Progress 03/01/02 to 02/28/07

Outputs
Progress Report Objectives (from AD-416) a) Plant Pathology: Optimize the artificial methods for screening resistance to Moniliophthora roreri, Ceratocystis fimbriata and Crinipellis perniciosa. Study the pathogenicity and the diversity of Crinipellis isolates. Study diversity and pathogenicity of Moniliophthora roreri populations. b) Germplasm evaluation: Nacional type clones (A types) Characterize with molecular markers cacao clones of Nacional type. The main goal this activity will be to identify the pure homozygous Nacional types with molecular markers. Pure Nacional clones serve as references for the Nacional flavor tests, as well as parents in the breeding programs. Molecular diversity analysis will be carried out on the 1996 collection (Coleccion Nueva) of Nacional clones. New collections could be made by searching for old trees showing molecular fingerprints of the Nacional type without taking into account agronomic measurements. Allen and Chalmers collections (B types) New plots will be established containing accessions of the Allen and Chalmers collections. New plots will be established from the original plants including those existing in the INIAP station of NAPO. Clones from these collections not existing in Ecuador but existing in other countries will be repatriated to complete the collection and to perform disease resistance screening. Disease resistance on these accessions will be evaluated for Moniliophthora roreri, Phytophthora sp., Ceratocystis fimriata and Crinipellis perniciosa. Other agronomic and quality traits will also be studied. These evaluations will combine field observations from the remaining plants in the original Allan and Chalmers plots and from artificial inoculation of clones or seedlings derived from original plots. The screening of grafted plants and seedlings from the Allen and Chalmers accessions using the early screening tests for witches broom will permit selection of parents for the establishment of new populations segregating for resistance. Germplasm Release Policy The research under this agreement will involve two different kinds of genetic resources: A: The Nacional types (including hybrid or pure Nacional genotypes) and B: the non-Nacional types. It is understood that the results of this research will be managed under two different policies: Clones or any varieties issued from this agreement from the study of genetic materials of the A type will be managed under the strict discretion of INIAP, as these materials possess particular national value. Those derived from type B will reside within the public domain. INIAP agrees to facilitate the sharing of scientific results from the utilization of type A individuals while permitting the dissemination of scientific results as well as clones or varieties derived from the utilization of type B individuals to the international community. Approach (from AD-416) Plant Pathology: Diversity analyses of Witches Broom: A diversity analysis with AFLP markers using isolates from different countries (included Ecuador) was performed in collaboration with University of Florida and showed the originality of the Ecuadorian isolates. Pathogenicity analyses will now be performed on a set of susceptible and resistant clones. Germplasm evaluations and breeding: Allen and Chalmers collections were evaluated for incidence of Witches Broom, Moniliosis and yield in Pichilingue. Thirteen individuals (LCT 368, EBC 148, TIP-1, UNAP-2, CUR-3, TAP-6, TAP-12, TAP-3, TAP-10, AMAZ-11, AMAZ-14, LCT-37 and LCT-46) were selected from these collections as parents for a recurrent selection program. The recurrent selection program mentioned above will be developed on three different groups or populations: a) Wilds or clones from the Allen and Chalmers collections, B) Known clones (clones known for their agronomic behavior) or selected from crosses already evaluated and C) Nacional type clones. Individuals within each group will be crossed among them and with a set of common clones to the three groups. Next crosses will depend on combining abilities displayed by individuals within each group. Many individuals from the Allen collection are absent in the Pichilingue station and are now being evaluated in the Napo station and moved to Pichilingue. Thirty individuals from the Allen and Chalmers collection from the quarantine station in Reading were also reintroduced and established in Pichilingue. F1s individuals from the following crosses EET6xEET6, EET61xEET166, EPCxEET196, EET95xSIL1, SIL5xCA12, SCA12xUnknown, were selected for yield and disease resistance for the above mentioned recurrent selection program. All individuals mentioned above were also fingerprinted and their identity verified with 13 microsatellites. The study of the Nacional clones originally included on this agreement will now be performed through CIRAD and financed with State Department funds. However, a group of Nacional clones will be crossed among them and represent one of the three populations of the recurrent selection program. Under the recurrent selection program from each of almost 200 crosses that are being performed, 50 individuals will be obtained. These individuals will be exposed to Witches Broom in a highly contaminated field. The 20 individuals showing the lower number of brooms will be planted in the field. Each pre-selected plant from each cross will be grafted four times and planted together with its clones. Significant Activities that Support Special Target Populations This report serves to document research conducted under a specific cooperative agreement between ARS and Estacion Experimental Tropical Pichilingue del Instituto Nacional Autonomo de Investigaciones Agropecuarias (INIAP) EET Pichilingue, Quevedo, Ecuador. Additional details of research can be found in the report for the parent project 6631-21000-012-00D Development of DNA markers associated with disease resistance in cacao. This serves as a final report for the project. The project is continuing under the new agreement numbered 6631-21000-012-13S. The Allen collection at the Napo Station has been duplicated in Pichilingue. Evaluation of the Chalmers collection for agronomic traits and molecular markers is complete and a publication is in preparation. To develop witches� broom (WB) resistant varieties, three segregating populations were made. These included within-population crosses of wild material, known clones, and Nacional types. Families from these crosses have been evaluated using the high inoculum pressure system. Correlation analysis between evaluations during the dry season and the rainy season demonstrated that there was no correlation between evaluations (r=0.14). The efficiency of the selection under high inoculum pressure was demonstrated by the difference in WB incidence between the different populations under study, especially between the known and Nacional population. The best cross within the Nacional group showed only 14% of healthy plants while in the known group the best cross showed 40%. This difference of 25% is quite important for selection purposes. A new crossing scheme was designed to recombine the most WB resistant clones (based on their combining ability for WB resistance presented here) with clones showing good combining ability for yield in INIAP and black pod in Africa. This new crossing scheme will be a source of very promising genotypes for future clone trials. Monitoring Activities: The research is monitored by site visits to inspect experimental field plots and meetings with the cooperator. In addition, telephonic and email communications occur as necessary.

