DEVELOPMENT OF PCR-BASED SNP MARKER OF RICE Waxy GENE WITH CONFRONTING TWO-PAIR PRIMERS.

Abstract

Rice amylose content (AC) is a key determinant for grain end-use quality attributes. The base substitution (G --> T) at +1 loci of the first intron (In1) of Waxy (Wx), a major gene controlling AC in rice, results in decreased AC. A new SNP typing method of Wx In1 based on polymerase chain reaction with confronting two-pair primers (PCR-CTPP) was reported here: first its practicability was confirmed by 23 varieties with known SN P and AC; and then the segregation ratio at target SN P loci were checked and it fitted well for 1 :2: 1 single gene segregation; at last SNP typing and AC assay with 150 mini core collections (MCC) in China showed that average AC of 53 G type varieties (22.5%) was significantly higher than that of 97 T type varieties (13.7%) (p < 0.01) and the target SNP loci explained 77.8% AC variation. So this method could be used to estimate AC of rice variety roughly or in marker-assisted-breeding, that is, using variety with known and desired AC as Wx allele donor parent and aided with crossbreed, backcross and marker-assisted selection (MAS) reported here rice breeders could improve AC of varieties with comprehensively excellent performance to meet special end-products.