Anthocyanins are a class of water-soluble flavonoid pigments that play crucial roles in plant physiology and human health. Their biosynthesis is regulated by the MYB-bHLH-WD40 transcriptional complex, in which MYB transcription factors serve as the key determinants. However, the function of repressor-type MYBs in tuber crops such as potato remains poorly understood. Here we show that the R2R3-MYB transcription factor StMYB3 acts as a repressor of anthocyanin biosynthesis in potato. Transient-expression assays revealed that co-expression of StMYB3 with StAN2 (an R2R3 MYB activator) markedly reduced anthocyanin accumulation in leaves, and tuber skins of StMYB3-over-expressing lines exhibited a significant decrease in anthocyanin content. Mechanistic analyses demonstrate that both StMYB3 and StAN2 interact with StAN1 (an anthocyanin related bHLH). StMYB3 not only suppresses the StAN2-mediated transcriptional activation of anthocyanin biosynthesis genes (StCHS, StF3H, StF3'5'H, and StGST) but also directly represses the promoter activity of bHLH transcription factor StAN1. Moreover, StMYB3 and StAN2 form a mutually reinforcing positive-feedback loop at the transcriptional level. These results uncovers a StMYB3-StAN1-StAN2 regulatory module whose dynamics, driven by competition and bidirectional feedback, precisely control anthocyanin accumulation. This finding provides a reference for breeding potatoes with high anthocyanin content.

Potato, the fourth largest food crop in the world, stores nutrients in underground tubers. However, light exposure induces tuber accumulation of chlorophyll and toxic steroidal glycoalkaloids (SGAs); this unwanted trait called tuber greening causes a decline in potato quality and renders parts of tuber inedible. Despite progress in enzymatic cascades governing SGAs biosynthesis, the regulatory scheme of SGAs and chlorophyll metabolism in light-exposed tubers persists as a critical knowledge gap. Here, we identify that the blue light receptor StCRY1 plays a predominant role in light-induced tuber greening and SGA elevation, functioning as a light-controlled transcriptional switch for genes involved in SGAs and chlorophyll biosynthesis. We show that the transcription factor StHY5 acts downstream of StCRY1 to coregulate both chlorophyll and SGA metabolism. However, StMYB4, a transcription factor regulated by StHY5, promotes SGA synthesis by directly binding to SGA biosynthetic genes without affecting chlorophyll homeostasis. Furthermore, StCRY1 employs a dual strategy by modulating StMYB4 expression and physically interacting with StMYB4 to regulate its transcriptional activity. Collectively, these findings uncover a modularly coordinated control of SGA accumulation and chlorophyll biosynthesis by bifurcation of the StCRY1-StHY5 axis, providing a promising strategy to concurrently curb light-induced tuber greening and glycoalkaloids accumulation.

The pigmentation patterns of potato tubers are complex and diverse, often exhibiting significant tissue specificity. This study was conducted to elucidate the molecular mechanisms underlying the differential pigmentation in different parts of potato tubers using two cultivars, ‘Huashu 12’ and 15EM36-26, which exhibit opposite pigmentation patterns between the bud eyes and the tuber periderm. Metabolomic analysis revealed that cyanidin, pelargonidin, and malvidin are the key anthocyanin components responsible for the observed pigmentation differences. A total of 118 common differentially expressed genes in the differentially pigmented tissues of both cultivars were identified in transcriptomic analysis, including key structural genes of the anthocyanin biosynthesis pathway (such as StPAL, StCHS, and StDFR). Weighted gene co-expression network analysis was further employed to screen modules significantly correlated with pigmentation phenotypes, and 28 candidate genes associated with anthocyanin biosynthesis were identified. Expression validation demonstrated that the expression of StbHLH14 was significantly higher in non-pigmented tissues compared to pigmented tissues. Functional analysis revealed that StbHLH14 can inhibit the activation of structural gene promoters (such as StCHS and StDFR) via the MYB transcription factor StAN2, thereby negatively regulating anthocyanin biosynthesis. This study unveils the metabolic and transcriptional basis of tissue-specific pigmentation in potato tubers and clarifies the negative regulatory role of StbHLH14.

