Integration of genomics into breeding in rice

Abstract

Elucidation of the association between nucleotide and phenotypic changes has been a big challenge in plant molecular genetics. Toward this goal, we have been involved in the genetic dissection of natural phenotypic variations in rice and have identified several genes involved in complex traits, including heading date, shattering habit, pre-harvest sprouting, root morphology, disease resistance and eating quality. To enhance the power of genetic dissection of complex phenotypes, we are developing several mapping populations, such as recombinant inbred lines and chromosome segment substitution lines, which will be required to extract the useful alleles from natural variants. Marker assisted selection has been applied for the development of heading date and durable resistance. To facilitate allele mining using novel plant materials, we have also embarked on the genome-wide discovery of single nucleotide polymorphisms (SNPs). In particular, to overcome a shortage of SNPs among temperate japonica cultivars, we have attempted whole-genome sequencing of several cultivars using next-generation sequencing approaches. Although Japanese cultivars are closely related genetically, about 67,000 SNPs have been discovered between Nipponbare (reference) and Koshihikari by this approach. This SNP discovery has led to the development of an array-based SNP genotyping system in Japanese rice cultivars. Large-scale 67 genotyping of these SNPs has made it possible to visualize pedigree haplotypes for the Japanese landraces and modern cultivars. These new efforts in genomics have opened up new opportunities to accelerate not only the genetic dissection of complex traits, but also the improvement of rice cultivars.