COMPREHENSIVE MOLECULAR GENETIC CHARACTERIZATION AMONG WEST

Transcription

1 COMPREHENSIVE MOLECULAR GENETIC CHARACTERIZATION AMONG WEST AFRICA AND BRAZIL LOCALLY ADAPTED POULTRY BREEDS: CREATION OF A BASIS FOR GERMPLASM EXCHANGE Report Call For Report Call for final report Africa-Brazil Projects funded in the 2011/12 Report Status Submitted Title COMPREHENSIVE MOLECULAR GENETIC CHARACTERIZATION AMONG WEST AFRICA AND BRAZIL LOCALLY ADAPTED POULTRY BREEDS: CREATION OF A BASIS FOR GERMPLASM EXCHANGE ID 2993 Thematic Area Productivity Enhancing Technologies Reporting period 09 Jan Jun 2015 Co-leader Institutions Obafemi Awolowo University & EMBRAPA Project Co-leaders Mrs. Ofelia Omitogun & ARTHUR MARIANTE Type of African Co-leader Institution UNIVERSITY Summary In this study, local chicken breeds with different types of feathers were collected in five Nigerian regions (South SS; Southwest SW; North NC; Northwest NW; Southeast SE), as well as the Shika-Brown type. Samples from 11 Brazilian chicken lines were included, provided by Embrapa Swine and Poultry and Embrapa Genetic Resources and Biotechnology, which were collected in two regions (South and Midwest). The TT is a meat-type paternal broiler line that has been selected for over 20 years. LLc and PPc are a paternal and maternal broiler lines, respectively, maintained without selection. CC and CCc are white eggtype lines, maintained with and without selection, respectively. The GG is a brown egg-type line. Cobb is a commercial broiler line and Indio is a backyard chicken collected in Southern Brazil. The GIG, GC and GIU are backyard chickens collected in different properties in Midwestern Brazil. A total of 16 chicken microsatellite markers was used to evaluate each sample. A region of 450 bp from D-Loop mitochondrial DNA was chosen to evaluate each sample. For large scale SNP genotyping, 112 samples from the two countries were selected, being 50 from all regions of Nigeria and 62 from CC, GG, Indio and TT Brazilians populations. The results suggest that ex situ conservation strategies for both countries (e.g. gonads vitrification) should be implemented in each country in order to preserve the genetic groups until, aiming at future germplasm exchange events. Country(ies) of Implementation NIGERIA and BRAZIL Project Results In this study, Nigerian s chickens with different types of feathers were collected from five regions (South; Southwest; North; Northwest; Southeast and Shika- Brown, total N=136) and Brazilian s chicken were collected from eleven lines/ genetic groups collected in the Midwest and South (total N= 717). Three different molecular markers were used to perform the comprehensive genetic characterization of Brazil and Nigeria breeds: sequence analysis of 450bp of mitochondrial DNA control region; 10 nuclear microsatellite loci and 580,000 SNPs markers. A total of 37 haplotypes were identified between Nigeria (18 haplotypes) and Brazil (19 haplotypes) populations and it was not identified any shared haplotype between the two countries. When the Nigeria samples were evaluated alone, it was observed that no haplotype grouped exclusively by geographic region or type of feather. This result suggests higher admixture and low phylogeographical signal among genetic groups. In addition, 65% of analyzed samples belong for just one haplotype (H_2). From Brazilian samples it was observed specific haplotypes for the line selected for meat (H_19, TT line). Brazilian and Nigeria shared haplotypes when sequences for NCBI were pooled in the analysis. In addition, it was possible to identify shared haplotypes between Nigeria breeds analyzed from different scientific groups in different moments. The nuclear analysis with microsatellites markers corroborate the mtdna study and principal coordinate analysis has showed that two main groups were formed, one containing the Brazilian populations and another one with the Nigerian populations. It was identified that most of Nigerian populations were very similar, except by Shika-Brown. The global Fst between the Nigeria and Brazil breeds was 17%. For the large-scale SNP analysis, 112 samples were genotyped from both countries using the Axiom Genome-Wide Chicken Genotyping Array (Affymetrix) with approximately 580,000 SNP markers. The analysis are still being generated as the results were released just late June by a third-party Company. In the end, the most important result was the creation of a concise genomic database for Brazilian and Nigerian chicken breeds that might be used as proxy for others scientific groups and livestock species. A complete set of Material and Methods as well as Results are presented as an Annex of this Report..