Impacts
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Publications

Progress 10/01/05 to 09/30/06

Outputs
Progress Report 4d Progress report. This report serves to document research conducted under a specific cooperative agreement between ARS and INIAP EET Pichilingue, Quevedo, Ecuador. Additional details of research can be found in the report for the parent project 6631-21000- 012-00D Development of DNA markers associated with disease resistance in cacao. Of the original 436 accessions from the Allen collection 276 (63%) remain at the Napo Station and 27% of the accessions are duplicated in Pichilingue. Evaluation of the Chalmers collection for agronomic traits and molecular markers is complete and a publication is in preparation. To develop WB resistant varieties three segregating populations were made. These included within population crosses of wild material, known clones and Nacional types. Families from these crosses have been evaluated using the high inoculum pressure system. Correlation analysis between evaluations during the dry season and the rainy season demonstrated that there was no correlation between evaluations (r=0.14). The efficiency of the selection under high inoculum pressure was demonstrated by the difference in WB incidence between the different populations under study, especially between the Known and Nacional population. The best cross within the Nacional group showed only 14% of healthy plants while in the known group the best cross showed 40%. This difference of 25% is quite important for selection purposes. A new crossing scheme was designed to recombine the most WB resistant clones (based on their combining ability for WB resistance presented here) with clones showing good combining ability for yield in INIAP and Black Pod in Africa. This new crossing scheme will be a source of very promising genotypes for future clone trials.

Impacts
(N/A)

Publications

Progress 10/01/04 to 09/30/05

Outputs
4d Progress report. This report serves to document research conducted under a specific cooperative agreement between ARS and INIAP EET Pichilingue, Quevedo, Ecuador. Additional details of research can be found in the report for the parent project 6631-21000- 012-00D Development of DNA Markers Associated With Disease Resistance in Cacao. Evaluations of the Nacional type germplasm continued. Weather favored more disease incidence in 2004 and the clones CCAT 46-48 and CCAT 45-83 were identified as the most productive in the collection. Evaluation of the Chalmers Collection has identified a valuable breeding resource for witches broom (WB) resistance. Clones TAP12, TIP1, TAP6, TAP10 and TAP11 are very resistant to the disease and this source is believed to be different from the SCA source of resistance. In the Allen Collection clones LCT 278 and LCT 254 have been identified as having tolerance to WB. In the breeding trials 53 hybrid families have been evaluated for WB resistance using the seedling inoculation method; however, the correlation with field resistance is not encouraging.

