Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia

Analyzing the Diversity of MYB Family Response Strategies to Drought Stress in Different Flax Varieties Based on Transcriptome Data

The MYB transcription factor family has numerous members, and is involved in biological activities, such as ABA signaling, which plays an important role in a plant's resistance to abiotic stresses such as drought. However, the diversity of MYB members that respond to drought stress and their regulatory mechanisms in different flax varieties were unclear. In this study, we obtained 855.69 Gb of clean data from 120 flax root samples from 20 flax (Linum usitatissimum L.) varieties, assembled 92,861 transcripts, and identified 434 MYB family members in each variety. The expression profiles of the MYB transcription factor family from 20 flax varieties under drought stress were analyzed. The results indicated that there are four strategies by which the MYB family responds to drought stress in these 20 flax varieties, each of which has its own specific processes, such as development, reproduction, and localization processes. The four strategies also include common biological processes, such as stimulus responses, metabolic processes, and biological regulation. The WGCNA method was subsequently employed to identify key members of the MYB family involved in response strategies to drought stress. The results demonstrated that a 1R-MYB subfamily gene co-expression network is significantly related to the gibberellin response and cytokinin-activated signaling pathway processes in the 'Strategy 4' for MYB family response to drought, identifying core genes such as Lus.scaffold70.240. Our results showed a diversity of MYB family responses to drought stress within flax varieties, and these results contribute to deciphering the mechanisms of the MYB family regulation of drought resistance. This will promote the more accurate breeding development of flax to adapt to agricultural production under drought conditions.

Molecular mechanism of thiamine in mitigating drought stress in Chinese wingnut (Pterocarya stenoptera): Insights from transcriptomics

Urban garden plants are frequently affected by drought, which can hinder their growth, development, and greening effect. Previous studies have indicated that Chinese wingnut (Pterocarya stenoptera) responds to drought stress by increasing the expression of thiamine synthesis genes. In this study, it was found that exogenous thiamine can effectively alleviate the negative effects of drought stress on plants. Forward transcriptome sequencing and physiological tests were further conducted to reveal the molecular mechanism of thiamine in alleviating drought stress. Results showed that exogenous thiamine activated the expression of eight chlorophyll synthesis genes in Chinese wingnut under drought stress. Moreover, physiological indicators proved that chlorophyll content increased in leaves of Chinese wingnut with thiamine treatment under drought stress. Photosynthesis genes were also activated in Chinese wingnut treated with exogenous thiamine under drought stress, as supported by photosynthetic indicators PIabs and PItotal. Additionally, exogenous thiamine stimulated the expression of genes in the auxin-activated signaling pathway, thus attenuating the effects of drought stress. This study demonstrates the molecular mechanism of thiamine in mitigating the effects of drought stress on non-model woody plants lacking transgenic systems. This study also provides an effective method to mitigate the negative impacts of drought stress on plants.

Comparative transcriptomics provides insights into the pathogenic immune response of brown leaf spots in weeping forsythia

Weeping forsythia is an important ornamental, ecological and medicinal plant. Brown leaf spots limit the large-scale production of weeping forsythia as a medicinal crop. Alternaria alternata is a pathogen causing brown leaf spots in weeping forsythia; however, its pathogenesis and the immune response mechanisms of weeping forsythia remain unclear. In this study, we identified two mechanisms based on morphological anatomy, physiological indexes and gene expression analyses. Our results showed that A. alternata induced leaf stomata to open, invaded the mesophyll, dissolved the cell wall, destroyed the cell membrane and decreased the number of chloroplasts by up-regulating the expression of auxin-activated signaling pathway genes. Alternaria alternata also down-regulated iron-ion homeostasis and binding-related genes, which caused an increase in the levels of iron ions and reactive oxygen species in leaves. These processes eventually led to programmed cell death, destroying palisade and spongy tissues and causing the formation of iron rust spots. Alternaria alternata also caused defense and hypersensitive responses in weeping forsythia through signaling pathways mediated by flg22-like and elf18-like polypeptides, ethylene, H2O2 and bacterial secretion systems. Our study provides a theoretical basis for the control of brown leaf spots in weeping forsythia.

