Quantitative expression of microRNAs in Brassica oleracea infected with Xanthomonas campestris pv. campestris

Souza, Lucas Santos; Maximiano, Mariana Rocha; Megías, Esaú; Pappas, Marília de Castro Rodrigues; Ribeiro, S. G.; Mehta, Ângela

doi:10.1007/s11033-019-04779-7

Cited by 12 publications

(6 citation statements)

References 39 publications

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“…In this work, we found that miR390a expression levels decreased 0.78-fold, and were ranked as the fourth most stable according to the geNorm and NormFinder programs, suggesting that miR390a is not the optimal reference gene in poplar under biotic stress. This is supported by a previous study, in which disease-resistant and disease-susceptible cultivars of Brassica oleracea were each inoculated with a pathogen; miR390 expression levels in disease-resistant cultivars increased 1.5-fold, whereas its levels decreased 1.7-fold in disease-susceptible cultivars [35]. It was reported that the expression of mi390a-5p increased 2.8-fold in Arabidopsis inoculated with Verticillium dahlia [36].…”

Section: Discussionsupporting

confidence: 77%

Identification and validation of miRNA reference genes in poplar under pathogen stress

et al. 2021

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Quantitative real time polymerase chain reaction (qRT-PCR) is a common method to analyze gene expression. Due to differences in RNA quantity, quality, and reverse transcription efficiency between qRT-PCR samples, reference genes are used as internal standards to normalize gene expression.However, few universal genes especially miRNAs have been identified as reference so far. Therefore, it is essential to identify reference genes that can be used across various experimental conditions, stress treatments, or tissues. In this study, 14 microRNAs (miRNAs) and 5.8S rRNA were assessed for expression stability in poplar trees infected with canker pathogen. Using three reference gene analysis programs, we found that miR156g and miR156a exhibited stable expression throughout the infection process. miR156g and miR156a were then tested as internal standards to measure the expression of miR1447 and miR171c, and the results were compared to small RNA sequencing (RNA-seq) data. We found that when miR156a was used as the reference gene, the expression of miR1447 and miR171c were consistent with the small RNA-seq expression profiles. Therefore, miR156a was the most stable miRNAs examined in this study, and could be used as a reference gene in poplar under canker pathogen stress, which should enable comprehensive comparisons of miRNAs expression and avoid the bias caused by different lenth between detected miRNAs and traditional referece genes. The present study has expanded the miRNA reference genes available for gene expression studies in trees under biotic stress.

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Section: Discussionsupporting

confidence: 77%

Identification and validation of miRNA reference genes in poplar under pathogen stress

et al. 2021

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“…The functional involvement of plant miRNAs in response to abiotic stresses was originally suggested by surveys of NCBI expressed sequence tags and profiling miRNA expression after challenging plants with certain stress stimuli to predict miRNA targets [40]. Flowering Chinese cabbage has much fewer miRNAs registered in miRBase compared to other vegetable crops and model plant Arabidopsis [11,41].…”

Section: Mirna In Flowering Chinese Cabbagementioning

confidence: 99%

Comparative Analysis of miRNA Expression Profiles between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing

Waqas

Xia

et al. 2020

Genes

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Heat stress disturbs cellular homeostasis, thus usually impairs yield of flowering Chinese cabbage (Brassica campestris L. ssp. chinensis var. utilis Tsen et Lee). MicroRNAs (miRNAs) play a significant role in plant responses to different stresses by modulating gene expression at the post-transcriptional level. However, the roles that miRNAs and their target genes may play in heat tolerance of flowering Chinese cabbage remain poorly characterized. The current study sequenced six small RNA libraries generated from leaf tissues of flowering Chinese cabbage collected at 0, 6, and 12 h after 38 °C heat treatment, and identified 49 putative novel miRNAs and 43 known miRNAs that differentially expressed between heat-tolerant and heat-sensitive flowering Chinese cabbage. Among them, 14 novel and nine known miRNAs differentially expressed only in the heat-tolerant genotype under heat-stress, therefore, their target genes including disease resistance protein TAO1-like, RPS6, reticuline oxidase-like protein, etc. might play important roles in enhancing heat-tolerance. Gene Ontology (GO) analysis revealed that targets of these differentially expressed miRNAs may play key roles in responses to temperature stimulus, cell part, cellular process, cell, membrane, biological regulation, binding, and catalytic activities. Furthermore, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analysis identified their important functions in signal transduction, environmental adaptation, global and overview maps, as well as in stress adaptation and in MAPK signaling pathways such as cell death. These findings provide insight into the functions of the miRNAs in heat stress tolerance of flowering Chinese cabbage.

