Routine genotyping at 384 SNP loci is currently possible
for rice, for both indica and japonica subspecies
(Boualaphanh et al. 2011b; Wright et al. 2010). However,
just as genotyping at 384 loci has become routine, the
number of loci on newly developed chips has risen to
44000, and is soon to reach 1, 000,000 loci (Tung et al.
2011). As this rich collection of SNPs are discovered, the
genotyping can be used to develop mapping populations
rapidly (Boualaphanh et al. 2011b), or used to associate
with phenotype data (Calingacion et al. 2011), or a particular
set of SNPs can be selected and used for specific
genotyping in a breeding program (Chen et al. 2011).