A putative R3 MYB repressor is the candidate gene underlying atroviolacium, a locus for anthocyanin pigmentation in tomato fruit

Cao, Xue; Qiu, Zhengkun; Wang, Xiaotian; Giang, Tong van; Liu, Xiaolin; Wang, Jing; Wang, Xiaoxuan; Gao, Jianchang; Guo, Yanmei; Du, Yan; Wang, Guoping; Huang, Zejun

doi:10.1093/jxb/erx382

Cited by 94 publications

(124 citation statements)

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“…In addition, it has been demonstrated that many transcription factors (TFs), including MYBs, NACs, basic helix-loop-helix (bHLH), WD40s, and WRKYs, are involved in the regulation of metabolic biosynthesis in plants and the regulatory pattern of these transcription factors is usually tissue-specific [43][44][45][46][47]. MYBs play a critical role in fruit and flower color formation via the regulation of structural genes in the flavonoid or anthocyanin biosynthetic pathway [43][44][45][48][49][50][51]. It has been reported that R2R3 MYB transcription factors act as important regulators in controlling the spatiotemporal biosynthesis of flavonoids during grape and apple fruit development [44,51].…”

Section: Discussionmentioning

confidence: 99%

Annotation of genes involved in high level of dihydromyricetin production in vine tea (Ampelopsis grossedentata) by transcriptome analysis

Cao

et al. 2020

BMC Plant Biol

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Background: Leaves of the medicinal plant Ampelopsis grossedentata, which is commonly known as vine tea, are used widely in the traditional Chinese beverage in southwest China. The leaves contain a large amount of dihydromyricetin, a compound with various biological activities. However, the transcript profiles involved in its biosynthetic pathway in this plant are unknown. Results: We conducted a transcriptome analysis of both young and old leaves of the vine tea plant using Illumina sequencing. Of the transcriptome datasets, a total of 52.47 million and 47.25 million clean reads were obtained from young and old leaves, respectively. Among 471,658 transcripts and 177,422 genes generated, 7768 differentially expressed genes were identified in leaves at these two stages of development. The phenylpropanoid biosynthetic pathway of vine tea was investigated according to the transcriptome profiling analysis. Most of the genes encoding phenylpropanoid biosynthesis enzymes were identified and found to be differentially expressed in different tissues and leaf stages of vine tea and also greatly contributed to the biosynthesis of dihydromyricetin in vine tea. Conclusions: To the best of our knowledge, this is the first formal study to explore the transcriptome of A. grossedentata. The study provides an insight into the expression patterns and differential distribution of genes related to dihydromyricetin biosynthesis in vine tea. The information may pave the way to metabolically engineering plants with higher flavonoid content.

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Section: Discussionmentioning

confidence: 99%

Annotation of genes involved in high level of dihydromyricetin production in vine tea (Ampelopsis grossedentata) by transcriptome analysis

Cao

et al. 2020

BMC Plant Biol

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“…Anthocyanin biosynthesis is regulated by several well-studied TFs, including MYB, bHLH, and WD40 [13,19,[55][56][57]. Yan et al [38] annotated 83 MYB family TFs in L. ruthenicum using RNA-Seq, and the observed expression patterns suggested that some MYB TFs might play a role in the regulation of anthocyanin synthesis during different fruit development periods.…”

Section: Discussionmentioning

confidence: 99%

Transcriptomic analysis of Lycium ruthenicum Murr. during fruit ripening provides insight into structural and regulatory genes in the anthocyanin biosynthetic pathway