Impacts
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Publications

Progress 10/01/03 to 09/30/04

Outputs
4. What were the most significant accomplishments this past year? D. Progress Report. This report serves to document research conducted under a specific cooperative agreement between ARS and INIAP EET Pichilingue, Quevedo, Ecuador. Additional details of research can be found in the report for the parent project 6631-21000- 012-00D, Development of DNA markers associated with disease resistance in cacao. Field evaluation continued on 67 accessions of the Collection Genotipos de Cacao Nacional (GCN) and 100 accessions of the Collection Selection Nacional Sabor 'Arriba' (SNA). Phenotypic and disease data were collected to estimate the yield for each accession. Budsticks from 40 cacao accessions from the original Allen and Chalmers collections were established in the Estacion Experimental Napo Payamino in July. These were grafted, and currently there are 120 plants in the nursery. These will be planted next January. The main purpose of this activity is to obtain duplicates of the original trees. Accessions from both collections already in the field at Pichilingue were confirmed to prevent mistakes when using the trees for propagation and data collection. Morphological characterization work on the trees from the original Allen and Chalmers collection at the Estacion Experimental Napo Payamino continues at a good pace. Results will be shown in detail in the next progress report. Leaf samples of the clones SCA-6, SCA-12, and SIL-1 were sent to the USDA-Miami laboratory for SSR fingerprinting to confirm identification. The morphological and phenotypic characterization is continuing as is the molecular analysis (samples have already been sent to Miami). Breeding Strategies: 1. Accessions collected from the wild (ie. Allen and Chalmers accessions and others): An incomplete diallel design was chosen for this population. A total of 67 crosses have been carried out so far. Incompatibility problems were detected in nine crosses. The remaining crosses have produced 315 pods which are developing in the field. It is estimated that this activity is 65% completed (Figure 1). 2. Known accessions: A factorial design was chosen for this diverse group and pollinations are still ongoing. Progeny production has been difficult due to absence of flowers on some clones (plants 2057, 2367 and 2416 used as male parent plants and SIL-1 and EET-58 used as female parents). A high incidence of cherelle wilt also has affected the development of pods. We now have 370 pods corresponding to 23 crosses developing in the field. The maximum number of pods per cross is 35 and the minimum is six. It is estimated that this activity is 80% completed (Figure 1). 3. Nacional type accessions: Six trips have been made to Las Brisas Farm and La Gloria Farm located in the Province of Manabi. During these trips pollen from Pichilingue trees was taken to pollinate selected Nacional trees in the aforementioned farms. A total of 21 crosses have been completed producing 45 pods which are under development. Cherelle wilt incidence has caused the loss of some pods. Nursery and field site preparation: Sowing of seeds from new hybrid progenies is underway in the nursery. To accommodate the progeny trials, we have prepared approximately 18 hectares, and the planting of shade trees for the cacao is currently underway. Last September, work started to clear out some additional 20 hectares of land. This was an abandoned pasture land, and it will be used to plant the new progenies being created within the project, as well as to plant observation plots with new promising material. In total, 38 hectares of evaluation plots will be planted eventually at the Pichilingue location. Ortets selection: Another group of seedlings, created some 52 years ago, were included as a project activity in December 2002. The parents of these seedlings are mostly of the Amazonian type, and earlier observations suggested an interesting potential for productivity and disease resistance. Pod production ranges from 100 to 250 per tree on selected trees. There are some trees showing low WB incidence, and no WB incidence has been detected on one tree that has a very good pod load. Some of the trees which have been identified are already being multiplied. Plant Pathology: 1. Compilation/organization of historical disease data on old cocoa progenies: Data tabulation for the SCA-12 x SIL-5 family has been completed. Data tabulation for the EET-95 x SIL-1 family will be completed by the end of the year (see Table 1). Data tabulation for SCA-6 x SIL-5 family will start in January 2004 and is expected to be completed by March of the same year. Table No.1. Actual situation of data tabulation for past records of the families under study. Family Data tabulated To be tabulated EET-95 x SIL-1 1970-1978 1979-1985 SCA-12 x Unknown 1970-1985 --- SCA-6 x SIL-1 1971-1985 --- SCA-12 x SIL-5 1971-1985 --- SCA-6 x SIL-5 --- 1971-1985 2. Rehabilitation and evaluation of old cocoa progenies: All cocoa progenies have been evaluated regularly, registering healthy and diseased pods as well as fresh bean weight per tree. Pruning and counting of number of brooms (vegetative and cushion) have been performed as planned in July-August for SCA-12 X Unknown, SCA-6 x SIL-1, SCA-12 x SIL-5, and SCA-6 x SIL-5 family. EET-95 x SIL-1 family - the largest population - has not been pruned or evaluated for WB infection yet; it is planned for next December-January. These data, together with the historical records, would allow the estimation of the stability of the family characters - mainly resistance - over time. The identification of promising trees within these families for their potential for breeding or commercial purposes has already begun, and more details on this will be shown in the next progress report. Mapping for QTL detection of disease resistance traits will be performed in these populations once phenotypic data and marker analysis are completed. 3. Rehabilitation of the AIS (Automated Inoculation System): The facility for the production of spores, needed to carry out the screening tests for WB resistance, was completely rebuilt. Reduced capacity, due to structural deterioration and difficulties with the irrigation system, caused failures in basidiocarp production. A new metallic structure was set up with a new roof and irrigation system, and a screen now covers the new facility. It is functioning now, and a significantly better performance of basidiocarp production is expected.

Impacts
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Publications