The MYB transcription factor (TF) family is one of the largest families in plants and performs highly diverse regulatory functions, particularly in relation to pathogen/pest resistance, nutrient/noxious substance absorption, drought/salt resistance, trichome growth, stamen development, leaf senescence, and flavonoid/terpenoid biosynthesis. Owing to their vital role in various biological regulatory processes, the mechanisms of MYB TFs have been extensively studied. Notably, MYB TFs not only directly regulate targets, such as phytohormones, reactive oxygen species signaling and secondary cell wall formation, but also serve as crucial points of crosstalk between these signaling networks. Here, we have comprehensively described the structures, classifications, and biological functions of MYB TFs, with a specific focus on their roles and mechanisms in the response to biotic and abiotic stresses, plant morphogenesis, and secondary metabolite biosynthesis. Different from other reported reviews, this review provides comprehensive knowledge on plant MYB TFs and will provide valuable insights in understanding regulatory networks and associated functions of plant MYB TFs to apply in resistance breeding and crop improvement. 

MYB transcription factors in plants: A comprehensive review of their discovery, structure, classification, functional diversity and regulatory mechanism

α-Farnesene, a crucial secondary metabolite in sesquiterpenes, is crucial for plant biotic and abiotic stress resistance. In this study, we screened an AFS gene from transcriptome data of tea plants (Camellia sinensis) intercropped with Chinese chestnut (Castanea mollissima), resulting in the cloning of CsAFS2. CsAFS2 expression increased following treatment with MJ (Methyl jasmonate), SA (Salicylic acid), GA3 (Gibberellin A3), and various plant growth regulators, as well as under high-salt, drought, and low-temperature conditions. The heterologous genetic transformation of tobacco with CsAFS2 led to an enhanced resistance to low-temperature stress and aphid feeding, evident from elevated levels of osmotic regulatory substances, increased protective enzyme activity, and the upregulation of cold and insect resistance-related genes. Trichomes, crucial in cold and insect resistance, exhibited significantly greater length and density in transgenic tobacco as compared to control plants. These results confirm the vital role of CsAFS2 in enhancing cold and insect resistance, providing comprehensive insights into stress regulation mechanisms in tea plants and advancing stress-resistant tea plant breeding.

CsAFS2 Gene from the Tea Plant Intercropped with Chinese Chestnut Plays an Important Role in Insect Resistance and Cold Resistance

The trichome is a specialized structure developed from the epidermal cells of plants. It serves as a protective tissue covering the surface of plants, playing a crucial role in shielding plants against biotic and abiotic stresses. The trichomeless trait is a necessary quality trait of seedling Chinese cabbage, contributing to the enrichment of Chinese cabbage germplasm resources. This study analyzed the trichomeless mutant Y358-10 and identified the trichomeless trait as being controlled by the recessive gene BrTRI1. Through BSA-seq (Bulked sergeant analysis) and KASP (Kompetitive allele-specific PCR) techniques, the BrTRI1 gene was located on chromosome A06 at 24.91–24.95 Mb. Functional annotation analysis revealed that BraA06g038610.3.5C is a homologous gene of Arabidopsis AtGL1 and induces trichome formation, which may be a candidate gene for BrTRI1. Sequence analysis revealed a 108 bp insertion in the promoter region and transposable element (TE) insertion in the third exon of BraA06g038610.3.5C, differing from the previously published mutation. The InDel markers BrTRI1-PI and BrTRI1-TE were developed and validated in the F2 population and 342 DH (Double haploid) and high inbred lines. We identified all reported variants of BrTRI1 and BrTTG1 among 342 DH and high inbred lines, which covered the widest variation range and the most germplasm resources. The results demonstrated that only the identical source Y358-10 and Y358P1 concomitantly conformed to BrTRI1-PI and BrTRI1-TE. RNA-seq and qRT-PCR analyses indicated that variations in BraA06g038610.3.5C and the differential expression of other genes involved in trichome development in Y358-10 resulted in the inhibition of trichome formation. This provides a new perspective for studying the molecular mechanism of Chinese cabbage trichome formation and genetic improvement. 

Identification of a unique allele BrTRI1 regulating the trichomeless trait of Chinese cabbage (Brassica rapa L. ssp. pekinensis)

RNA sequencing (RNA-seq) enables the accurate measurement of multiple transcriptomic phenotypes for modeling the impacts of disease variants. Advances in technologies, experimental protocols, and analysis strategies are rapidly expanding the application of RNA-seq to identify disease biomarkers, tissue- and cell-type-specific impacts, and the spatial localization of disease-associated mechanisms. Ongoing international efforts to construct biobank-scale transcriptomic repositories with matched genomic data across diverse population groups are further increasing the utility of RNA-seq approaches by providing large-scale normative reference resources. The availability of these resources, combined with improved computational analysis pipelines, has enabled the detection of aberrant transcriptomic phenotypes underlying rare diseases. Further expansion of these resources, across both somatic and developmental tissues, is expected to soon provide unprecedented insights to resolve disease origin, mechanism of action, and causal gene contributions, suggesting the continued high utility of RNA-seq in disease diagnosis. Expected final online publication date for the Annual Review of Genomics and Human Genetics, Volume 25 is August 2024. Please see http://www.annualreviews.org/page/journal/pubdates for revised estimates.

