Tagging salinity tolerance genes in rice using amplified fragment length polymorphism (AFLP)

The genetic basis of salinity tolerance of the indica cross IR66946 (IR29-salt susceptible improved variety x Pokkali-tolerant traditional tall variety) was determined through PCR-based AFLP. The F8 recombinant inbred lines (RILs) of IR66946 were used to map the genes for salinity tolerance in Pokkali. Phenotyping was done at seedling stage using salinized (EC=12d S/m) culture solution under controlled condition in IRRI phytotron. Combining the AFLP technique with selective genotyping, a linkage map for rice was established. Each linkage group was assigned to corresponding chromosome. The AFLP map consisting of 206 AFLP markers was generated from 32 primer combinations of Pst 1 and Mse 1 using the 80 RILs which were selected from the extreme tails of the population in response to salinity tolerance. The level of polymorphism for individual primer combination varied from 0-39.3 percent with overall polymorphism of 19.1 percent. The map length was 181.4 cM with an average interval size of 10.53 cM. To assign the linkage groups to chromosome, 42 published-mapped AFLP markers were used as anchor markers distributed over the 12 chromosomes. The remaining AFLP markers were then assigned to specific chomosomes based on their linkage to anchor markers. The AFLP map was equivalent to the reference RFLP/AFLP, having the anchors in the same order with the reference maps. Further, tests with an STS marker showed that it mapped in the expected position in the AFLP map. With the constructed AFLP map, a major gene for salinity tolerance designated saltol was mapped between flanking AFLP markers P 3/M9-8 and P1/M9-3 on chromosome 1 with 14.7 cM and 18.6 cM distance, respectively, from the gene. QTL associated with salinity tolerance (high K absorption, low Na absorption, and low Na-K absorption ratio) were tagged on chromosomes 1, 3, 4, 10, and 12. Single marker analysis and interval marker analysis were used to detect QTL and both produced basically the same results. High K absorption had 3 QTL, low Na absorption had 4 and low Na-K ratio absorption had 3. A common QTL for the 3 quantitative traits for salinity tolerance was observed in chromosome 1. This segment contained the saltol gene and explained a range of 64.3-80.2 percent of the phenotypic variation with LOD 14.5. The study also showed that a combination of rapid generation of AFLP map and selective genotyping would make QTL detection fast, easy and cost effective