Horticulture Research最新文献

Temporal fruit microbiome and immunity dynamics in post-harvest apple (Malus x domestica)

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-25 DOI: 10.1093/hr/uhaf063

Roselane Kithan-Lundquist, Hannah M McMillan, Sheng-Yang He, George W Sundin

{"title":"Temporal fruit microbiome and immunity dynamics in post-harvest apple (Malus x domestica)","authors":"Roselane Kithan-Lundquist, Hannah M McMillan, Sheng-Yang He, George W Sundin","doi":"10.1093/hr/uhaf063","DOIUrl":"https://doi.org/10.1093/hr/uhaf063","url":null,"abstract":"The plant immune response plays a central role in maintaining a well-balanced and healthy microbiome for plant health. However, insights on how the fruit immune response and the fruit microbiome influence fruit health after harvest are limited. We investigated the temporal dynamics of the fruit microbiota and host defense gene expression patterns during post-harvest storage of apple fruits at room temperature. Our results demonstrate a temporal dynamic shift in both bacterial and fungal community composition during post-harvest storage that coincides with a steep-decline in host defense response gene expression associated with pattern-triggered immunity. We observed the gradual appearance of putative pathogenic/spoilage microbes belonging to genera Alternaria (fungi) and Gluconobacter and Acetobacter (bacteria) at the expense of Sporobolomyces and other genera, which have been suggested to be beneficial for plant hosts. Moreover, artificial induction of pattern-triggered immunity in apple fruit with the flg22 peptide delayed the onset of fruit rot caused by the fungal pathogen Penicillium expansum. Our results suggest that the fruit immune response helps to orchestrate a microbiome and that the collapse of the immunity results in the proliferation of spoilage microbes and fruit rot. These findings hold implications for the development of strategies to increase fruit quality and prolong shelf life in fruits and vegetables.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"27 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495163","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Developmental landscape and asymmetric gene expression in the leaf vasculature of Brassica rapa revealed by single-cell transcriptome

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-25 DOI: 10.1093/hr/uhaf060

Xinlei Guo, Jingping Yuan, Yuanyuan Zhang, Jian Wu, Xiaowu Wang

{"title":"Developmental landscape and asymmetric gene expression in the leaf vasculature of Brassica rapa revealed by single-cell transcriptome","authors":"Xinlei Guo, Jingping Yuan, Yuanyuan Zhang, Jian Wu, Xiaowu Wang","doi":"10.1093/hr/uhaf060","DOIUrl":"https://doi.org/10.1093/hr/uhaf060","url":null,"abstract":"Leaf vasculature not only acts as a channel for nutrients and signaling information but also influences leaf morphology. It consists of several distinct cell types with specialized functions. Cell type-specific characterizations based on single-cell RNA sequencing technology could aid in understanding the identities of vascular tissues and their roles in leaf morphogenesis in Brassica rapa. Here, we generated a single-cell transcriptome landscape of the Chinese cabbage leaf vasculature. A total of 12 cell clusters covering 7 known cell types were identified. Different vascular cell types were characterized by distinct identities. The xylem parenchyma and companion cells exhibited an active expression pattern of amino acid metabolism genes. Tracheary elements and sieve elements were enriched in many genes related to cell wall biosynthesis, and the phloem parenchyma was enriched in many sugar transporter-encoding genes. Pseudo-time analyses revealed the developmental trajectories of the xylem and phloem and the potential roles of auxin and ethylene in xylem development. Furthermore, we identified key candidate regulators along the differentiation trajectory of the sieve elements and companion cells. Most of the homoeologous genes in the syntenic triads from the three subgenomes showed asymmetric gene expression patterns in different vascular cell types. Collectively, our study revealed that Chinese cabbage leaf vasculature cells had highly heterogeneous transcriptomes, providing new insights into the complex processes of leaf vasculature development in B. rapa leafy vegetables and other Brasscia crops.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"66 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495171","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Stable isotope labelling and gene expression analysis reveal dynamic nitrogen-supply mechanisms for rapid growth of Moso bamboo