MYB transcription factors represent one of the largest transcription factor families in plants and play a critical role in regulating rind coloration. However, key MYB genes directly involved in rind color formation in watermelon have not yet been systematically identified or functionally characterized. In this study, a total of 115 MYB genes were systematically identified from the watermelon genome and classified into 25 distinct subclades based on phylogenetic analysis. Combined with bioinformatic characterization of conserved domains, motif composition, gene structure, and promoter cis-elements, the molecular features of this gene family were comprehensively elucidated. Transcriptome analysis revealed significant differences in the expression levels of structural genes involved in chlorophyll biosynthesis during fruit development among watermelon accessions with different rind colors. WGCNA further identified key modules highly associated with rind color formation, from which two core candidate regulators, ClaMYB79 (Cla97C08G155540.2) and ClaMYB71 (Cla97C07G140720.1), were selected, and their regulatory networks were constructed. The reliability of the transcriptome results was further confirmed by qRT-PCR validation. This research lays a solid foundation for future research to elucidate the molecular mechanisms by which MYB genes regulate rind color formation in watermelon.

Light is a key factor for inducing anthocyanin biosynthesis; however, its regulatory mode in potato anthocyanin biosynthesis remains unclear. Previous research identified a specific genotype that causes the tuber skin to gradually turn purple when exposed to light of different wavelengths. In the present study, we conducted metabolome and transcriptome analyses on tuber samples during anthocyanin accumulation. The metabolome data showed that the contents of naringenin chalcone, naringenin, dihydrokaempferol, and cyanidin gradually increased during anthocyanin accumulation. The transcriptome data showed that the expression levels of most structural genes increased gradually during anthocyanin accumulation, especially the StF3'H gene that promotes cyanidin formation. Moreover, the photo-responsive transcription factor StHY5 was specifically expressed at high levels before anthocyanin accumulation, occurring 2 h after light induction. Establishment of transgenic lines demonstrated that StHY5 overexpression could promote the accumulation of anthocyanin in potato tubers, along with a parallel increase in the transcription levels of StAN2, StMYBA1, StCHI, StF3H, StF3'H, and StDFR. Electrophoretic mobility shift and dual luciferase assays showed that StHY5 can enhance the promoter activity of the MYB transcription factors StAN2 and StMYBA1 as well as the structural genes StCHI and StF3H through binding to the G-box motif. StAN2 activated the expression of StF3'H (a newly identified purple gene locus in potato) and StDFR by binding to the MYB-binding site in the promoters, thereby promoting anthocyanin biosynthesis. This study provides a theoretical basis for revealing the molecular mechanism of light-regulated anthocyanin biosynthesis in potatoes.

Loquat (Eriobotrya japonica) is an important subtropical evergreen fruit tree of the Rosaceae family that possesses significant edible and economic value. The NAC transcription factor family, as plant-specific regulatory factors, not only participated in plant growth and development but also played crucial roles in fruit quality formation. Through genome-wide analysis, this study identified 117 NAC family members in loquat, which were phylogenetically classified into 14 distinct subfamilies. Chromosomal localization revealed that 114 genes were unevenly distributed across 17 chromosomes, while the remaining 3 were located in genomic scaffold regions. Collinearity analysis indicated that loquat NAC genes primarily underwent purifying selection and showed high homology with NAC genes from other Rosaceae species. Cis-acting element prediction analysis suggested these genes were extensively involved in various biological processes, including abiotic stress responses, hormone signal transduction, and growth regulation. Expression pattern analysis based on transcriptome data further uncovered differential expression characteristics of NAC genes across different loquat cultivars and fruit developmental stages. Notably, correlation analysis identified several NAC candidate genes that were significantly associated with fruit sugar-acid content. This study provided the first comprehensive and systematic characterization of the NAC gene family in loquat, establishing an important foundation for elucidating the molecular mechanisms by which NAC transcription factors regulate loquat fruit flavor quality.

