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Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice
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Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice
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Journal Article
Pan-genome analysis highlights the extent of genomic variation in cultivated and wild rice
2018
Overview
The rich genetic diversity in
Oryza sativa
and
Oryza rufipogon
serves as the main sources in rice breeding. Large-scale resequencing has been undertaken to discover allelic variants in rice, but much of the information for genetic variation is often lost by direct mapping of short sequence reads onto the
O. sativa japonica
Nipponbare reference genome. Here we constructed a pan-genome dataset of the
O. sativa
–
O. rufipogon
species complex through deep sequencing and de novo assembly of 66 divergent accessions. Intergenomic comparisons identified 23 million sequence variants in the rice genome. This catalog of sequence variations includes many known quantitative trait nucleotides and will be helpful in pinpointing new causal variants that underlie complex traits. In particular, we systemically investigated the whole set of coding genes using this pan-genome data, which revealed extensive presence and absence of variation among rice accessions. This pan-genome resource will further promote evolutionary and functional studies in rice.
A pan-genome dataset of the
Oryza sativa
–
Oryza rufipogon
species complex generated through deep sequencing and de novo genome assembly of 66 divergent accessions will be helpful in pinpointing new causal variants underlying complex traits and in promoting evolutionary and functional studies in rice.
Publisher
Nature Publishing Group US,Nature Publishing Group
