Extrapolation of significant genes and transcriptional regulatory networks involved in Zea mays in response in UV-B stress

Recent advances in exploring transcriptional regulatory landscape of crops

Crop breeding entails developing and selecting plant varieties with improved agronomic traits. Modern molecular techniques, such as genome editing, enable more efficient manipulation of plant phenotype by altering the expression of particular regulatory or functional genes. Hence, it is essential to thoroughly comprehend the transcriptional regulatory mechanisms that underpin these traits. In the multi-omics era, a large amount of omics data has been generated for diverse crop species, including genomics, epigenomics, transcriptomics, proteomics, and single-cell omics. The abundant data resources and the emergence of advanced computational tools offer unprecedented opportunities for obtaining a holistic view and profound understanding of the regulatory processes linked to desirable traits. This review focuses on integrated network approaches that utilize multi-omics data to investigate gene expression regulation. Various types of regulatory networks and their inference methods are discussed, focusing on recent advancements in crop plants. The integration of multi-omics data has been proven to be crucial for the construction of high-confidence regulatory networks. With the refinement of these methodologies, they will significantly enhance crop breeding efforts and contribute to global food security.

Multi-Omic Analysis Reveals the Molecular Mechanism of UV-B Stress Resistance in Acetylated RcMYB44 in Rhododendron chrysanthum

Ultraviolet-B (UV-B) radiation is a significant environmental factor influencing the growth and development of plants. MYBs play an essential role in the processes of plant responses to abiotic stresses. In the last few years, the development of transcriptome and acetylated proteome technologies have resulted in further and more reliable data for understanding the UV-B response mechanism in plants. In this research, the transcriptome and acetylated proteome were used to analyze Rhododendron chrysanthum Pall. (R. chrysanthum) leaves under UV-B stress. In total, 2348 differentially expressed genes (DEGs) and 685 differentially expressed acetylated proteins (DAPs) were found. The transcriptome analysis revealed 232 MYB TFs; we analyzed the transcriptome together with the acetylated proteome, and screened 4 MYB TFs. Among them, only RcMYB44 had a complete MYB structural domain. To investigate the role of RcMYB44 under UV-B stress, a homology tree was constructed between RcMYB44 and Arabidopsis MYBs, and it was determined that RcMYB44 shares the same function with ATMYB44. We further constructed the hormone signaling pathway involved in RcMYB44, revealing the molecular mechanism of resistance to UV-B stress in R. chrysanthum. Finally, by comparing the transcriptome and the proteome, it was found that the expression levels of proteins and genes were inconsistent, which is related to post-translational modifications of proteins. In conclusion, RcMYB44 of R. chrysanthum is involved in mediating the growth hormone, salicylic acid, jasmonic acid, and abscisic acid signaling pathways to resist UV-B stress.

Supplementary UV-B Radiation Effects on Photosynthetic Characteristics and Important Secondary Metabolites in Eucommia ulmoides Leaves

