AFRICAN HAPMAP FOR RUMINANTS-CONSTRUCTION OF RESOURCE POPULATIONS
Bovine Functional Genomics
2012 Annual Report
1a.Objectives (from AD-416):
Develop scientifically-based tools for animal improvement programs in Africa and establish a cooperative network that individual country breeding programs can leverage the efforts of one another. Provide a nexus to enhance the cooperative efforts of advanced research institutions, such as ARS and International Livestock Research Institute (ILRI). ILRI has expertise in locally adapted breeds and livestock animal improvement programs in Africa, and has facilities for hosting laboratory activities for isolating genomic DNA from tissue samples. The facilities are located in the region of relevant resource target populations, and ILRI’s location will likely act as a hub of future scientific activities for this cooperative network of researchers studying genomics in ruminants of Africa.
1b.Approach (from AD-416):
ILRI will host visiting scientists that are working with ARS in collecting samples to generate the resource population of cattle that will make up a HapMap population of cattle representing locally adapted breeds of importance. The overall goal of this cooperation is to provide a suitable environment to ensure reliable extraction of genomic DNA from tissues that may not be importable into the U.S., and also provide training for outside scientists participating in this project.
The objective was to catalyze a cooperative effort to apply genomic tools to characterize the ruminant genomes of locally-adapted, native breeds throughout sub-Saharan Africa. This information will help to develop genomic tools for animal improvement programs in Africa and provide a nexus to enhance the cooperative efforts of advanced research institutions, such as ARS and ILRI. ILRI scientists helped to train a Nigerian graduate student in genomic DNA extraction techniques. The training was done by extracting 350 ear-punch samples derived from 12 native breeds of African cattle. A subset of these samples have been genotyped by BFGL scientists on the BovineHD SNP beadchip assay. The information obtained on more than 700,000 SNP will be used to complete the Ph.D. training of the Nigerian student, who will assess breed diversity and purity of these samples to help guide conservation decisions in Nigeria and Uganda. This research supported two objectives of an in-house project to develop biological resources and computational tools to enhance characterization of the bovine genome sequence (obj. #1), and.
2)to characterize conserved genome elements and identify functional genetic variation (obj. #3).