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-25 DOI: 10.1093/hr/uhaf062

Junbo Zhang, Man Shi, Chenglei Zhu, Kebin Yang, Quan Li, Xiaoming Song, Zhimin Gao, Tingting Cao, Dezheng Zhu, Xinzhang Song

{"title":"Stable isotope labelling and gene expression analysis reveal dynamic nitrogen-supply mechanisms for rapid growth of Moso bamboo","authors":"Junbo Zhang, Man Shi, Chenglei Zhu, Kebin Yang, Quan Li, Xiaoming Song, Zhimin Gao, Tingting Cao, Dezheng Zhu, Xinzhang Song","doi":"10.1093/hr/uhaf062","DOIUrl":"https://doi.org/10.1093/hr/uhaf062","url":null,"abstract":"Rapid growth of Moso bamboo (Phyllostachys edulis) shoots (offspring ramet) is primarily fuelled by nitrogen (N) derived from parent ramet and absorbed by rhizome roots. However, the extent to which each N source supports the growth of offspring ramet and the underlying molecular mechanisms of N transport remain unclear. Here, clonal fragments consisting of a parent ramet, an offspring ramet, and an interconnected rhizome were established in a Moso bamboo forest. Additionally, 15N isotope tracing and transcriptome profiling were conducted concurrently to quantify the N contribution from the parent ramet and rhizome roots to the offspring ramet, and to reveal the molecular mechanisms underlying N transport during rapid growth (i.e., early, peak, branching, and leafing stages). The N acquisition strategy of offspring ramet shifted from being primarily provided by the parent ramet (72.53%) during early stage to being predominantly absorbed by rhizome roots (69.85%) during the leafing stage. Approximately equal N contributions (45.82–54.18%) from the parent ramet and rhizome roots were observed during peak and branching stages. PeAAP29123 was identified as a key gene for N transport, being most closely correlated with 15N content. Biomolecular assays demonstrated that PeHDZ23987 could activate the expression of PeAAP29123 via two types of HD-motifs. Overexpression of PeHDZ23987 and PeAAP29123 significantly enhanced N starvation tolerance in transgenic rice with significantly improved N uptake efficiency. Our findings clarify the pattern and mechanisms of N supply for the rapid growth of Moso bamboo offspring ramet and provide transcriptomic evidence for long-distance N transport between clonal ramets.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"23 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495164","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ethylene Modulates the Phenylpropanoid Pathway by Enhancing VvMYB14 Expression via the ERF5-Melatonin-ERF104 Pathway in Grape Seeds

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-25 DOI: 10.1093/hr/uhaf061

Shiwei Gao, Fei Wang, Shengnan Wang, Jiapeng Diao, Shuxia Lan, Yujiao Xu, Xinning Lyu, Hui Kang, Yuxin Yao

{"title":"Ethylene Modulates the Phenylpropanoid Pathway by Enhancing VvMYB14 Expression via the ERF5-Melatonin-ERF104 Pathway in Grape Seeds","authors":"Shiwei Gao, Fei Wang, Shengnan Wang, Jiapeng Diao, Shuxia Lan, Yujiao Xu, Xinning Lyu, Hui Kang, Yuxin Yao","doi":"10.1093/hr/uhaf061","DOIUrl":"https://doi.org/10.1093/hr/uhaf061","url":null,"abstract":"The interaction between ethylene and melatonin in the regulation of polyphenol metabolism and the underlying mechanism remain largely unclear. This work demonstrated that ethylene treatment increased melatonin biosynthesis by inducing the VvASMT expression in grape seeds. Ethylene-induced VvERF5 transactivated VvASMT via binding to the ERE element in its promoter. VvERF5 overexpression led to an increase in melatonin biosynthesis while its suppression generated the opposite results in grape seeds, calli and/or Arabidopsis seeds. A melatonin responsive element (MTRE) was identified, and melatonin-induced VvERF104 was found to bind to the MTRE of the VvMYB14 promoter and activate its expression. VvMYB14 overexpression widely modified the expression of genes in phenylpropanoid pathway and phenolic compound content in grape seeds. DAP-seq revealed that the MEME-1 motif was the most likely binding sites of VvMYB14. VvPAL, VvC4H and VvCHS were verified to be the target genes of VvMYB14. Additionally, the overexpression of VvERF5 or VvERF104 increased the expression of VvPAL, VvC4H and VvCHS, as well as the levels of the corresponding metabolites. Moreover, the roles of VvERF5, VvASMT and VvERF104 in mediating ethylene-induced changes in phenylpropanoid pathway were elucidated using their suppressing seeds. Collectively, ethylene increased the VvMYB14 expression via the pathway of ERF5-melatonin-ERF104 and thereby modified phenylpropanoid pathway.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"27 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495168","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Ethylene positively regulates anthocyanin synthesis in 'Viviana' lily via the LvMYB5-LvERF113-LvMYB1 module

