In silico analysis of motifs in promoters of Differentially Expressed Genes in rice (Oryza sativa L.) under anoxia

While COVID-19 liver injuries have been reported in various studies, concerns are raised about disease-drug reactions in COVID-19 patients. In this study, we examined the hypothesis of gene-disease interactions in an in-silico model of gene expression to seek changes in cytochrome P450 genes. The Gene Expression Omnibus dataset of the liver autopsy in deceased COVID-19 patients (GSE150316) was used in this study. Non-alcoholic fatty liver biopsies were used as the control (GSE167523). Besides, gene expression analysis was performed using the DESeq/EdgeR method. The GO databases were used, and the paths were set at p<0.05. The drug-gene interaction database (DGIdb) was searched for interactions. According to the results, 5,147 genes were downregulated, and 5,122 genes were upregulated in SARS-CoV-2 compared to healthy livers. Compared to the cytochromes, 34 cytochromes were downregulated, while 4 cytochromes were upregulated among the detected differentially expressed genes (DEG). The drug-gene interaction database (DGIdb) provided a list of medications with potential interactions with COVID-19 as well as metacetamol, phenethyl isocyanate, amodiaquine, spironolactone, amiloride, acenocoumarol, clopidogrel, phenprocoumon, trimipramine, phenazepam, etc. Besides, dietary compounds of isoflavones, valerian, and coumarin, as well as caffeine metabolism were shown to have possible interactions with COVID-19 disease. Our study showed that expression levels of cytochrome P450 genes could get altered following COVID-19. In addition, a drug-disease interaction list is recommended to be used for evaluations in clinical considerations in further studies.

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In silico analysis of the fragrance gene (badh2) in Asian rice (Oryza sativa L.) germplasm and validation of allele specific markers

Plant Genetic Resources ◽

10.1017/s1479262120000015 ◽

2020 ◽

Vol 18 (2) ◽

pp. 71-80

Author(s):

Withanage Vidyani Erandika Withana ◽

Rathanyaka Maudiyanselage Ramesha Eshani Kularathna ◽

Nisha Sualri Kottearachchi ◽

Deepthika S. Kekulandara ◽

Jagath Weerasena ◽

...

Keyword(s):

Oryza Sativa ◽

In Silico ◽

Oryza Sativa L ◽

Major Gene ◽

In Silico Analysis ◽

Betaine Aldehyde Dehydrogenase ◽

Nucleotide Polymorphisms ◽

Rice Varieties ◽

Asian Rice ◽

Allele Specific

AbstractBadh2 of rice is considered to be the major gene responsible for the fragrance in rice. The wild type badh2 allele encodes betaine aldehyde dehydrogenase 2 (BADH2) enzyme while the mutated version of badh2 gene encodes non-functional BADH2 enzyme that leads to the accumulation of 2-acetyl-1-pyrroline (2AP), the principal fragrant compound in rice. There are many mutated recessive alleles causing fragrance in global rice germplasm, although the badh2.1 allele present in Basmati type rice is the most well-known among breeders. In this study, we attempted to reveal potential fragrance causing mutations, and the respective varieties carrying them, through in silico analysis based on the sequences available in the Rice SNP-Seek-Database of International Rice Research Institute. The sequences of 1878 rice accessions from 22 countries were analysed to identify mutations in each exon of badh2 comparatively with the non-fragrant ‘wildtype’ GenBank sequence in Nanjing11, Oryza sativa indica (EU770319.1). Results revealed that 63 varieties from 12 countries possessed the most prevalent allele, badh2.1 having an 8 bp deletion and three single nucleotide polymorphisms in the 7th exon. The second most prevalent allele in genotypes from Asia was badh2.7 having a ‘G’ insertion in the 14th exon. A novel allele with a T deletion in 9th exon was detected in a Thai rice accession. Rice varieties containing either badh2.1 or badh2.7 alleles could be identified with DNA markers for badh2.1 (frg) and badh2.7 (Bad2.7CAPS). The marker, Bad2.7CAPS, co-segregated with the fragrance phenotype in two crosses, confirming the possibility of employing it in marker assisted breeding.

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