The association between alleles of the Waxy gene, defined by the number of CT repeats on exon 1, and traits of grain quality was carried out using 47 Philippine Seed Board rice varieties. The major alleles of the Waxy gene in the set of 47 were (CT)10, (CT)11, (CT)17 and (CT)20. Varieties were divided into four clusters based on the metric of each trait of grain quality. (CT)10 (27-32% amylose content (AC)) and (CT)11 (22-30% AC) were mainly in clusters 3 and 4 (hard texture), and (CT)17 (20-24% AC) and (CT)20 (18-27% AC) were exclusively in grain quality cluster 1 (soft texture) and 2 (medium texture). (CT)n associated negatively with AC in this set. Only six (CT)11 and one (CT)10 rices were in cluster 4 (high-AC low-GT) and had high RVA consistency (final viscosity – trough viscosity) > 200 RVU. (CT)17 seemed to be the preferred source of low-intermediate AC in the Philippine rice breeding program, followed by (CT)20.

Key Words: apparent amylose content, cooked rice hardness, cluster, CT polymorphism, gelatinization temperature, PSB Rc varieties, RVA,Waxy gene

Abbreviations: AC – apparent amylose content, CT – cytosine and thymine, DNA – deoxyribonucleic acid, GBSS I – granule-bound starch synthase I, GQNPC – Grain Quality, Nutrition and Postharvest Centre, GT – gelatinization temperature, IRRI – International Rice Research Institute, PhilRice – Philippine Rice Research Institute, PSB Rc – Philippine Seed Board rice, RVA – Rapid Visco Analyser, RVU – Rapid Visco units