Abstract
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.
Highlights
Weedy rice (Oryza sativa f. spontanea Rosh.), commonly known as red rice, is one of the most noxious weeds in rice growing areas worldwide[1,2]
PSRR-1 showed higher degree of shattering compared to Bengal and Nona Bokra. Both PSRR-1 and Nona Bokra are intensely dormant compared to non-dormant Bengal
The percentage of high quality (HQ) filtered reads ranged from 92% to 95% (Table 1) and all HQ filtered reads were used for mapping
Summary
Weedy rice (Oryza sativa f. spontanea Rosh.), commonly known as red rice, is one of the most noxious weeds in rice growing areas worldwide[1,2]. There are two major genetically distinct groups of weedy rice in the United States such as the straw hulled (SH) and black hulled with long awns (BHA), which are believed to have originated in domesticated indica and aus rice background, respectively[13] Recent studies involving both morphological data as well as whole genome sequences of weedy, cultivated, and wild rice have supported the evolution of US weedy rice by de-domestication[12,19]. A recent study on African rice has revealed role of SH4 in controlling grain length[35,36] Another QTL of seed shattering, qSH1 encodes a member of homeobox TF with a SNP in 5′ regulatory region causing a failure in abscission layer formation[37]. The largest QTL on chromosome 4 overlapped with the Sh4, the presence of the non-shattering SNP allele in the weedy rice accession suggested involvement of a linked locus[26] or alternative genetic mechanisms[45]
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