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-25 DOI: 10.1093/hr/uhaf059

Yibing Zhang, Yibo Sun, Weifeng Du, Shaokun Sun, Shimiao Zhang, Mengyao Nie, Yudong Liu, Muhammad Irfan, Li Zhang, Lijing Chen

{"title":"Ethylene positively regulates anthocyanin synthesis in 'Viviana' lily via the LvMYB5-LvERF113-LvMYB1 module","authors":"Yibing Zhang, Yibo Sun, Weifeng Du, Shaokun Sun, Shimiao Zhang, Mengyao Nie, Yudong Liu, Muhammad Irfan, Li Zhang, Lijing Chen","doi":"10.1093/hr/uhaf059","DOIUrl":"https://doi.org/10.1093/hr/uhaf059","url":null,"abstract":"Ethylene (ET) influences the synthesis of anthocyanins, although its regulatory effects can differ significantly across various plant species. In apples (Malus domestica), ET promotes anthocyanin synthesis, whereas in Arabidopsis thaliana, it inhibits its accumulation. Our research showed that ethephon (Eth), an ET derivative, promotes anthocyanin synthesis in 'Viviana' lilies, which has great potential in the cut flower industry. The regulatory mechanism whereby ethylene influences anthocyanin synthesis in lilies remains unclear. In this study, we screened and characterized an ET-induced ET response factors (ERFs), LvERF113, with inhibitory function. Our analyses suggested that LvERF113 could inhibit the negative regulatory function of LvMYB1 at transcriptional and posttranslational levels, promoting anthocyanin synthesis in 'Viviana' lily tepals. In addition, LvERF113 is positively regulated by LvMYB5, forming the LvMYB5-LvERF113-LvMYB1 module controlling anthocyanin synthesis by ET in 'Viviana' lily. These findings offer new insights into the ET regulatory network of anthocyanin synthesis and provide a theoretical basis for the application of ET derivatives in the cut flower industry.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"68 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-25","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143495165","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Integration of digital phenotyping, GWAS and transcriptomic analysis revealed a key gene for bud size in tea plant (Camellia sinensis)

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-20 DOI: 10.1093/hr/uhaf051

Shuran Zhang, Si Chen, Zhilu Fu, Fang Li, Qiyu Chen, Jianqiang Ma, Yuanquan Chen, Liang Chen, Jiedan Chen

