Awais Rasheed, Yuanfeng Hao, Xianchun Xia, Awais Khan, Yunbi Xu, Rajeev K. Varshney, Zhonghu He

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 at both the technological level due to cost ineffectiveness, and at the knowledge level due to large genotype-phenotype gaps in crop plants. It is expected that such genotyping platforms can be achieved in next 10 years in major crops in consideration of, a) very rapid developments in gene discovery of important traits, b) understanding of quantitative traits through new analytical models and population designs, c) integrating multi-layer -omics data leading to identification of genes and pathways responsible for important breeding traits, and d) improvement in cost of genotyping large populations in parallel to improvement in cost of per data point. Crop breeding chips and genotyping platforms will provide unprecedented opportunities to accelerate development of cultivars with the desired yield potential, quality and enhanced adaptation to mitigate the effects of climate change.