A genotyping platform assembled with high-throughput DNA extraction, codominant functional markers, and automated CE system to accelerate marker-assisted improvement of rice

The introgression of multiple genes into traditional cultivars using marker-assisted selection (MAS) in order to obtain favorable traits is an effective strategy to achieve improved rice lines. Genotyping of markers is a central component of the evaluation of germplasm and the selection of progeny lines. However, efficient DNA extraction and genotyping of large breeding populations still remain limiting factors in rice molecular breeding programs. This study has developed and validated a cost-effective, rapid (<1 h for 96 samples), and high-throughput (96-well format) total DNA-extraction method based on magnetic particle technology. To improve the grain-quality traits of two rice varieties, we have designed and employed an efficient codominant functional marker system (including Wx, ALK, Chalk5, and fgr genes), in combination with genotyping based on automated capillary electrophoresis. Rice lines with simultaneous improvement at multiple loci were obtained and found to have superior grain quality and to be fragrant. The genotyping pipeline established in this study represents an efficient, reliable, and precise platform for MAS.