During harvesting, storage, transportation, and processing, potato ( Solanum tuberosum L . ) tubers undergo greening after exposure to light, leading to the accumulation of toxic glycoside alkaloids, resulting in quality deterioration and economic losses. However, the underlying mechanisms are unclear. This study compared the transcriptome and proteome differences among four potato cultivars during the light-induced greening process, identifying 3,751 unique proteins (high confidence; ≥91.7%). The levels of enzymes involved in steroidal glycoalkaloid biosynthesis varied among the cultivars. In addition, coexpression network analysis of the transcriptomic data identified the transcription factor MYB113 (Soltu.DM.10G020780.1) as a potential positive regulator of steroidal glycoalkaloid biosynthesis. The dual-luciferase assay revealed that StMYB113 could bind to the promoters of steroidal glycoalkaloid biosynthesis-related genes and activate them. The transgenic lines overexpressing Solanum tuberosum L. Myb domain protein ( StMYB113 ) exhibited greater mRNA abundance of these genes and elevated levels of steroidal glycoalkaloids. This study provided a theoretical basis for exploring the impact of light on the synthesis of solanine in potatoes.

The R2R3-MYB proteins comprise the largest class of MYB transcription factors, which play an essential role in regulating anthocyanin synthesis in various plant species. Ananas comosus var. bracteatus is an important colorful anthocyanins-rich garden plant. The spatio-temporal accumulation of anthocyanins in chimeric leaves, bracts, flowers, and peels makes it an important plant with a long ornamental period and highly improves its commercial value. We conducted a comprehensive bioinformatic analysis of the R2R3-MYB gene family based on genome data from A. comosus var. bracteatus. Phylogenetic analysis, gene structure and motif analysis, gene duplication, collinearity, and promoter analysis were used to analyze the characteristics of this gene family. In this work, a total of 99 R2R3-MYB genes were identified and classified into 33 subfamilies according to phylogenetic analysis, and most of them were localized in the nucleus. We found these genes were mapped to 25 chromosomes. Gene structure and protein motifs were conserved among AbR2R3-MYB genes, especially within the same subfamily. Collinearity analysis revealed four pairs of tandem duplicated genes and 32 segmental duplicates in AbR2R3-MYB genes, indicating that segmental duplication contributed to the amplification of the AbR2R3-MYB gene family. A total of 273 ABRE responsiveness, 66 TCA elements, 97 CGTCA motifs, and TGACG motifs were the main cis elements in the promoter region under response to ABA, SA, and MEJA. These results revealed the potential function of AbR2R3-MYB genes in response to hormone stress. Ten R2R3-MYBs were found to have high homology to MYB proteins reported to be involved in anthocyanin biosynthesis from other plants. RT-qPCR results revealed the 10 AbR2R3-MYB genes showed tissue-specific expression patterns, six of them expressed the highest in the flower, two genes in the bract, and two genes in the leaf. These results suggested that these genes may be the candidates that regulate anthocyanin biosynthesis of A. comosus var. bracteatus in the flower, leaf, and bract, respectively. In addition, the expressions of these 10 AbR2R3-MYB genes were differentially induced by ABA, MEJA, and SA, implying that these genes may play crucial roles in hormone-induced anthocyanin biosynthesis. Our study provided a comprehensive and systematic analysis of AbR2R3-MYB genes and identified the AbR2R3-MYB genes regulating the spatial-temporal anthocyanin biosynthesis in A. comosus var. bracteatus, which would be valuable for further study on the anthocyanin regulation mechanism of A. comosus var. bracteatus.