To explore the effects of ultraviolet light supplementation on the photosynthetic characteristics and content of secondary metabolites in the leaves of Eucommia ulmoides Oliver (E. ulmoides), the effects of supplementary UV-B (sUV-B) radiation on the medicinally active components of E. ulmoides were comprehensively evaluated. In our study, we selected leaves of five-year-old E. ulmoides seedlings as experimental materials and studied the effect of supplemental ultraviolet-B (sUV-B) radiation on growth, photosynthetic parameters, photosynthetic pigments, fluorescence parameters, and secondary metabolites of E. ulmoides using multivariate analysis. The results showed that the leaf area and the number of branches increased after sUV-B radiation, which indicated that sUV-B radiation was beneficial to the growth of E. ulmoides. The contents of chlorophyll a and chlorophyll b increased by 2.25% and 4.25%, respectively; the net photosynthetic rate increased by 5.17%; the transpiration rate decreased by 35.32%; the actual photosynthetic efficiency increased by 10.64%; the content of the secondary metabolite genipin increased by 12.9%; and the content of chlorogenic acid increased by 75.03%. To identify the genes that may be related to the effects of sUV-B radiation on the growth and development of E. ulmoides leaves and important secondary metabolites, six cDNA libraries were prepared from natural sunlight radiation and sUV-B radiation in E. ulmoides leaves. Comparative analysis of both transcriptome databases revealed a total of 3698 differential expression genes (DEGs), including 1826 up-regulated and 1872 down-regulated genes. According to the KOG database, the up-regulated unigenes were mainly involved in signal transduction mechanisms [T] and cell wall/membrane biogenesis [M]. It is also involved in plant hormone signal transduction and phenylpropanoid biosynthesis metabolic pathways by the KEGG pathway, which might further affect the physiological indices and the content of chlorogenic acid, a secondary metabolite of E. ulmoides. Furthermore, 10 candidate unigenes were randomly selected to examine gene expression using qRT-PCR, and the six libraries exhibited differential expression and were identical to those obtained by sequencing. Thus, the data in this study were helpful in clarifying the reasons for leaf growth after sUV-B radiation. And it was beneficial to improve the active components and utilization rate of E. ulmoides after sUV-B radiation.

Effect of enhanced UV-B radiation on growth and photosynthetic physiology of Iris tectorum maxim

Iris tectorum Maxim. is an important plant that plays a very crucial role in the ecological welfare of wetlands. In this study, the effects of different intensities of UV-B radiation on the growth, photosynthetic pigment content, chlorophyll fluorescence characteristics, chloroplast ultrastructure, and gas exchange parameters of Iris tectorum Maxim. were studied. The results showed that enhanced UV-B radiation had a significant influence on the above-mentioned parameters of iris. Compared with the control, enhanced UV-B radiation caused certain damage to the leaf appearance. With the increasing intensity of radiation, the apparent damage degree became more serious. Enhanced UV-B radiation significantly decreased leaf chlorophyll contents, and the effect accumulated with the exposure time. Enhanced UV-B radiation increased Fo, significantly increased the non-photochemical quenching coefficient NPQ, reduced PSII and Qp, and significantly decreased the Fm, Fv/Fm, and Fv/Fo in leaves. The effect of UV-B radiation on PSII destruction of Iris tectorum Maxim. increased as the radiation intensity increased and the exposure time prolonged. The chloroplast structure was damaged under the enhanced UV-B radiation. More specifically, thylakoid lamellae were distorted, swelling and even blurred, and a large number of starch granules appeared. The effect of the high intensity of radiation on chloroplast ultrastructure was greater than that of lower intensity. Enhanced UV-B radiation reduced significantly the net photosynthetic rate, stomatal conductance, and transpiration rate, and the degree of degradation increased with the increasing irradiation intensity. However, the intercellular CO₂ content increased, which suggests that the main reason for the decrease of photosynthetic rate was the non-stomatal factors.

UV-B induces the expression of flavonoid biosynthetic pathways in blueberry (Vaccinium corymbosum) calli

Ultraviolet-B (UV-B) radiation is an environmental signal that affects the accumulation of secondary metabolites in plants. In particular, UV-B promotes flavonoid biosynthesis, leading to improved fruit quality. To explore the underlying molecular mechanism, we exposed blueberry (Vaccinium corymbosum) calli to UV-B radiation and performed a transcriptome deep sequencing (RNA-seq) analysis to identify differentially expressed genes (DEGs). We detected 16,899 DEGs among different treatments, with the largest number seen after 24 h of UV-B exposure relative to controls. Functional annotation and enrichment analysis showed a significant enrichment for DEGs in pathways related to plant hormone signal transduction and phenylpropanoid and flavonoid biosynthesis. In agreement with the transcriptome data, flavonol, anthocyanin and proanthocyanidin accumulated upon UV-B radiation, and most DEGs mapping to the phenylpropanoid and flavonoid biosynthetic pathways using the KEGG mapper tool were upregulated under UV-B radiation. We also performed a weighted gene co-expression network analysis (WGCNA) to explore the relationship among genes involved in plant hormone signal transduction, encoding transcription factors or participating in flavonoid biosynthesis. The transcription factors VcMYBPA1, MYBPA2.1, MYB114, MYBA2, MYBF, and MYB102 are likely activators, whereas MYB20, VcMYB14, MYB44, and VcMYB4a are inhibitors of the flavonoid biosynthetic pathway, as evidenced by the direction of correlation between the expression of these MYBs and flavonoid biosynthesis-related genes. The transcription factors bHLH74 and bHLH25 might interact with MYB repressors or directly inhibited the expression of flavonoid biosynthetic genes to control flavonoid accumulation. We also observed the downregulation of several genes belonging to the auxin, gibberellin and brassinosteroid biosynthetic pathways, suggesting that MYB inhibitors or activators are directly or indirectly regulated to promote flavonoid biosynthesis under UV-B radiation.

