Integration Of Data To Study Goat Diversity and Adaptation: The AdaptMap Project

The ADAPTmap (http://bioinformatics.tecnoparco.org/adaptmap/) is an International effort developed to improve coordination among otherwise independent projects for genotyping and re-sequencing of goat breeds. The objective is to explore diversity and adaptation of goat populations around the world by using traditional and novel approaches. A number of international projects aim to disentangle diversity of goat breeds/populations by recording and relating genomic diversity, morphological traits and several geo-climatic parameters for characterizing the breeding environment.  In addition, large projects have been carried out for genomic analyses of complex traits, providing extensive datasets on commercial populations.  Genomic analyses typically comprise extensive genotyping with the Illumina 50k SNP panel. However, re-sequencing and genotyping by sequencing techniques will be applied on some of the same local and commercial populations and de-novo sequencing approaches will be applied to wild ancestors. Integrating of data from the various sources is an essential step to allow a comprehensive application of population genomics.  However, heterogeneity of sampling designs, studies objectives, resources and methods of sample collection and recording poses a great challenge in data integration for storage, querying and analysis.  Bioinformatic solutions have been developed for efficient merging of genomic data from independent sources. Genomic and phenotypic data can be transferred to the centralized database using a multi-file web uploader. SNPage software was developed to easily handle and safely merge SNP genomic information. Methods for identification of hidden relationships among morphological, phenotypic, environmental and geo-climatic data are being applied for the calculation of synthetic indicators.