Crop breeding chips and genotyping platforms: progress, challenges and perspectives (original) (raw)

There is a rapidly rising trend in development and application of molecular marker assays for gene mapping and discovery in field crops and trees. Thus far more than 50 SNP arrays and 15 different types of genotyping-by-sequencing (GBS) platforms have been developed in more than 25 crop species and perennial trees. However, much less has been emphasized on developing ultra-high-throughput and cost-effective genotyping platforms for applied breeding programs. We discuss the scientific bottlenecks in existing SNP arrays and GBS technologies and the strategy to develop targeted platforms for crop molecular breeding. The concept of true breeding platforms implies to automated genotyping technologies, either array- or sequencing-based, targeting functional polymorphisms underpinning economic traits, providing desirable prediction accuracy for quantitative traits, and have universal application across genetic backgrounds in a crop. The development of such platforms face serious challenges...