Marker Validation: The Key to Development of Breeder's Chipset

Many abiotic stress tolerances, as well as some forms of disease resistances are controlled by multiple genes. The integration of molecular technology into rice breeding schemes dealing with multiple genes must coincide with the improvement of the marker system.  Marker validation is the first initiative for a more precise and efficient strategy aiding several breeding objectives. Marker validation consists of step-by-step procedures, ultimately replacing low-throughput gel-based system (QTL/gene-specific markers, indel size markers) with high-throughput marker system (Fluidigm™ SNP and Infinium™ SNP). With the help of bioinformatics tools, accurate single-nucleotide polymorphism system enhances the capacity and reliability of molecular breeding. Currently developed and newly developed markers are initially tested on a standard variety panel composed of 96 purified diverse varieties, and a segregating population containing multiple QTLs/genes (Pup1, Sub1, Saltol, AG1, DTY_2.2, DTY_4.1, qHTSF_4.1, RTSV) using the Fragment Analyzer (FA) and Fluidigm SNP. Data collected using marker-assisted system is combined with screening data of different target traits for further validation. At the end of the validation process, foreground, recombinant and background markers will be integrated into a single marker chipset, called the breeder’s chipset, for a specific trait-packaging program. Improved donor development is achieved with great accuracy and precision at a shorter timeframe and at a lower cost.