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Abstract
The discovery of single nucleotide polymorphisms (SNPs) and insertions/deletions,
which are the basis of most differences between alleles, has been simplified by recent
developments in sequencing technology. SNP discovery in many crop species, such as
corn and soybean, is relatively straightforward because of their high level of intraspecific
nucleotide diversity, and the availability of many gene and expressed sequence tag
(EST) sequences. For these species, direct readout of SNP haplotypes is possible.
Haplotype-based analysis is more informative than analysis based on individual SNPs,
and has more power in analyzing association with phenotypes. The elite germplasm of
some crops may have been subjected to bottlenecks relatively recently, increasing
the amount of linkage disequilibrium (LD) present and facilitating the association
of SNP haplotypes at candidate gene loci with phenotypes. Whole-genome scans may help
identify genome regions that are associated with interesting phenotypes if sufficient
LD is present. Technological improvements make the use of SNP and indel markers attractive
for high-throughput use in marker-assisted breeding, EST mapping and the integration
of genetic and physical maps.