I don't know if this is the case, but I guess it is. I know nothing about rice genetics, and your question is too broad. But let's try.

If the genome is haploid, then you don't need to clone.

On the other hand, if the allele is diploid and you have 2 SNPs, at least one of them heterozygote, in sucesive positions, then you will have to clone to assess the haplotype. Example: A/C (1st SNP) G/T (2nd SNP). Then, one haplotype one could be A-G, A-T, C-G or C-T. Cloning will tell.

You could also use ARMS-PCR to assess haplotypes, though.

Hope it helps.