Evolution in the Genotyping Platforms for Plant Breeding

Improving the crop productivity, resilience to climate extremes, resistance to biotic stress and improving the quality are the main breeding objectives. Different tools, resources and strategies are used to precisely select the desirable cultivars in crop breeding. One of such tools is the genomics-assisted breeding (GAB), which improves selection accuracy during breeding cycles. However, practicing GAB depends on the availability of molecular markers for selecting the desired phenotypes. Once a marker is available for use in breeding, the efforts are then made to make it cost-effective and high-throughput to integrate its use in applied breeding. However, different breeding scenario like gene tagging, marker-assisted recurrent selection (MARS), background selection, diversity estimates, and genomic selection require different genotyping platforms, and there is no ‘one-size-fits-all’ solution. We provided an overview of the efforts around developing cost-effective, high-throughput and breeding-oriented crop genotyping platforms. A successful genotyping platform would have the features of high genome coverage, least ascertainment bias, high power in gene discovery studies, balance between throughput and flexibility, provide high prediction accuracy in genomic selection, and, above all, affordable for most of the crop breeding programs.