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“…miRNAs are conserved and are involved in many molecular interaction networks including plant-pathogen interactions ( Sunkar et al, 2012 ; Islam W. et al, 2017 ). The role of miRNAs in plants was examined in response to Xcc infection and four miRNAs (miR156, miR167, miR169, and miR390) were found to be differentially expressed showing a down and up-regulated expression profile in the susceptible and resistant cultivars, respectively ( Santos L.S. et al, 2019 ).…”

Section: Advances In Omics Technologiesmentioning

confidence: 99%

Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L.

et al. 2021

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Brassica oleracea is one of the most important species of the Brassicaceae family encompassing several economically important vegetables produced and consumed worldwide. But its sustainability is challenged by a range of pathogens, among which black rot, caused by Xanthomonas campestris pv. campestris (Xcc), is the most serious and destructive seed borne bacterial disease, causing huge yield losses. Host-plant resistance could act as the most effective and efficient solution to curb black rot disease for sustainable production of B. oleracea. Recently, ‘omics’ technologies have emerged as promising tools to understand the host-pathogen interactions, thereby gaining a deeper insight into the resistance mechanisms. In this review, we have summarized the recent achievements made in the emerging omics technologies to tackle the black rot challenge in B. oleracea. With an integrated approach of the omics technologies such as genomics, proteomics, transcriptomics, and metabolomics, it would allow better understanding of the complex molecular mechanisms underlying black rot resistance. Due to the availability of sequencing data, genomics and transcriptomics have progressed as expected for black rot resistance, however, other omics approaches like proteomics and metabolomics are lagging behind, necessitating a holistic and targeted approach to address the complex questions of Xcc-Brassica interactions. Genomic studies revealed that the black rot resistance is a complex trait and is mostly controlled by quantitative trait locus (QTL) with minor effects. Transcriptomic analysis divulged the genes related to photosynthesis, glucosinolate biosynthesis and catabolism, phenylpropanoid biosynthesis pathway, ROS scavenging, calcium signalling, hormonal synthesis and signalling pathway are being differentially expressed upon Xcc infection. Comparative proteomic analysis in relation to susceptible and/or resistance interactions with Xcc identified the involvement of proteins related to photosynthesis, protein biosynthesis, processing and degradation, energy metabolism, innate immunity, redox homeostasis, and defence response and signalling pathways in Xcc–Brassica interaction. Specifically, most of the studies focused on the regulation of the photosynthesis-related proteins as a resistance response in both early and later stages of infection. Metabolomic studies suggested that glucosinolates (GSLs), especially aliphatic and indolic GSLs, its subsequent hydrolysis products, and defensive metabolites synthesized by jasmonic acid (JA)-mediated phenylpropanoid biosynthesis pathway are involved in disease resistance mechanisms against Xcc in Brassica species. Multi-omics analysis showed that JA signalling pathway is regulating resistance against hemibiotrophic pathogen like Xcc. So, the bonhomie between omics technologies and plant breeding is going to trigger major breakthroughs in the field of crop improvement by developing superior cultivars with broad-spectrum resistance. If multi-omics tools are implemented at the right scale, we may be able to achieve the maximum benefits from the minimum. In this review, we have also discussed the challenges, future prospects, and the way forward in the application of omics technologies to accelerate the breeding of B. oleracea for disease resistance. A deeper insight about the current knowledge on omics can offer promising results in the breeding of high-quality disease-resistant crops.

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Quantitative expression of microRNAs in Brassica oleracea infected with Xanthomonas campestris pv. campestris

Cited by 12 publications

References 39 publications

Identification and validation of miRNA reference genes in poplar under pathogen stress

Identification and validation of miRNA reference genes in poplar under pathogen stress

Comparative Analysis of miRNA Expression Profiles between Heat-Tolerant and Heat-Sensitive Genotypes of Flowering Chinese Cabbage Under Heat Stress Using High-Throughput Sequencing

Advances in Multi-Omics Approaches for Molecular Breeding of Black Rot Resistance in Brassica oleracea L.

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