Classification of rice germplasm. II. Discrimination of indica from japonica via analysis of amplicon length polymorphisms

The polymerase chain reaction (PCR) was used to survey DNA sequence variation among 12 indica and 10 japonica rice cultivars. Of the 143 primer pairs used, 37 detected amplicon length polymorphism (ALP) and 11 revealed PCR banding patterns paralleled with the indica/japonica differentiation. Thus the 11 primer pairs were used to discriminate the two rice subspecies. A collection of 116 accessions representing the breadth of rice germplasm was analyzed for ALP at the 11 loci. Rice accessions with scores of 0.3 or more were classified as indica while those with -0.3 or less were classified as japonica. Those with scores from -0.3 to 0.3 were considered intermediate. With this criterion, 70 accessions were classified as indica, 35 accessions as japonica, and 11 accessions as intermediate. The concept and the approach used here for rice should be equally applicable for classifying other plant species.