Research Areas

Animal Genetic Resources 2013 -

Researcher: Samuel Rezende Paiva

1.       Summary

Research, development and preservation of Genetic Resources (GR) have been one of Embrapa’s major efforts over the past 38 years. Along the same direction the National Center for Genetic Resources Preservation (NCGRP/ARS/USDA) has achieved excellence in the preservation and security of genetic resources for use in food production and many other uses. This work plan proposes to promote a robust research cooperation with ARS and Land Grand Universities as well diminish technical and organizational issues of Embrapa’s Genetic Resources System represented by the main problems: (a) there is a lack of a robust, active and fully implemented data information system in Embrapa to document and facilitate the management of the genetic resources; (b) currently genetic characterization activities are fragmented throughout the Brazilian network and many of the analytical tools employed are out of date, providing incomplete or inaccurate information about the conserved germplasm; (c) routine cryopreservation methods for some plant species and for gametes and embryos of some animal species are still suboptimal, requiring further R&D; (d) the introduction and exchange of genetic materials, do not fully meet Embrapa’s (and its partners) needs and standards.

2.       Goals of Labex Genetic Resources

2.1.    Information System

Monitor and test the advances of the new GRIN-Global Plant System in NCGRP and to guarantee the incorporation of GIS and genomic data as well the use of the new version of the Animal Information System (Animal GRIN v2) by the Brazilian Animal Genetic Resources Network;

2.2.    Genetic characterization

Develop and adapt methods and strategies to optimize the genotyping of plant and animal genetic germplasm banks;

2.3.    Cryopreservation

Develop and adapt cryopreservation methods for plants, animal and microorganisms species of common interest for US and Brazil;

2.4.    Exchange

Optimize and document the main procedures for exchange as well as give support for the ongoing and new exchange events for genetic resources between ARS and Embrapa;

 3. Project(s):

3.1.   Implementation and adaptation of Information systems in genetic resources programs and update them to the new Era of Genomics (Goals 2.1 and 2.4) 

3.1.1.Research Group

 Animal Genetic Resources - Harvey D. Blackburn (Animal Geneticist, NCGRP/ARS/US); Carrie S. Welsh (Animal Scientist, NCGRP/ARS/US); Theodore J. Manahan (Information Technology - IT Specialist, NCGRP/ARS/US); Yves Plante (Animal Geneticist, Agriculture and Agri-Food Canada - AAFC/Canada); Wenkai Fu (IT Specialist, AAFC/Canada); Arthur da Silva Mariante (Animal Scientist, Cenargen/Embrapa/Brazil); Eduardo Vaz de Mello Cajueiro (IT Specialist, Cenargen/Embrapa/Brazil)

Plant Genetic Resources - Josef M Pohl (Information Technology - IT Specialist, NCGRP/ARS/US); David Dierig (Research Leader, NCGRP/ARS/US); Peter D. Cyr (IT Specialist, PIRU/MWA/ARS/US); Ivo Roberto Sias Costa (Plant Scientist, Cenargen/Embrapa/Brazil); Gilberto de Oliveira Hiragi (IT Specialist, Cenargen/Embrapa/Brazil)

3.1.2.Objectives

a)      Implement the version 2.0 of the Animal-GRIN database in the Brazilian Animal Genetic Resources Program; b)      Evaluate a design addition of genomic data in a future version of Animal-GRIN; c)       Evaluate the compatibility of the Plant information systems GRIN-Global used by ARS and ALELO used by Embrapa; and d)      Support the genetic resources exchange between Brazil and US.

3.1.3.Approach

Animal Genetic Resources - a)      Elaboration of Agreement among ARS, Embrapa and Agri-Canada to use the new Animal Information System; b)      Review descriptors of database in order to assure the addition of Geographic Information Systems (GIS) data; c)       Elaboration of manuals for the new version of the database, including the exchange procedures to send/receive material from/to US and Brazil; d)      Training of regular users in Brazil and US; e)      Support the upload of Brazilian data into the information system; f)       Develop of possible solutions to incorporate genomic data in the system g)      Development and coding of IT solutions for genomic data; h)      Perform Beta tests for genomic pages;

Plant Genetic Resources - a)      Monitor and evaluate the implementation of GRIN-Global by PGRPP (Plant Genetic Resources Preservation Program); and b)      Analyze and Identify an approaches to migrate data between Brazilian ALELO and GRIN-Global;

General - a)      Elaboration and/or adaptation of tutorials to help Brazilian Institutions and researcher scientists to send plant, animal and microorganism germplasm to the USA, without violating Brazilian and American Environmental and Health legislations.

3.1.4.Expected Results

Animal Genetic Resources - a) Agreement signed by US, Canada and Brazil for an Animal Information System; b) Documentation available for general and specialized public with the launch of a Manual elaborated in two languages (English and Portuguese) for the Animal Information System; c) Training of 15 research scientists/ technicians in order to expand the number of the regular system users; d) Upload of 80% of Conservation Nuclei and Gene Banks from the Brazilian Animal Genetic Resources Program that represents public data available from 20 In situ and Ex situ conservation programs form Embrapa; e) Genomic module available in Animal Information System as well training of one person from Brazil in this module.
Plant Genetic Resources – a) Report to Brazilians Curators Identifying the qualities of GRIN Global that can be incorporated in Brazilian ALELO System; b) Develop schema, design and coding export and import tool between ALELO and GRIN-Global as well training one person from Brazil with this tool.
General – a) Release at least three Manuals/ tutorials elaborated in two languages (English and Portuguese);

Project: Development and adaptation of genetic and geographical tools to optimize Germplasm collections
Animal Genetic Resources - a) Customized SNP panel for sheep (parentage, traceability and candidate genes); b) Generation of raw data to reinforce the difficult of implementation of Nagoya Protocol Animal Genetic Resources and publication of one article in higher impact peer review periodical; c) Comparison of main livestock species from Brazil and US by molecular markers and GIS techniques; Publication of at least three articles in higher impact peer review periodicals; training at least two persons in those methodologies; d) Assembly two eukaryotes genomes by means of two different techniques of Next Generation Sequence and Publication of at least one article in higher impact peer review periodical; e) Enhance the exchange of Genetic material from Brazil to US by implementation of best practices to exchange animal DNA/ RNA material from Brazil and US.
Plant Genetic Resources – a) Identification of a cost effective strategy to genotype crops from collections between US and Brazil and at least one Cooperation Agreement signed by US and Brazil Research Scientists.

Project: Development and adaptation cryopreservation methods for plants, animal and microorganisms
Animal Genetic Resources - a) Report with the main goals of the workshop registered and training of three researchers; b) Cryopreservation method adapted and protocol validated with germplasm incorporation of two breeds/ populations in the NCGRP repositorium;
Plant Genetic Resources – a) Cryopreservation/ in vitro method adapted and protocol validated with incorporation of germplasm for collection; b) Germplasm exchanged between US/Brazil;
Microbes Genetic Resources – a) Report with the main goals of the meeting/workshop registered with the definition of main lines of collaboration; b) Cryopreservation method adapted and protocol validated with incorporation of germplasm for collection; c) Germplasm exchanged between US/Brazil