Résumé
Current advances in sequencing technologies and bioinformatics revealed
the genomic background of rice, a staple food for the poor people, and
provided the basis to develop large genomic variation databases for
thousands of cultivars. Proper analysis of this massive resource is
expected to give novel insights into the structure, function, and
evolution of the rice genome, and to aid the development of rice varieties
through marker assisted selection or genomic selection. In this work we
present sequencing and bioinformatics analyses of 104 rice varieties
belonging to the major subspecies of Oryza sativa. We identified
repetitive elements and recurrent copy number variation covering about 200
Mbp of the rice genome. Genotyping of over 18 million polymorphic
locations within O. sativa allowed us to reconstruct the individual
haplotype patterns shaping the genomic background of elite varieties used
by farmers throughout the Americas. Based on a reconstruction of the
alleles for the gene GBSSI, we could identify novel genetic markers for
selection of varieties with high amylose content. We expect that both the
analysis methods and the genomic information described here would be of
great use for the rice research community and for other groups carrying on
similar sequencing efforts in other crops.