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

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.

Comparative Genomic Analysis of Rice with Contrasting Photosynthesis and Grain Production under Salt Stress

“…With an in-depth analysis of the potential polymorphisms responsible for filled grain number under salt stress of flowering rice, the annotation of polymorphisms observed in MY/KK-JK/NN revealed that only ~3% of SNPs and ~2% of InDels were detected in CDSs, whereas the remaining ~35% of SNPs and ~36% of InDels were detected in upstream regions (Figure 4C,D). The larger number of variations in regulatory regions other than genic regions found in this study corresponds to the results of previous studies in rice [74,75]. We identified 722 high-impact variants resulting in changes such as frameshifts, exon loss and stop loss and 5120 moderate-impact variants, such as missense variants (non-synonymous) (Table S4).…”

Whole-genome sequencing and phenotyping revealed structural variants and varied level of resistance against leaf crumple disease in diverse lines of snap bean (Phaseolus vulgaris)

“…A higher ratio is an indicator of good quality SNPs as sequencing errors and false positive variants have a ratio closer to one [28].We found SNP transitions (A/G and C/T) are the most common substitution in the genome, which is consistent with other crop species like foxtail millet (Setaria italica) [29], tea (Camellia sinensis) [30], soybean [31], rice [22]. We observed a Ts/Tv ratio of 1.71 is however less than the ratios reported in crops like rice [22], maize (Zea mays) [32] and tea [30]. The higher Ts/Tv could be because of more synonymous mutations resulting due to transitions than transversions, which brings out the change in protein structure and function.…”

“…Despite having uniform genome coverage of mapped reads several empty bins were identified because of the stringent variant calling parameters used as indicated in the methods section. Such significant differential distribution of DNA polymorphisms has also been reported in Arabidopsis and rice [20][21][22].…”

Comparative Transcriptomics of Rice Genotypes with Contrasting Responses to Nitrogen Stress Reveals Genes Influencing Nitrogen Uptake through the Regulation of Root Architecture

“…Dular is a lowland drought tolerant cultivar with deep roots [63]; Nona Bokra and Pokkali are salt tolerant land races [64,65]. PSRR-1 is a weedy rice genotype from Louisiana [66] and is closely related to indica subspecies [67].…”