Simple sequence repeats (SSRs) have been the marker of choice for rice molecular breeding due to the high level of polymorphism, technical simplicity and low cost. Recent advances in rice genomics have led to the discovery of abundant single nucleotide polymorphism (SNPs) which have enormous potential for rice molecular breeding. To assess both marker systems for molecular breeding in rice, SSR and SNP markers were evaluated on a set of 23 genotypes representing indica germplasm for their usefulness in molecular research and breeding program. Seven hundred SSR and sequence tagged sites (STS) markers and 384 SNPs were screened for polymorphism. Highly polymorphic markers based on polymorphic information content (PIC) values were identified, which will be useful for molecular breeding. Data was used to identify an “indica genotyping set” based on high level of polymorphism, chromosome position and marker quality which will provide kits of markers for marker assisted selection (MAS). Genetic diversity analysis using SSR data was more consistent with pedigrees compared to analysis with SNP data indicating that more than 384 SNPs are required when elite indica breeding material is used. The results also indicated that there were polymorphic “blind spots” for the fixed SNP set suggesting that SSRs could still be used to complement fixed-SNP genotyping platforms for some molecular breeding applications.

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The increased severity and frequency of flooding is causing greater yield reductions in most rice-growing areas. To address this, popular cultivars were improved through introgression of SUB1, an FR13A-derived QTL conferring submergence tolerance at the vegetative stage, using marker-assisted backcrossing (MABC). Ciherang-Sub1, one of these improved near isogenic lines (NILs), showed significantly higher tolerance compared to the original cultivar while retaining its desirable agronomic qualities. However, due to the current shift to direct seeding, seed germination may also be adversely affected by flooding; thus the addition of major QTLs which can confer anaerobic germination (AG) tolerance will be highly beneficial. The AG tolerance QTL, qAG-9-2, also referred to as AG1, derived from Khao Hlan On, a Myanmar landrace, has been introgressed into the elite cultivar IR64 to produce IR64-AG1. This research focused on the transfer of AG1 to Ciherang-Sub1 via MABC, using IR64-AG1, a closely-related donor. Introgression of AG1 and recovery of the Ciherang genome was done in two backcross generations followed by one generation of selfing. The use of a closely-related donor shortened the development period to two years which could have been further reduced if a larger BC₁F₁ population had been used. Phenotypic evaluation showed that introgression of AG1 significantly increased AG tolerance compared to Ciherang-Sub1, and that the newly developed Ciherang-Sub1+AG1 retained the submergence tolerance from SUB1. The approach is very promising for faster development of improved lines using closely-related cultivars or improved lines as donors for introducing key traits.

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