Biology subjects

Gupta, O. P.

Publications and source records attributed to Gupta, O. P..

4 recordsLinked to original sources

bioRxiv2021

An innovative approach for determining composite wheat quality index to identify quality enriched genotypes - insights and implications

Ranking test entries or test sites on a quality basis is very difficult in wheat as value addition is perceived by several grain properties and end-products. Here, a novel approach has been developed and tested by deriving wheat quality index based on principal component analysis of 13 physico-chemical grain parameters and 3 end products of 45 wheat varieties. Depending upon the observed index range (0.15 to 0.71), the cultivars were assorted into 3 distinct classes i.e. elite, moderate and poor. The top group ascertained high quality standards of grain suited for bread and chapati whereas bottom group assured better cookies quality. This technique was also tested to differentiate quality enriched test sites within a zone or demarcate the most suited production environments to harness good quality wheat. The index will have an implication on farmers (premium price for varietal segregation), industry (product specific quality cultivars), and consumers (superior quality products).

biochemistry↗

bioRxiv2021

Genome-wide comprehensive analysis of miRNAs and their target genes expressed in resistant and susceptible Capsicum annuum landrace during Phytophthora capsici infection

MiRNAs regulate plants responses to fungal infection and immunity by modulating the gene expression. Despite extensive works on miRNAs role during plant-fungus interaction, work in Capsicum annuum-Phytophthora capsici pathosystem is limited. Therefore, in the current study, genome-wide known and novel miRNAs were identified in two contrasting chilli pepper landraces, i.e. GojamMecha_9086 (resistant) and Dabat_80045 (susceptible) during P. capsici infection. The small RNA deep sequencing resulted in 79 known miRNAs corresponding to 24 miRNAs families and 477 novel miRNAs along with 22,895 potential targets, including 30 defence-related genes against P. capsici infection. The expression analysis of [~]29 known & 157 novel miRNAs in resistant and 30 known and 176 novel miRNAs in susceptible landrace revealed differential accumulation pattern. RT-qPCR of a set of 8 defence related miRNAs representing 4 novel (Pz-novel-miR428-1, Pz-novel-miR160-1, Pz-novel-miR1028-1, Pz-novel-miR204-1) and 4 known (Pz-known-miR803-1, Pz-known-miR2059-1, Pz-known-miR2560-1, Pz-known-miR1872-1) revealed differential accumulation pattern in both resistant and susceptible landrace. Additionally, validation of 8 target genes of corresponding miRNAs using RA-PCR, which as good as 5 RLM-RACE, revealed an inverse relation with their corresponding miRNAs suggesting their key role during disease response. This study provides comprehensive genome-wide information about the repertoire of miRNAs and their target genes expressed in resistant and susceptible chilli pepper landrace, which can serve as a valuable resource for better understanding the post-transcriptional regulatory mechanism during C. annuum - P. capsici pathosystem.

genomics↗

bioRxiv2021

Integrative RNA-Seq analysis of Capsicum annuum L.-Phytophthora capsici L. pathosystem reveals molecular cross-talk and activation of host defence response

BackgroundChili pepper (Capsicum annuum L.) being one of an important member of the Solanaceae family, and its productivity is highly affected by the fungal pathogen Phytophthora capsici L. Other to CM-344, the unavailability of resistant landraces to all possible strains of P. capsici imposes a serious threat to its global production. This is because of our current understanding of the molecular mechanisms associated with the defence response in C. annuum-P. capsici pathosystem is limited. Therefore, the current study used RNA-seq technology to dissect the genes associated with defence response against P. capsici infection in two contrasting landraces, i.e. GojamMecha_9086 (Resistant) and Dabat_80045 (susceptible) exposed to P. capsici infection. ResultsThe transcriptomes from 4 leaf samples (RC, RI, SC and SI) of chili pepper resulted in a total of 1,18, 879 assembled transcripts (with a mean TL of 813.23bp and N50 of 1,277bp) along with 52,384 pooled unigenes with (mean UL of 1029.36 bp and N50 of 1,403bp). The enrichment analysis of the transcripts indicated 23 different KEGG pathways under five main categories. Further, 774 and 484 differentially expressed genes (DEGs) were obtained from RC vs. RI and SC vs. SI leaf samples, respectively. Of these, 57 DEGs were found to be associated with defence responses against P. capsici infection. The defence-related genes, such as LTPL, defensin J1-2-like, peroxidase 5-like, UGT, and GRP proteins-like, were more significantly upregulated in RC vs. RI. Furthermore, RT-qPCR analysis of six randomly selected genes validated the results of Illumina NextSeq500 sequencing results. Furthermore, a total of 58 TF families (bHLH most abundant) and 2,095 protein families (Protein kinase, PF00069, most abundant) were observed across all the samples with maximum hits in RI and SI samples. ConclusionsRNA-Seq analysis of chili peppers during P.capsici infection revealed differential regulation of genes associated with defence and signaling response with shared coordination of molecular function, cellular component and biological processing. The results presented here would enhance our present understanding of the defence response in chili pepper against P. capsici infection, which could be utilized by the molecular breeders to develop resistant chili genotypes.

genomics↗

bioRxiv2021

Integrative physiological, biochemical and transcriptomic analysis of hexaploid wheat roots and shoots provides new insights into the molecular regulatory network during Fe & Zn starvation

In plants, iron (Fe) & zinc (Zn) uptake and transportation from the rhizosphere to the grain is a critical process regulated by complex transcriptional regulatory networks. However, understanding the combined effect of Fe & Zn starvation on their uptake and transportation and the molecular regulatory networks that control them lack in wheat. Here, we performed a comprehensive physiological, biochemical and transcriptome analysis in two bread wheat genotypes, i.e. Narmada 195 and PBW 502, differing in inherent Fe & Zn content to understand the mechanism of Fe & Zn homeostasis. Compared to PBW 502, Narmada 195 exhibited increased tolerance to Fe & Zn withdrawal by an increased level of antioxidant enzymes and DPPH radical scavenging activity along with less malondialdehyde (MDA), H2O2 level, increased PS accumulation and lower reduction of root and shoot Fe & Zn content and length, leaf chlorosis, and leaf area. By integrating physiological and biochemical data along with co-expression & functional genome annotation and gene expression analysis, we identified 25 core genes associated with four key pathways, i.e. Met cycle (10), PS biosynthesis (4), antioxidant (3) and transport system (8) that were significantly modulated by Fe & Zn withdrawal in both the genotypes. Genes of these four pathways were more considerably up-regulated in Narmada 195, allowing better tolerance to Fe & Zn withdrawal and efficient uptake and transportation of Fe & Zn. Chromosomal distribution and sub-genome wise mapping of these genes showed a contribution from all the chromosomes except group 5 chromosomes with the highest number of genes mapped to chromosome 4 (24%) and sub-genome D (40%). Besides, we also identified 26 miRNAs targeting 14 core genes across the four pathways. Together, our work provides a crucial angle for an in-depth understanding of regulatory cross-talk among physiological, biochemical and transcriptional reprogramming underlying Fe & Zn withdrawal in wheat. Core genes identified can serve as valuable resources for further functional research for genetic improvement of Fe & Zn content in wheat grain. HighlightOur work provides a crucial angle for a comprehensive understanding of the regulatory mechanism underlying Fe & Zn withdrawal associated with physiological, biochemical and transcriptional reprogramming in wheat.

molecular biology↗