A microsatellite marker and a codominant PCR-based marker for marker-assisted selection of submergence tolerance in rice

Abstract

Submergence tolerance is an important trait for rice (Oryza sativa L.) in rainfed lowland conditions and is being evaluated as a weed control strategy for rice seeded directly into standing water. The trait is largely controlled by a major gene designated Sub1. The present study was conducted to assess the use of the microsatellite marker RM219 and the codominant PCR -based marker RM464A (derived from a microsatellite marker, RM464) to select for submergence tolerance. The two markers RM219 and RM464A were found to be linked to Sub1 by 3.4 and 0.7 cM, respectively. These two markers were further tested in 55 diverse indica and japonica rice cultivars and breeding lines. RM219 was highly polymorphic in this set of cultivars, showing 14 different alleles, and none of the 55 cultivars had the same allele as the submergence tolerance source IR40931-26. RM464A showed three different alleles in the 55 cultivars. The allele of RM464A of most japonica genotypes was 231 bp in size, 5 bp larger than that of IR40931-26, whereas the allele of most indica rice samples was the same as that of IR40931-26. This indicated that the marker RM219 could be used in breeding programs to select for the Sub1 gene in a wide range of backgrounds, whereas RM464A was more useful in selection for the Sub1 gene in japonica rice background. The two markers were used to identify lines from backcrossing a submergence tolerance donor to the temperate japonica cultivar M-202. Several lines were identified that were homozygous for RM219, RM464A, and Sub1, and were otherwise genetically similar to M-202. Near isogenic lines (NILs) developed from these sources will be a valuable tool for genetic and physiological studies of submergence tolerance and will also be valuable for evaluating submergence tolerance as a useful trait in water-seeded temperate rice production