2 Scalability and replicability This project can be a pilot for broader and future initiatives with livestock. In order to reach optimal results it will be necessary that all teams involved have to perform a careful review of the sampling strategies and legislation involved before sampling biological material. In addition, the students involved should be trained in advance to bring and deliver better samples. Using this project as example, a better training on sampling and DNA extraction from Africa breeds is advisable. Impacts of project results One of the hypotheses of this project was that there would be a high similarity among Nigerian and Brazilian chicken breeds due to the informal exchange of germplasm during the period of slavery, when millions of slaves from Africa were brought o Brazil. Domestic animals from Africa, and of different species, were brought along to feed the passengers during the long journey across the Atlantic Ocean. Due to their smaller size when compared to other domestic animals, chickens were one of the preferred species to be included in such journeys. Unfortunately, the chicken breeds of the two countries included in this study did not show any similarity that suggest that a germplasm exchange program should be developed among these two countries in the near future. In addition the database created in this study will help to increase the understanding about the connection of livestock species among both continents. However, efforts should be made to include samples of these breeds in animal gene banks to avoid their disappearance. With the same effort, those locally adapted breeds should be tested for production and health traits to test their importance in different production systems. Sustainability of project The results of this project have shown that the Brazilian and Nigerian chicken populations did not present the expected genetic similarities. Therefore, it is prudent not to exchange genetic material at this moment. We suggest that some sort of cryopreservation techniques (e.g. gonads vitrification) been implemented in both countries in order to make possible future exchange events as well as to guarantee the preservation of these ecotypes. Moreover, it is indicated that Nigerian Research Institutions should make efforts to organize and keep track of the germplasm ecotypes in characterized DNA banks and perform sound phenotypic and performance analysis when compared with industrial lines. Issues in project implementation It was very difficult to collect part of samples from the local Nigerian chicken breeds. The time taken to process and extract the DNA from the biological material was not enough for Nigerian students bring high quality DNA to Brazil. Many samples were discarded due to low quality DNA or even due to problems in their identification. This was the main problem that caused the delay in the analysis of the SNP data. However the data has been generated and it is under analysis. Lessons Learned This was the first effort to study molecular data from Brazilian and Nigerian local chicken breeds in order to improve the understanding of the distribution of genetic variability between the two continents. The genetic characterization of breeds is one of the first steps to create and/or optimize conservation programs within/ between countries. After the execution of this project it was possible to identify new models to improve sampling and management of biological material collected. Suggestions for improvement In future projects, when more than one student comes to be trained in Brazil, it would be better if they are from the same gender to optimize the lodging costs. This simple practice can let them stay for a longer period with the same initial budget. Publications Nothing has been published until now in order to not expose each country results until fully analysis and discussion by the research teams from both countries. It is expected at least one full paper in a higher impact international journal and 2 or 3 small papers in lower impact journals. Quantitative Project Results Quantitative - Project Results Knowledge Generated Technologies Products Services Number of Key Project Outputs 1. mitochondrial and nuclear (microsatellites and SNps) genetic characterization of Nigerian local chickens 2. Comparison of biodiversity of Brrazilian and Nigerian local chickens Methods for merging and analyzing molecular data generated by different facilities Chicken genomic information data to be deposited in a public database 1. Germplasm conservation for local farmers, academic and research institutes 2. Genotyping of improved and local chicken strains 3. Training Nigerian students on molecular techniques and conservation of animal genetic resources Training and Technical Visits Name Country/city Number of Days Gender Arthur Mariante Nigeria, Ile-ife and Ibadan 4 days Male Monica Ledur Nigeria, Ibadan 3 days Female Lucky Akpere Brazil: Brasilia and Concordia 34 days Male

3 Events Organized Germplasm Exchange Number of Participating Professionals (in the project team as a whole) Ronke Bolatito Event Name Indigenous Chikens in Brazil, Conservation and Utilization National Nigerian Poultry Workshop Nigerial Indigenous Chickens, conservation and Utilization Nigerial Indigenous Chickens, conservation and Utilization Species Gallus gallus (DNA and blood samples) Female Brazil: Brasilia and Concordia Country/City 34 days Female Event Type (workshop, forum, symposium, etc.) Year OAU, Ile-Ife Seminar 2013 NACGRAB, Ibadan Brazil: Concordia Brazil: Brasilia Number of Accessions 5 breeds/ samples of 150 animals Male 4 3 Workshop, Symposium Seminars by Akpere, Bolatito and Mariante Seminars by Akpere and Bolatito Recipient Country Brazil Attachments (photos and other documents)

4 Nigerian students being trained at the Animal Genetics Laboratory at Embrapa Swine and Poultry Research Center in Concordia SC - Brazil

5 Visit of Arthur Mariante, the Brazilian co-leader to Obafemi Awolowo University, Ile-Ife, Nigeria Visit of Arthur Mariante and Monica Ledur to the Animal Genetic Laboratory at the National Centre for Genetic Resources and Biotechnology - NACGRAB - Ibadan, Nigeria