MYB transcription factors play a key role in anthocyanin biosynthesis. However, there are few reports on MYB transcription factors that can regulate anthocyanin biosynthesis in potato. In this study, the StMYB113 gene was isolated from potato and characterized. Transient activation experiments showed that the StMYB113 gene could promote anthocyanin biosynthesis in tobacco leaves by enhancing the expression of genes encoding anthocyanin biosynthesis-related enzymes. In addition, overexpression of the StMYB113 gene promoted anthocyanin accumulation in potato tuber skin. Furthermore, transient luciferase analysis showed that StMYB113 enhanced the promoter activities of StF3H and StDFR genes significantly. These results indicated that the StMYB113 gene could promote anthocyanin accumulation in potato tuber skin by directly activating the expression of StF3H and StDFR. The promoter activity of StMYB113 was significantly higher in light than in dark conditions, suggesting that the expression of StMYB113 is induced by light. These findings illustrate the role and regulation of the StMYB113 gene in potato anthocyanin biosynthesis and enrich the regulatory theory of potato anthocyanin biosynthesis.

Anthocyanins, which are natural pigments and serve as important natural antioxidants scavenging free radicals, are rich in a variety of compounds that are important in health care. Anthocyanins affect the ripening, taste and color of fruits and vegetables, and prevent plants from abiotic and biotic stresses. Therefore, optimizing anthocyanin content is regarded as the breeding goal in many horticultural crops. As the secondary ethylene signaling transcription factors, ethylene response factors（ERFs） respond to plant hormone signaling and can result in feedback regulation, and these genes are known to modulate the process of ethylene regulating anthocyanin biosynthesis via various mechanisms. In terms of the molecular mode, ERFs in regulation of anthocyanin biosynthesis rely on the physical interaction with transcription factors, activating transcription factors, forming regulatory complexes with MBW or directly activating structural gene promoters. This study aims to provide a theoretical basis for further elucidating the mechanism of ERF regulating anthocyanin biosynthesis, and to explore the relationship between the rapid accumulation of anthocyanins and the increase of ethylene release in fruits and vegetables at the late ripening stage.

园艺植物遗传学是园艺专业的核心基础课程之一,在培养高素质应用型本科园艺人才方面发挥着重要作用.本研究立足知识、能力、价值"三育人"理念,深挖课程思政元素并融入知识教学,实现了专业教育与思政教育的有机融合.

Anthocyanin biosynthesis is affected by light, temperature, and other environmental factors. The regulation mode of light on anthocyanin synthesis in apple, pear, tomato and other species has been reported, while not clear in potato. In this study, potato RM-210 tubers whose peel will turn purple gradually after exposure to light were selected. Transcriptome analysis was performed on RM-210 tubers during anthocyanin accumulation. The expression of StMYBA1 gene continued to increase during the anthocyanin accumulation in RM-210 tubers. Moreover, co-expression cluster analysis of differentially expressed genes showed that the expression patterns of StMYBA1 gene were highly correlated with structural genes CHS and CHI . The promoter activity of StMYBA1 was significantly higher in light conditions, and StMYBA1 could activate the promoter activity of structural genes StCHS , StCHI , and StF3H . Further gene function analysis found that overexpression of StMYBA1 gene could promote anthocyanin accumulation and structural gene expression in potato leaves. These results demonstrated that StMYBA1 gene promoted potato anthocyanin biosynthesis by activating the expression of structural genes under light conditions. These findings provide a theoretical basis and genetic resources for the regulatory mechanism of potato anthocyanin synthesis.