Expression dosage effects of a small number of genes after the artificial doubling of weeping forsythia

Whole genome doubling (WGD) plays a critical role in plant evolution, yet the mechanisms underlying the maintenance of overall equilibrium following an artificial doubling event, as well as its impact on phenotype and adaptability, remain unclear. By comparing the gene expression of naturally occurring weeping forsythia diploids and colchicine-induced autotetraploids under normal growth conditions and cold stress, we identified gene expression dosage responses resulting from ploidy change. Only a small proportion of effectively expressed genes showed dosage effect, and most genes did not exhibit significant expression differences. However, the genes that showed expression dosage effect were largely random. The autotetraploids had slower overall growth rates, possibly resulting from negative gene dosage effects on zeatin synthesis and multiple metabolic delays caused by other negative dosage genes. Our comparative analysis of cold response genes in diploids and autotetraploids revealed that genes related to "response to abscisic acid" and "cold acclimation" were key factors contributing to greater cold tolerance in the autotetraploids. In particular, gene expression related to "cold acclimation" might mitigate the effects of cold stress. Taken together, our findings suggested that overall gene expression equilibrium following WGD of weeping forsythia autotetraploids was achieved through the inactivation of the majority of duplicated genes. Our research provides new insights into the mechanisms regulating expression dosage balance following polyploidization events.

Genome-wide investigation of the WRKY transcription factor gene family in weeping forsythia: expression profile and cold and drought stress responses

Weeping forsythia is a wide-spread shrub in China with important ornamental, medicinal and ecological values. It is widely distributed in China's warm temperate zone. In plants, WRKY transcription factors play important regulatory roles in seed germination, flower development, fruit ripening and coloring, and biotic and abiotic stress response. To date, WRKY transcription factors have not been systematically studied in weeping forsythia. In this study, we identified 79 WRKY genes in weeping forsythia and classified them according to their naming rules in Arabidopsis thaliana. Phylogenetic tree analysis showed that, except for IIe subfamily, whose clustering was inconsistent with A. thaliana clustering, other subfamily clustering groups were consistent. Cis-element analysis showed that WRKY genes related to pathogen resistance in weeping forsythia might be related to methyl jasmonate and salicylic acid-mediated signaling pathways. Combining cis-element and expression pattern analyses of WRKY genes showed that more than half of WRKY genes were involved in light-dependent development and morphogenesis in different tissues. The gene expression results showed that 13 WRKY genes were involved in drought response, most of which might be related to the abscisic acid signaling pathway, and a few of which might be regulated by MYB transcription factors. The gene expression results under cold stress showed that 17 WRKY genes were involved in low temperature response, and 9 of them had low temperature responsiveness cis-elements. Our study of WRKY family in weeping forsythia provided useful resources for molecular breeding and important clues for their functional verification.

Genome-wide analysis of the carotenoid cleavage dioxygenases gene family in Forsythia suspensa: Expression profile and cold and drought stress responses

Forsythia suspensa is a famous ornamental and medicinal plant in Oleaceae. CCD family is involved in the synthesis of pigments, volatiles, strigolactones, and abscisic acid (ABA) in plants. In this study, the CCD family in F. suspensa was analyzed at the genome level. A total of 16 members of the CCD family were identified, which included 11 members of the carotenoid cleavage dioxygenases (CCD) subfamily and 5 members of the 9-cis epoxycarotenoid dioxygenases (NCED) subfamily. The expression analysis of different tissues demonstrated that three FsCCD1 genes might be involved in the synthesis of pigments and volatiles in flowers and fruits. Three CCD4 genes were effectively expressed in flowers, while only FsCCD4-3 was effectively expressed in fruits. Comparison of CCD4 between Osmanthus fragrans and F. suspensa showed that the structure of FsCCD4-1 is was comparable that of OfCCD4-1 protein, indicating that the protein might be performing, especially in catalyzing the synthesis of β-ionone. However, further comparison of the upstream promoter regions showed that the proteins have major differences in the composition of cis-elements, which might be responsible for differences in β-ionone content. On the other hand, four NCED genes were significantly up-regulated under cold stress while two were up-regulated in drought stress. The data showed that these genes might be involved in the synthesis of ABA. Taken together, our data improves understanding of the CCD family and provides key candidate genes associated with cold and drought stresses in F. suspensa.