High resolution genotyping by restriction enzyme-phased sequencing of advanced backcross lines of rice exhibiting differential cold stress recovery

Advanced backcross rice lines MIb 4853-9 and 6885-2 harbor major seedling cold tolerance QTL qCTS4 and qCTS12 from the temperate japonica M202 in the genetic background of the indica IR50. Previous studies have shown that these lines exhibit the same tolerance, based on visual ratings, under constant and intermittent exposure to cold stress. However, some differences between the MIb lines with regard to physiological stress indicators are observed under constant exposure and a clear difference is detected using a cold stress recovery assay. Genotyping with over 120 SSR markers did not detect any polymorphisms. Here we report using a reduced representation sequencing method called Restriction Enzyme Site Comparative Analysis to identify M202 introgressions unique to each MIb line as candidate loci for the cold stress recovery trait.