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Analyzing the genome level DNA polymorphisms between weedy and cultivated rice is crucial to elucidate the molecular basis of weedy and agronomic traits, which in turn can enhance our ability to control weedy rice and its utilization for rice improvement. Here, we presented the genome-wide genetic variations between a weedy rice accession PSRR-1 and two cultivated rice accessions, Bengal and Nona Bokra, belonging to  japonica  and  indica  subspecies, respectively. The total number of SNPs and InDels in PSRR/Bengal was similar to that of Nona Bokra/Bengal, but was three times greater than that of PSRR/Nona Bokra. There were 11546 large-effect SNPs/InDels affecting 5673 genes, which most likely differentiated weedy rice from cultivated rice. These large effect DNA polymorphisms were mostly resulted in stop codon gain and least by start codon loss. Analysis of the molecular functions and biological processes of weedy rice specific SNPs/InDels indicated that most of these genes were involved in protein modification/phosphorylation, protein kinase activity, and protein/nucleotide binding. By integrating previous QTL mapping results with the DNA polymorphisms data, the candidate genes for seed dormancy and seed shattering were narrowed down. The genomic resource generated in this study will facilitate discovery of functional variants for weedy and agronomic traits.

Genome-wide discovery of DNA polymorphisms by whole genome sequencing differentiates weedy and cultivated rice