Deciphering the transcriptomic insight during organogenesis in Castor (Ricinus communis L.), Jatropha (Jatropha curcas L.) and Sunflower (Helianthus annuus L.)

Cultivation of the castor crop is hindered by various factors and one of the approaches for genetic improvement of the crop is through exploitation of biotechnological tools. Response of castor tissues to in vitro culture is poor which necessitated this study on understanding the molecular basis of organogenesis in cultured tissues of castor, through de novo transcriptome analysis and by comparing with jatropha and sunflower having good regeneration ability. Transcriptome profiling analysis was carried out with hypocotyl explants from castor, jatropha and cotyledons from sunflower cultured on MS media supplemented with different concentrations of hormones. Differentially expressed genes 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, vacuolar transporter genes, transcription factors like short root like protein were down-regulated while genes like DELLA were up-regulated accounting for regeneration recalcitrance. Validation of 62 DEGs through qRT-PCR showed a consensus of 77.4% of the genes expressed. Overall study provides 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.

Whole Genome Sequencing and Comparative Genomic Analysis Reveal 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, 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 the purple, red coloration of grain and other plant parts. Comparative genomic analysis using 'a panel of 108 rice lines' revealed a total of 3,200,951 variants including 67,774 unique variations in Purpleputtu (PP) genome. Multiple sequence alignment uncovered a 14 bp 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 Oryza rufipogon and O. nivara. In addition, PP genome exhibits a well conserved 4.5 Mbp region on chromosome 5 that harbors several loci associated with domestication of rice. Further, PP showed 1,387 unique when SNPs compared to 3,023 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.

Deciphering genome-wide WRKY gene family of Triticum aestivum L. and their functional role in response to Abiotic stress

WRKY transcription factors (TFs) act in regulating plant growth and development as well as in response to different stress. Some earlier studies done by individual researchers reported different wheat WRKY TFs. Although, the recently released wheat genome has opened an avenue to investigate wheat WRKYs (TaWRKY) TFs. Prime objective of this study to performed genome-wide classifications of TaWRKYs and their functional annotation. The classification of 107 individual identified characterized sequences of TaWRKY (IICS-TaWRKY) and 160 uncharacterized draft sequences of TaWRKY (UDS-TaWRKY), along with their gene structures and motifs analysis was performed. Along with comparative sequence analysis and microarray analysis was performed to mimic out TaWRKYs functions in response to different abiotic stresses, accompanied by in-vitro validation. The comparative phylogenetic analysis and estimation of Ka/Ks ratio with Triticum urartu, illustrate group based clasifications of TaWRKYs and evolutionary divergences. Furthermore, motif-based and protein-DNA interaction analysis of TaWRKYs helps to identify, their putative function in target DNA recognition sites. Subsequently, results of microarray and comparative sequence analysis provides the evidence of TaWRKYs involved in heat and/or drought stress. Further, in-vitro results validates that TaWRKY014, TaWRKY090 are found to participate in response of drought stress, whereas TaWRKY008, TaWRKY122, and WRKY45 are involved in response of heat and drought stress. These findings can be utilized in developing novel heat and drought-tolerant wheat cultivars using marker-assisted breeding and transgenic development.