Integration of genomics into rice breeding

One of the major challenges in genetics has been to identify the nucleotide polymorphisms responsible for phenotypic variation. Through intensive analysis, several major quantitative trait loci (QTLs) for agronomic traits in rice have been identified and the underlying candidate genes have been delimited. Advanced mapping populations, including chromosome segment substitution lines, have enhanced the power of genetic analysis to detect QTL alleles, even those with minor effects. Recent examples of marker-assisted selection have proven the potential of this strategy for crop improvement. The genome-wide discovery of single nucleotide polymorphisms (SNPs), even among closely related cultivars, has enhanced the power of allele mining in a wide range of rice breeding materials. An arraybased SNP genotyping system can be used to visualize pedigree haplotypes in breeding materials, including landraces and modern cultivars. All of these technologies are accelerating the genetic dissection of complex agronomic traits and further improvement of rice.