Duan

Zhang

et al. 2018

PLoS ONE

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Fruit development in Lycium ruthenicum Murr. involves a succession of physiological and biochemical changes reflecting the transcriptional modulation of thousands of genes. Although recent studies have investigated the dynamic transcriptomic responses during fruit ripening in L. ruthenicum, most have been limited in scope, and thus systematic data representing the structural genes and transcription factors involved in anthocyanin biosynthesis are lacking. In this study, the transcriptomes of three ripening stages associated with anthocyanin accumulation, including S1 (green ripeness stage), S2 (skin color change) and S3 (complete ripeness stage) in L. ruthenicum were investigated using Illumina sequencing. Of a total of 43,573 assembled unigenes, 12,734 were differentially expressed during fruit ripening in L. ruthenicum. Twenty-five significantly differentially expressed structural genes (including PAL, C4H, 4CL, CHS, CHI, F3H, F3'H, F3'5'H, DFR, ANS and UFGT) were identified that might be associated with anthocyanin biosynthesis. Additionally, several transcription factors, including MYB, bHLH, WD40, NAC, WRKY, bZIP and MADS, were correlated with the structural genes, implying their important interaction with anthocyanin biosynthesisrelated genes. Our findings provide insight into anthocyanin biosynthesis and regulation patterns in L. ruthenicum and offer a systematic basis for elucidating the molecular mechanisms governing anthocyanin biosynthesis in L. ruthenicum.

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“…A bioinspired, genome editing and transgene-free alternative to this approach, we suggest, would be to emulate the existing genetic diversity of tomato cultivars. Specifically, a 4-bp frameshift indel mutation in the SlMYBATV transcription factor gene acts as a spectacular switch that boosts anthocyanin production in a wild tomato from the Galápagos Islands (Cao et al, 2017). This knockout would be easy to reproduce using CRISPR, and could be combined with other anthocyanin variation loci that are currently under investigation.…”

Section: The Advantages Of Bioinspired Genome Editingmentioning

confidence: 99%

The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing

Courtier‐Orgogozo

Martin

2020

Journal of Experimental Biology

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One promising application of CRISPR/Cas9 is to create targeted mutations to introduce traits of interest into domesticated organisms. However, a major current limitation for crop and livestock improvement is to identify the precise genes and genetic changes that must be engineered to obtain traits of interest. Here, we discuss the advantages of bio-inspired genome editing, i.e. the engineered introduction of natural mutations that have already been associated with traits of interest in other lineages (breeds, populations or species). To obtain a landscape view of potential targets for genome editing, we used Gephebase (www.gephebase.org), a manually curated database compiling published data about the genes responsible for evolutionary and domesticated changes across eukaryotes, and examined the >1200 mutations that have been identified in the coding regions of more than 700 genes in animals, plants and yeasts. We observe that our genetic knowledge is relatively important for certain traits, such as xenobiotic resistance, and poor for others. We also note that protein-null alleles, often owing to nonsense and frameshift mutations, represent a large fraction of the known loci of domestication (42% of identified coding mutations), compared with intraspecific (27%) and interspecific evolution (11%). Although this trend may be subject to detection, publication and curation biases, it is consistent with the idea that breeders have selected large-effect mutations underlying adaptive traits in specific settings, but that these mutations and associated phenotypes would not survive the vagaries of changing external and internal environments. Our compilation of the loci of evolution and domestication uncovers interesting options for bio-inspired and transgene-free genome editing.

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A putative R3 MYB repressor is the candidate gene underlying atroviolacium, a locus for anthocyanin pigmentation in tomato fruit

Abstract: Fine-mapping of the atv locus identifies a putative R3 MYB repressor SLMYBATV as its candidate gene. We present a model of the anthocyanin gene regulation network in the peel of tomato fruit.

Cited by 94 publications

References 54 publications

Annotation of genes involved in high level of dihydromyricetin production in vine tea (Ampelopsis grossedentata) by transcriptome analysis

Annotation of genes involved in high level of dihydromyricetin production in vine tea (Ampelopsis grossedentata) by transcriptome analysis

Transcriptomic analysis of Lycium ruthenicum Murr. during fruit ripening provides insight into structural and regulatory genes in the anthocyanin biosynthetic pathway

The coding loci of evolution and domestication: current knowledge and implications for bio-inspired genome editing

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