Indica and Japonica differentiation under the species of Oryza sativa L. ha
s been documented using morphological characters, isozyme and DNA markers.
We illustrate marker assisted analysis of genetic differentiation with a sa
mple of RFLP and isozyme data from 111 accessions of rice lines and compare
it to morphological differentiation based on Cheng and Wang' morphological
character index. The results lead to three main conclusions: (1) Among the
92 polymorphic cloned probes deliberately selected, 41 were highly associa
ted with Indica-Japonica differentiation, suggesting such differentiation w
as an accumulative process of gene change at multiple loci; (2) There exist
two main types of relationships between morphological and genetic differen
tiation. For well differentiated Indica and Japonica (as the case in the co
ntrol subset), morphology and genomic constitutions are synchronously speci
alized. For incompletely differentiated rice lines (as the case in the subs
et of DH lines), morphological differentiation and genetic differentiation
are asynchronous. (3) Synthetic or incompletely differentiated rice lines w
ith different genomic constitutions are often adapted to specific environme
nts. These results indicate that marker alleles provide applied breeders wi
th effective ways to identify, track, and incorporate regions of chromosome
s governing adaptedness to specific target environments into improved culti
vars.