Plant Cis-regulatory elements: methods of identification and applications

Ijaz, Usman

doi:10.35495/ajab.2019.08.352

Cited by 21 publications

(8 citation statements)

References 134 publications

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“…Cis-regulatory elements are linear fragments of non-coding DNA. Cis-regulatory elements provide the binding sites for transcription factors [ 45 ]. They have many localizations, orientations, and activities in relation to genes.…”

Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses

Azeem

Ijaz

Ali

et al. 2021

Plants

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Potassium (K+) is one of the most important cations that plays a significant role in plants and constitutes up to 10% of plants’ dry weight. Plants exhibit complex systems of transporters and channels for the distribution of K+ from soil to numerous parts of plants. In this study, we have identified 39 genes encoding putative K+ transport-related genes in Vigna radiata. Chromosomal mapping of these genes indicated an uneven distribution across eight out of 11 chromosomes. Comparative phylogenetic analysis of different plant species, i.e., V. radiata, Glycine max, Cicer arietinum, Oryza sativa, and Arabidopsis thaliana, showed their strong conservation in different plant species. Evolutionary analysis of these genes suggests that gene duplication is a major route of expansion for this family in V. radiata. Comprehensive promoter analysis identified several abiotic stresses related to cis-elements in the promoter regions of these genes, suggesting their role in abiotic stress tolerance. Our additional analyses indicated that abiotic stresses adversely affected the chlorophyll concentration, carotenoids, catalase, total soluble protein concentration, and the activities of superoxide and peroxidase in V. radiata. It also disturbs the ionic balance by decreasing the uptake of K+ content and increasing the uptake of Na+. Expression analysis from high-throughput sequencing data and quantitative real-time PCR experiments revealed that several K+ transport genes were expressed in different tissues (seed, flower, and pod) and in abiotic stress-responsive manners. A highly significant variation of expression was observed for VrHKT (1.1 and 1.2), VrKAT (1 and 2) VrAKT1.1, VrAKT2, VrSKOR, VrKEA5, VrTPK3, and VrKUP/HAK/KT (4, 5, and 8.1) in response to drought, heat or salinity stress. It reflected their potential roles in plant growth, development, or stress adaptations. The present study gives an in-depth understanding of K+ transport system genes in V. radiata and will serve as a basis for a functional analysis of these genes.

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Section: Resultsmentioning

confidence: 99%

Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses

Azeem

Ijaz

Ali

et al. 2021

Plants

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“…In the promoter sequences, cis -elements were predicted to gain a better understanding of the role of DcSOD genes under different environmental conditions (Ijaz et al, 2020 ). Similar to tomato SlSOD genes, different stress, hormone, and light-responsive elements were identified, which were related to drought, anaerobic induction, and low temperature (Zhang et al, 2015 ).…”

Section: Discussionmentioning

confidence: 99%

Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H2O2) Under Abiotic Stress Condition

et al. 2022

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Superoxide dismutase (SOD) proteins are important antioxidant enzymes that help plants to grow, develop, and respond to a variety of abiotic stressors. SOD gene family has been identified in a number of plant species but not yet in Daucus carota. A total of 9 DcSOD genes, comprising 2 FeSODs, 2 MnSODs, and 5 Cu/ZnSODs, are identified in the complete genome of D. carota, which are dispersed in five out of nine chromosomes. Based on phylogenetic analysis, SOD proteins from D. carota were categorized into two main classes (Cu/ZnSODs and MnFeSODs). It was predicted that members of the same subgroups have the same subcellular location. The phylogenetic analysis was further validated by sequence motifs, exon–intron structure, and 3D protein structures, with each subgroup having a similar gene and protein structure. Cis-regulatory elements responsive to abiotic stresses were identified in the promoter region, which may contribute to their differential expression. Based on RNA-seq data, tissue-specific expression revealed that DcCSD2 had higher expression in both xylem and phloem. Moreover, DcCSD2 was differentially expressed in dark stress. All SOD genes were subjected to qPCR analysis after cold, heat, salt, or drought stress imposition. SODs are antioxidants and play a critical role in removing reactive oxygen species (ROS), including hydrogen peroxide (H2O2). DcSODs were docked with H2O2 to evaluate their binding. The findings of this study will serve as a basis for further functional insights into the DcSOD gene family.

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“…Various previous researchers who used SSR markers for sunflower characterization at molecular data also found that sunflower lines had a clear tendency of grouping restorer and CMS lines into different clusters. For examining the genetic diversity in sunflower SSR, markers are a powerful as it reveals high level of polymorphism among sunflower lines (Lochner, 2011 ; Zia et al, 2014 ; Suresha et al, 2017 ; Ijaz et al, 2020 ).…”

Section: Discussionmentioning

confidence: 99%

Molecular markers-based DNA fingerprinting coupled with morphological diversity analysis for prediction of heterotic grouping in sunflower (Helianthus annuus L.)

et al. 2022

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Cultivated sunflower holds a very narrow genetic base and the efficient utilization of available genetic diversity is very important for a successful breeding program. In the present study, 109 sunflower genotypes were assessed for diversity paneling through a combined approach of morphological and molecular markers analysis. Morphological parameters including days to flower initiation, days to flower completion, plant height, stem curvature, number of leaves per plant, leaf area, head diameter, hundred seed weight, and seed yield per plant were studied. Simple sequence repeats (40 DNA markers) were deployed for diversity profiling. Data were analyzed by both univariate and multivariate statistics. SD and coefficient of variation confirm the presence of significant amounts of genetic variation for all the morphological parameters. Cluster Analysis and Principal Component Analysis further confirm the presence of distinct grouping patterns in the studied material. Cluster analysis of both morphological and molecular analysis revealed that restorer lines tend to group separately from A, B, and open-pollinated lines. Further grouping, at the sub-cluster level, revealed six distinct sub-clusters in each of the two major clusters. In total, 12 genotypes, 6 CMS lines (CMS-HAP-12, CMS-HAP-54, CMS-HAP-56, CMS-HAP-99, CMS-HAP-111, and CMS-HAP-112) and 6 restorer lines (RHP-38, RHP-41, RHP-53, RHP-68, RHP-69, and RHP-71) could be used as potential parents for hybrid development. As genotypes of similar genetic backgrounds tend to group closer, it is deduced that one genotype with the highest seed yield per plant could be used for further hybrid breeding programs in sunflowers.

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Plant Cis-regulatory elements: methods of identification and applications

Cited by 21 publications

References 134 publications

Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses

Genome-Wide Identification and Expression Profiling of Potassium Transport-Related Genes in Vigna radiata under Abiotic Stresses

Genome-Wide Characterization of Superoxide Dismutase (SOD) Genes in Daucus carota: Novel Insights Into Structure, Expression, and Binding Interaction With Hydrogen Peroxide (H2O2) Under Abiotic Stress Condition

Molecular markers-based DNA fingerprinting coupled with morphological diversity analysis for prediction of heterotic grouping in sunflower (Helianthus annuus L.)

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