Biology subjects

Daware, A.

Publications and source records attributed to Daware, A..

4 recordsLinked to original sources

bioRxiv2022

GWAShub: A Web-based Resource to Democratize Genome-Wide Association Studies in Crop Plants

Genome-wide association study (GWAS) is a popular approach for linking natural genetic variation with phenotype variation and thus is central to crop quantitative genetics. The ever-increasing wealth of publicly available genomic sequence information for crop plants presents an unprecedented opportunity for utilizing GWAS for the identification of genes governing a plethora of agronomic traits. However, the lack of technical expertise and computational infrastructure is still hindering the ability of plant breeders to conduct GWAS in a self-reliant manner. Here, we present a GWAShub web server that provides a user-friendly interface for performing comprehensive GWAS and post-GWAS in crop plants utilizing publicly available genomic sequence variation data, comprehensive annotation data and diverse computational tools. The utility of GWAS-hub was further demonstrated by conducting large-scale GWAS for flowering/maturity time traits in chickpea. This analysis identified three different flowering/maturity time associated genes, all encoding different histone methyltransferases. Thus, epigenetic regulation is identified as vital mechanism regulating flowering time and maturity duration in chickpea. Finally, we hope GWAShub (www.gwashub.com) will enable resource-scarce researchers to join the GWAS revolution fueled by advancements in next-generation sequencing and computational genomics

bioinformatics↗

bioRxiv2022

Rice Pan-genome Array (RPGA): an efficient genotyping solution for pan-genome-based accelerated crop improvement in rice

The advent of the pan-genome era has unraveled previously unknown genetic variation existing within diverse crop plants including rice. This untapped genetic variation is believed to account for a major portion of phenotypic variation existing in crop plants and might be responsible for missing heritability. However, the use of conventional single reference-guided genotyping often fails to capture large portion of this genetic variation leading to a reference bias. This makes it difficult to identify and utilize novel population/cultivar-specific genes for crop improvement. To overcome this challenge, we developed a rice pan-genome genotyping array (RPGA) includes 80K genome-wide SNPs which provides simple, user-friendly and cost-effective solution for rapid pan-genome-based genotyping in rice. The GWAS conducted using RPGA-SNP genotyping data of a rice diversity panel detected total of 42 loci, including previously known as well as novel genomic loci regulating grain size/weight traits in rice. Eight of the identified trait-associated loci (dispensable loci) could not be detected with conventional single reference genome-based GWAS and found to be missing from the commonly used Nipponbare reference genome. WD repeat-containing PROTEIN 12 gene underlying one of such dispensable locus on chromosome 7 (qLWR7) along with few other non-dispensable loci was subsequently detected using high-resolution QTL mapping confirming authenticity of RPGA-led GWAS. This demonstrates the potential of RPGA-based genotyping to overcome reference bias. Besides GWAS, the application of RPGA-based genotyping for natural allelic diversity and population structure analysis, seed purity and hybridity testing, ultra-high-density genetic map construction and chromosome level genome assembly, and marker-assisted foreground/background selection was successfully demonstrated. Based on these salient outcomes, a web application (http://www.rpgaweb.com) was also developed to provide easy to use platform for imputation of RPGA-based genotyping data using 3K Rice Reference Panel and subsequent GWAS in order to drive genetic improvement of rice.

genomics↗

bioRxiv2019

Genome-wide analysis of polymorphisms identified domestication-associated polymorphism desert carrying important rice grain size/weight QTL

Rice grain size and weight are major determinant of grain quality and yield and so have been under rigorous selection since domestication. However, genetic basis for contrasting grain size/weight trait among indian germplasm, and their association with domestication shaped evolutionary region is not studied before. To identify genetic basis of grain size/weight two long (LGG) and two short grain genotypes (SGG) were resequenced. LGG (LGR and Pusa Basmati 1121) differentiated from SGG (Sonasal and Bindli) by 504439 SNPs and 78166 InDels. The LRK gene cluster was significantly affected and a truncation mutation in the LRK8 kinase domain was uniquely associated with LGG. Phylogeny with 3000 diverse rice accessions revealed four sequenced genotypes belonged to japonica group and were at the edge of clades indicating source of genetic diversity available in Asian rice population. Five SNPs significantly were associated with grain size/weight and top three SNPs were validated in RIL mapping populations, suggesting this study as a valuable resource for high-throughput genotyping. A contiguous [~]6 Mb polymorphism desert region carrying a major grain weight QTL was identified on chromosome 5 in four sequenced genotypes. Further, among 3000, this region was identified as evolutionary important site with significant positive selection, elevated LD, and multiple selection sweeps, stabilising many domestication-related traits including grain size/weight. The aus group genotype retained more allelic variations in the desert region than japonica and indica, and likely to be one of the differentiation point for aus group. We suggest this desert region as an important evolutionary node that can be selected in breeding programs for improvement of grain yield and quality. All data and analysis can be accessed from RiceSzWtBase database.\n\nSignificance statementBeing an important trait, rice grain size/weight has been under rigorous selection since domestication. However, a link between this trait and domestication is not so directly established. In addition to characterization of novel grain size/weight-associated SNPs, in this study, [~] 6 Mb polymorphism desert region harboring major grain weight QTL was identified on chromosome 5, which turned out to be an evolutionary important site with multiple selection sweeps and introgression events, significantly correlated with domestication-related traits.

plant biology↗

bioRxiv2018

Vitexin alters Staphylococcus aureus surface hydrophobicity to interfere with biofilm formation.

Bacterial surface hydrophobicity is one of the determinant biophysical parameters of bacterial aggregation for being networked to form biofilm. Phytoconstituents like vitexin have long been in use for their antibacterial effect. The present work is aimed to characterise the effect of vitexin on S. aureus surface hydrophobicity and corresponding aggregation to form biofilm. We have found that vitexin shows minimum inhibitory concentration at 252 g/ml against S. aureus. Vitexin reduces cell surface hydrophobicity and membrane permeability at sub-MIC dose of 126 g/ml. The in silico binding analysis showed higher binding affinity of vitexin with surface proteins of S. aureus. Down regulation of dltA, icaAB and reduction in membrane potential under sub-MIC dose of vitexin, explains reduced S. aureus surface hydrophobicity. Vitexin has substantially reduced the intracellular adhesion of planktonic cells to form biofilm through interference of EPS formation, motility and subsequent execution of virulence. This was supported by the observation that vitexin down regulates the expression of icaAB and agrAC genes of S. aureus. In addition, vitexin also found to potentiate antibiofilm activity of sub-MIC dose of gentamicin and azithromycin. Furthermore, CFU count, histological examination of mouse tissue and immunomodulatory study justifies the in vivo protective effect of vitexin from S. aureus biofilm associated infection. Finally it can be inferred that, vitexin has the ability to modulate S. aureus cell surface hydrophobicity which can further interfere biofilm formation of the bacteria.\n\nImportanceThere has been substantial information known about role of bacterial surface hydrophobicity during attachment of single planktonic bacterial cells to any surface and the subsequent development of mature biofilm. This study presents the effect of flavone phytoconstituent vitexin on modulation of cell surface hydrophobicity in reducing formation of biofilm. Our findings also highlight the ability of vitexin in reducing in vivo S. aureus biofilm which will eventually outcompete the corresponding in vitro antibiofilm effect. Synergistic effect of vitexin on azithromycin and gentamicin point to a regime where development of drug tolerance may be addressed. Our findings explore one probable way of overcoming drug tolerance through application of vitexin in addressing the issue of S. aureus biofilm through modulation of cell surface hydrophobicity.

microbiology↗