Gene annotation is essential for genome-based studies. However, algorithm-based genome annotation is difficult to fully and correctly reveal genomic information, especially for species with complex genomes. Artemisia annua L. is the only commercial resource of artemisinin production though the content of artemisinin is still to be improved. Genome-based genetic modification and breeding are useful strategies to boost artemisinin content and therefore, ensure the supply of artemisinin and reduce costs, but better gene annotation is urgently needed. In this study, we manually corrected the newly released genome annotation of A. annua using second- and third-generation transcriptome data. We found that incorrect gene information may lead to differences in structural, functional, and expression levels compared to the original expectations. We also identified alternative splicing events and found that genome annotation information impacted identifying alternative splicing genes. We further demonstrated that genome annotation information and alternative splicing could affect gene expression estimation and gene function prediction. Finally, we provided a valuable version of A. annua genome annotation and demonstrated the importance of gene annotation in future research.

Ananas comosus var. bracteatus is an important tropical ornamental plant because of its green/white chimeric leaves. The accumulation of anthocyanin makes the leaf red especially the white margin. However, the leaves lost red color in summer and winter. Light intensity is one of the most important factors affecting leaf color along the season. In order to understand the effects of light intensity on the growth and coloration of the chimeric leaves, Ananas comosus var. bracteatus was grown under full sunlight, 50% shade and 75% shade for 75 days to evaluate the content of pigments, the color parameters (value L*, a*, b*) and structural histocytology characteristics of chimeric leaves. The results showed that high irradiance was beneficial to keep the chimeric leaves red. However, prolonged exposure to high irradiance caused light damage, some of the leaves wrinkled and even burned. Shading decreased the content of anthocyanin and increased the content of chlorophyll especially in the white margin of the leaves. Numerous chloroplasts were found in the mesophyll cells of the white margin part of chimeric leaves under shading for 75 days. The increase of chlorophyll content resulted in better growth of plants. In order to balance the growth and ornamental value of the leaves, approximately 50% shade is suggested to be the optimum light irradiance condition for Ananas comosus var. bracteatus in summer.

After anthocyanin synthesis, a variety of anthocyanin compounds are produced through further methylation, glycosylation, and acylation. However, the effect of the potato methylase gene on anthocyanin biosynthesis has not been reported. Red and purple mutation types appear in tubers of the potato cultivar 'Purple Viking' with chimeric skin phenotypes. In this study, transcriptome and anthocyanin metabolome analyses were performed on skin of Purple Viking tubers and associated mutants. According to the metabolome analysis, the transformation of delphinidin into malvidin-3-O-glucoside and petunidin 3-O-glucoside and that of cyanidin into rosinidin O-hexoside and peonidin-3-O-glucoside were hindered in red tubers. Expression of methyltransferase gene OMT30376 was significantly lower in red tubers than in purple ones, whereas the methylation level of OMT30376 was significantly higher in red tubers. In addition, red skin appeared in tubers from purple tuber plants treated with S-adenosylmethionine (SAM), indicating the difference between purple and red was caused by the methylation degree of the gene OMT30376. Thus, the results of the study suggest that the OMT30376 gene is involved in the transformation of anthocyanins in potato tubers. The results also provide an important reference to reveal the regulatory mechanisms of anthocyanin biosynthesis and transformation.

花青素是植物中重要的类黄酮化合物,在果实着色、抗逆境等方面起着重要的生理作用.富含花青素的食物对人体也有良好的保健作用,如抗衰老、防止血管硬化等.花青素的生物合成与积累不仅受到自身结构基因、调节基因以及植物激素的影响,也会受到外界环境因素(如光照、温度等)的影响.其中,光照是影响植物花青素合成与积累的重要因素之一,因此解析植物从接收光信号到影响花青素合成的调控机制有重要的生物学意义.HY5(ELONGATED HYPOCOTYL5)作为碱性亮氨酸拉链(bZIP,basic leucine zipper)类转录因子,在调控植物生长发育的过程中发挥着重要的作用,它是第一个被发现参与光形态建成的转录因子,在植物花青素生物合成的过程中也发挥着关键性的调控作用.本文综述了 HY5蛋白在植物花青素合成通路中响应光信号机制并激活下游转录因子和结构基因的转录特征,概述了该转录因子与BBX蛋白互作进而调控花青素合成积累过程,旨在为后续深入阐明HY5介导植株类黄酮化合物代谢及响应光信号机理提供理论依据.

