Biology subjects

Chakravartty, N.

Publications and source records attributed to Chakravartty, N..

4 recordsLinked to original sources

bioRxiv2021

Identification of heat responsive genes in pea stipules and anthers through transcriptional profiling

Field pea (Pisum sativum L.), a cool-season legume crop, is known for poor heat tolerance. Our previous work identified PR11-2 and PR11-90 as heat tolerant and susceptible lines in a recombinant inbred population. CDC Amarillo, a Canadian elite pea variety, was considered as another heat tolerant variety based on its similar field performance as PR11-2. This study aimed to characterize the differential transcription. Plants of these three varieties were stressed for 3h at 38{degrees}C prior to self-pollination, and RNAs from heat stressed anthers and stipules on the same flowering node were extracted and sequenced via the Illumina NovaSeq platform for the characterization of heat responsive genes. In silico results were further validated by qPCR assay. Differentially expressed genes (DEGs) were identified at log2 fold change, the three varieties shared 588 DEGs which were up-regulated and 220 genes which were down-regulated in anthers when subjected to heat treatment. In stipules, 879 DEGs (463/416 upregulation/downregulation) were consistent among varieties. The above heat-induced genes of the two plant organs were related to several biological processes i.e., response to heat, protein folding and DNA templated transcription. Ten gene ontology (GO) terms were over-represented in the consistently down-regulated DEGs of the two organs, and these terms were mainly related to cell wall macromolecule metabolism, lipid transport, lipid localization, and lipid metabolic processes. GO enrichment analysis on distinct DEGs of individual pea varieties suggested that heat affected biological processes were dynamic, and variety distinct responses provide insight into molecular mechanisms of heat-tolerance response. Several biological processes, e.g., cellular response to DNA damage stimulus in stipule, electron transport chain in anther that were only observed in heat induced PR11-2 and CDC Amarillo, and their relevance to field pea heat tolerance is worth further validation.

plant biology↗

bioRxiv2019

Deciphering the transcriptomic insight during organogenesis in castor (Ricinus communis L.), jatropha (Jatropha curcas L.) and sunflower (Helianthus annuus L.)

BackgroundCastor is a non-edible oilseed crop with a multitude of pharmaceutical and industrial uses. Profitable cultivation of the crop is hindered by various factors and one of the approaches for genetic improvement of the crop belonging to a monotypic genus is to exploit biotechnological tools. The major limitation for successful exploitation of biotechnological tools is the in vitro recalcitrance of castor tissues. Response of castor tissues to in vitro culture is poor which necessitated study on understanding the molecular basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis, by comparing with two other crops (jatropha and sunflower) with good regeneration ability.\n\nResultsRNA-seq analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from sunflower cultured on MS media supplemented with different concentrations of hormones. Genes that showed strong differential expression analysis during dedifferentiation and organogenic differentiation stages of callus included components of auxin and cytokinin signaling, secondary metabolite synthesis, genes encoding transcription factors, receptor kinases and protein kinases. In castor, many genes involved in auxin biosynthesis and homeostasis like WAT1 (Wall associated thinness), vacuolar transporter genes, transcription factors like short root like protein were down-regulated while genes like DELLA were upregulated accounting for regeneration recalcitrance. Validation of 62 differentially expressed genes through qRT-PCR showed a consensus of 77.4% with the RNA-Seq analysis.\n\nConclusionThis study provides information on the set of genes involved in the process of organogenesis in three oilseed crops which forms a basis for understanding and improving the efficiency of plant regeneration and genetic transformation in castor.

plant biology↗

bioRxiv2019

Deciphering the unique SNPs among leading Indian Tomato Cultivars using Double Digestion Restriction Associated DNA sequencing

World-wide grown and consumed tomato (Solanum lycopersicum) crop used as model system for new cultivar and fruit development. Genetic and genomic research of Indian tomato cultivars will provide an insight to develop new breeding strategies and crop improvement. The present study aimed to identify the high quality common and unique single nucleotide polymorphisms (SNPs), present in 9 different Indian tomato cultivars using double digestion restriction associated DNA sequencing (ddRAD-seq). Total of 36,847,092 raw reads (3.68 GB) were generated for all samples and 3,329,625 of high-quality reads were aligned uniquely to the reference tomato genome. Using stringent filtering, a total of 1,165 SNPs and 69 INDELs were found in genic regions, along with the unique variants to each cultivar was observed. Similarly, 7 and 33 variants were identified in chloroplast and mitochondrial genome of tomato. In addition, the population structure and genetic relationship among these cultivars suggested 4 well-differentiated sub-populations. Functional annotation of SNP/INDLEs associated with flanking sequences along with gene ontology and pathway analysis was performed. Identified SNPs/INDELs could be useful as markers for variety identification for genetic purity analysis. Findings from this work will be useful to plant breeders and research community to deepen their understanding and enhance tomato breeding programs.

genomics↗

bioRxiv2019

Whole genome sequencing and comparative genomic analysis reveal novel allelic variations unique to a purple colored rice landrace (Oryza sativa ssp. indica cv. Purpleputtu)

Purpleputtu (Oryza sativa ssp. indica cv. Purpleputtu) is a unique rice landrace from southern India that exhibits predominantly purple color. This study reports the underlying genetic complexity of the trait and associated domestication and de-domestication processes during its coevolution with present day cultivars. Along-with genome level allelic variations in the entire gene repertoire associated with purple, red coloration of grain and other plant parts. Comparative genomic analysis of the whole genome sequence of Purpleputtu (PP) revels total of 3,200,951 variants including 67,774 unique variations were observed in PP when compared with 108 rice genomes. Multiple sequence alignment uncovered a 14bp deletion in Rc (Red colored, a transcription factor of bHLH class) locus of PP, a key regulatory gene of anthocyanin biosynthetic pathway. Interestingly, this deletion in Rc gene is a characteristic feature of the present-day white pericarped rice cultivars. Phylogenetic analysis of Rc locus revealed a distinct clade showing proximity to the progenitor species rufipogon and nivara. In addition, PP genome exhibits a well conserved a 4.5Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique SNPs compared to 3,024 lines of rice (SNP-Seek database). The results indicate that PP genome is rich in allelic diversity and can serve as an excellent resource for rice breeding for a variety of agronomically important traits such as disease resistance, enhanced nutritional values, stress tolerance and protection from harmful UV-B rays.

genomics↗