RNA Sequencing in Disease Diagnosis.

Differential expression (DE) analysis is a widely used method for identifying genes that are functionally relevant for an observed phenotype or biological response. However, typical DE analysis includes selection of genes based on a threshold of fold change in expression under the implicit assumption that all genes are equally sensitive to dosage changes of their transcripts. This tends to favor highly variable genes over more constrained genes where even small changes in expression may be biologically relevant. To address this limitation, we have developed a method to recalibrate each gene’s differential expression fold change based on genetic expression variance observed in the human population. The newly established metric ranks statistically differentially expressed genes not by nominal change of expression, but by relative change in comparison to natural dosage variation for each gene. We apply our method to RNA sequencing datasets from rare disease and in-vitro stimulus response experiments. Compared to the standard approach, our method adjusts the bias in discovery towards highly variable genes, and enriches for pathways and biological processes related to metabolic and regulatory activity, indicating a prioritization of functionally relevant driver genes. With that, our method provides a novel view on DE and contributes towards bridging the existing gap between statistical and biological significance. We believe that this approach will simplify the identification of disease causing genes and enhance the discovery of therapeutic targets.

Recalibrating differential gene expression by genetic dosage variance prioritizes functionally relevant genes

A 448 kb region on chromosome B02 was delimited to be associated with trichome trait in Brassica juncea, in which the BjuVB02G54610 gene with a structural variation of 3 kb structure variation (SV) encoding a MYB transcription factor was predicted as the possible candidate gene. Mustards (Brassica juncea) are allopolyploid crops in the worldwide, and trichomes are essential quality attributes that significantly influence its taste and palpability in vegetable-use cultivars. As important accessory tissues from specialized epidermal cells, trichomes also play an important role in mitigating biotic and abiotic stresses. In this study, we constructed a F2 segregating population using YJ27 with intensive trichome leaves and 03B0307 with glabrous leaves as parents. By bulked segregant analysis (BSA-seq), we obtained a 2.1 Mb candidate region on B02 chromosome associated with the trichome or glabrous trait formation. Then, we used 13 Kompetitive Allele Specific PCR (KASP) markers for fine mapping and finally narrowed down the candidate region to about 448 kb in length. Interestingly, among the region, there was a 3 kb sequence deletion that located on the BjuVB02G54610 gene in the F2 individuals with trichome leaves. Genotyping results of F2 populations confirmed this deletion (R2 = 81.44%) as a major QTL. Natural population re-sequencing analysis and genotyping results further validated the key role of the 3 kb structure variation (SV) of insertion/deletion type in trichome development in B. juncea. Our findings provide important information on the formation of trichomes and potential target gene for breeding vegetable mustards. 

/pdf/structural-variation-of-gl1-gene-determines-the-trichome-2dnqxe0c.pdf

Structural variation of GL1 gene determines the trichome formation in Brassica juncea

Understanding dosage sensitivity or why Mendelian diseases have dominant vs. recessive modes of inheritance is crucial for uncovering the etiology of human disease. Previous knowledge of dosage sensitivity is mainly based on observations of rare loss-of-function mutations or copy number changes, which are underpowered due to ultra rareness of such variants. Thus, the functional underpinnings of dosage constraint remain elusive. In this study, we aim to systematically quantify dosage perturbations from cis-regulatory variants in the general population to yield a tissue-specific dosage constraint map of genes and further explore their underlying functional logic. We reveal an inherent divergence of dosage constraints in genes by functional categories with signaling genes (transcription factors, protein kinases, ion channels, and cellular machinery) being dosage sensitive, while effector genes (transporters, metabolic enzymes, cytokines, and receptors) are generally dosage resilient. Instead of being a metric of functional dispensability, we show that dosage constraint reflects underlying homeostatic constraints arising from negative feedback. Finally, we employ machine learning to integrate DNA and RNA metrics to generate a comprehensive, tissue-specific map of dosage sensitivity (MoDs) for autosomal genes. 

An RNA-informed dosage sensitivity map reflects the intrinsic functional nature of genes

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Structural variation of GL1 gene determines the trichome formation in Brassica juncea

An RNA-informed dosage sensitivity map reflects the intrinsic functional nature of genes