. Analysis (continued) • Mislabeling • Homonymous or ‘intra-plant’ error • Synonymous or ‘duplicate’ error • Non-match error • Synonymous multi-locus fingerprint profiles condensed into a single profile • 139 unique profiles used for subsequent analysis

  12. Accessions grouped into four main clusters • Based on geographic and common genetic background • Trinitarios/Criollos • Lower A. Forasteros • Upper A. Forasteros • Hybrids

  13. 0.00 0.68 0.34 Genetic Distance Coefficient CC10 B EET353[ECU] B EET381[ECU] P10[MEX] A P22[MEX] P43[MEX] RIM105[MEX] RIM13[MEX] A RIM15[MEX] RIM2[MEX] RIM34[MEX] RIM41[MEX] RIM48[MEX] RIM52[MEX] RIM6[MEX] RIM75[MEX] RIM78[MEX] RIM10[MEX] SGU69 ICS39 POUND7[POU] B SIC72 B SC49[COL] GS46 UF668 ICS40 GS7 ICS29 UF601 Mislabeling: e.g., RIM group • RIM identical (SSRs) • Yellow/green highlighted • (A/B) ending • More than one genotype • e.g., RIM13 [MEX] • Several clones don’t belong in this group • CC10, EET 353, SGU69

  14. RIM 2 [MEX] RIM 6 [MEX] RIM 10 [MEX] RIM 13 [MEX] A RIM 2 [MEX] RIM 15 [MEX] RIM 34 [MEX] RIM 41 [MEX] RIM 48 [MEX] RIM 52 [MEX] RIM 75 [MEX] RIM 105 [MEX] P 10 [MEX] P 22 [MEX] P 43 [MEX] RIM 13 [MEX] B RIM 30 [MEX] EET 381 EET 353 SGU 69

  15. Table 2. Fourteen synonymous groups (including 49 accessions) within the USDA-ARS Mayaguez cacao collection identified by microsatellite DNA analysis. Accessions in the same synonymous set shared identical multi-locus microsatellite profiles.

  16. Table 1. Name, source and results of identification verification (RIV) of cacao accessions maintained at the USDA-ARS Tropical Agriculture Research Station in Mayaguez, PR.

  17. Summary • Multilocus profiles, dendrogram, assignment test and reference genotypes help sort out mistakes • Allelic diversity proportional to CATIEs and not very different for major alleles • Genetic redundancy does exist • Shannon’s diversity index • Rationalization of collection is an option, but only after field characterization • Agronomic traits

  18. THANK YOU. QUESTIONS?

More Related