This study exploring the molecular mechanism of stamen petaloid development of Alcea rosea L., a popular ornamental of the region, using a comparative transcriptome analysis between multi-petal red flowers (stamen petaloid) and single petal red flowers (no-stamen petaloid) by RNA-seq technology fetched interesting observations. It is found that the 3375 differently expressed unigenes (DEGs), out of the total 132,569 unigenes, including 1550 were up-regulated and the remaining 1825 were down-regulated at the transcript levels. The average length of these DEGs was 741 bp, and the N50 was 1090 bp. A large number of DEGs related to stamen petaloid were identified by GO and KEGG annotation. Some of them get involved in the synthesis and signal transduction of plant hormones, such as auxin, gibberellin, cytokinin, ethylene, and brassinosteroid, while others are closely related to some key transcription factors, such as bHLH, MYB, GATA, MADS-box. These DEGs provide important clues of the regulatory pathway and offer valuable information for studying the mechanism of stamen petaloid.

Anthocyanins are biosynthesized on the cytoplasmic surface of the endoplasmic reticulum and then transported to the vacuole for storage. Glutathione S -transferases (GSTs) are involved in the transport of anthocyanins. However, the regulatory mechanism of GSTs in potato is unclear. In this study, the glutathione S -transferase gene StGST1 was isolated from potato and characterized. Expression analysis revealed that StGST1 transcript levels were higher in pigmented tubers than in white tubers. Overexpression of StGST1 promoted anthocyanin accumulation in the tuber. Transient luciferase analysis revealed that the promoter of StGST1 was activated by the transcription factors StAN2 and StAN11 . These results indicated that StGST1 promotes anthocyanin accumulation in potato tubers. These findings have important implications for improvement of anthocyanin accumulation in pigmented potato tubers.

Ananas comosus var. bracteatus f. tricolor (GL1) is a red pineapple accession whose mostly green leaves with chimeric white leaf margins turn red in spring and autumn and during flowering. It is an important ornamental plant and ideal plant research model for anthocyanin metabolism, chimeric leaf development, and photosynthesis. Here, we generated a highly contiguous chromosome-scale genome assembly for GL1 and compared it with other 3 published pineapple assemblies (var. comosus accessions MD2 and F153, and var. bracteatus accession CB5). The GL1 assembly has a total size of ∼461 Mb, with a contig N50 of ∼2.97 Mb and Benchmarking Universal Single-Copy Ortholog score of 97.3%. More than 99% of the contigs are anchored to 25 pseudochromosomes. Compared with the other 3 published pineapple assemblies, the GL1 assembly was confirmed to be more continuous. Our evolutionary analysis showed that the Bromeliaceae and Poaceae diverged from their nearest common ancestor ∼82.36 million years ago (MYA). Population structure analysis showed that while GL1 has not undergone admixture, bracteatus accession CB5 has resulted from admixture of 3 species of Ananas. Through classification of orthogroups, analysis of genes under positive selection, and analysis of presence/absence variants, we identified a series of genes related to anthocyanin metabolism and development of chimeric leaves. The structure and evolution of these genes were compared among the published pineapple assemblies with reveal candidate genes for these traits. The GL1 genome assembly and its comparisons with other 3 pineapple genome assemblies provide a valuable resource for the genetic improvement of pineapple and serve as a model for understanding the genomic basis of important traits in different pineapple varieties and other pan-cereal crops.

园艺植物育种学是高等院校园艺专业的核心课程之一,发挥着培养高素质应用型园艺人才的重要作用.以"立德树人"为核心,明确课程思政教学目标,深挖课程的思政内容,采用正确的思政路径,将思政教育贯穿于课程教学的全过程,实现专业知识传播、能力培养、素质提升与价值引领的有机统一.