The Role of Genomics Tools for Genetic Improvement and Their Potential Application in Developing Countries

The performance of an agricultural industry in a particular management and environmental circumstance depends upon the suitability of the germplasm that comprised the founder nucleus population, ongoing genetic improvement in the nucleus since the founder generation was formed, and the genetic lag that exists between the nucleus and the commercial populations.  In developed countries, ongoing genetic improvement in most species relies on multiple trait selection, traditionally based on measured phenotypes of large cohorts of individuals within a pedigree structure, but these analyses now commonly enhanced using whole-genome SNP information.  Genetic lag is minimized by exploiting reproductive technologies such as artificial insemination and/or embryo transfer.  In developing countries, pedigree information can be problematic to collect, cohorts of contemporaries are often of inadequate size, and advanced reproductive technologies can be difficult to employ.   In developing countries, case-control protocols for use in genome-wide association studies offer promise for identifying genomic regions with major gene effects that could be used for marker-assisted selection or introgression.   In both developed and developing countries, genomic tools such as exome annotation offer promise for identifying mutations that might be useful to introduce into nucleus populations by introgression or preferably by gene editing.