{"title":"Integration of digital phenotyping, GWAS and transcriptomic analysis revealed a key gene for bud size in tea plant (Camellia sinensis)","authors":"Shuran Zhang, Si Chen, Zhilu Fu, Fang Li, Qiyu Chen, Jianqiang Ma, Yuanquan Chen, Liang Chen, Jiedan Chen","doi":"10.1093/hr/uhaf051","DOIUrl":"https://doi.org/10.1093/hr/uhaf051","url":null,"abstract":"Tea plant (Camellia sinensis) is among the most significant beverage crops globally. The size of tea buds not only directly affects the yield and quality of fresh leaves, but also plays a key role in determining the suitability of different types of tea. Analyzing the genetic regulation mechanism of tea bud size is crucial for enhancing tea cultivars and boosting tea yield. In this study, a digital phenotyping technology was utilized to collected morphological characteristics of the apical buds of 280 tea accessions of representative germplasm at the ‘two and a bud’ stage. Genetic diversity analysis revealed that the length, width, perimeter, and area of tea buds followed a normal distribution and exhibited considerable variation across natural population of tea plants. Comparative transcriptomic analysis of phenotypic extreme materials revealed a strong negative correlation between the expression levels of four KNOX genes and tea bud size. A key candidate gene, CsKNOX6, was confirmed by further genome-wide association studies (GWAS). Its function was preliminarily characterized by heterologous transformation of Arabidopsis thaliana. Overexpression of CsKNOX6 reduced the leaf area in transgenic plants, which initially determined that it is a key gene negatively regulating bud size. These findings enhance our understanding of the role of KNOX genes in tea plants and provides some references for uncovering the genetic regulatory mechanisms behind tea bud size.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"25 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462791","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The genome of Vitis vinifera cv. Mgaloblishvili reveals resistance and susceptibility factors to downy mildew in the Rpv29 and Rpv31 loci

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-20 DOI: 10.1093/hr/uhaf055

Valentina Ricciardi, Andrea Minio, Melanie Massonnet, Alexander H J Wittenberg, Rosa Figueroa-Balderas, David Maghradze, Silvia Laura Toffolatti, Osvaldo Failla, Dario Cantu, Gabriella De Lorenzis

{"title":"The genome of Vitis vinifera cv. Mgaloblishvili reveals resistance and susceptibility factors to downy mildew in the Rpv29 and Rpv31 loci","authors":"Valentina Ricciardi, Andrea Minio, Melanie Massonnet, Alexander H J Wittenberg, Rosa Figueroa-Balderas, David Maghradze, Silvia Laura Toffolatti, Osvaldo Failla, Dario Cantu, Gabriella De Lorenzis","doi":"10.1093/hr/uhaf055","DOIUrl":"https://doi.org/10.1093/hr/uhaf055","url":null,"abstract":"Mgaloblishvili, a grapevine variety from Georgia (Southern Caucasus), exhibits a unique resistance mechanism against downy mildew. Mgaloblishvili resistance mechanism, involving pathogen recognition, activation of ethylene signalling pathway, structural and chemical defences, is mediated by the resistance loci Rpv29, Rpv30, and Rpv31. Mgaloblishvili genome was sequenced using PacBio HiFi, resulting in a chromosome-scale diploid assembly of 986 Mbp, including 58,912 predicted protein-coding genes across two phased chromosome sets. Comparative analysis with the susceptible PN40024 genome allowed us to identify differences in structure, gene content, and gene expression, as well as the impact of structural variants (SVs) and single nucleotide polymorphisms (SNPs) between Mgaloblishvili and PN40024 loci. Resistance haplotypes were identified through DNA sequencing of a self-pollinated Mgaloblishvili population. Compared to orthologous regions in PN40024, the Rpv29 locus in Mgaloblishvili exhibits reduced gene content, while the Rpv31 locus has similar gene content. In both Mgaloblishvili and PN40024, most genes within these loci are associated with plant defence pathways. While genes in both genotypes perform similar functions, SVs and SNPs were identified as key determinants of the structural differences between the genomes. Defining the Rpv30 locus was challenging due to ambiguous marker localization. DNA sequencing allowed us to identify resistance haplotypes for both Rpv30 and Rpv31 on Mgaloblishvili haplotype 2, though insights into the Rpv29 locus remain limited. Our results indicate that Mgaloblishvili's resistance is driven by numerous small SVs and SNPs, which lead to the loss of susceptibility factors and unique transcriptional regulation of defence-related genes.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"15 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462790","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic origin of Citrus reticulata “Unshiu”

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-20 DOI: 10.1093/hr/uhaf015

Shengjun Liu, Luoyun Wang, Xiang Zhang, Lifang Sun, Fuzhi Ke, Yue Huang, Lizhi Song, Haiping Ye, Jianguo Xu, Yuantao Xu, Xia Wang, Xiuxin Deng, Gaoping Liu, Qiang Xu

{"title":"Genomic origin of Citrus reticulata “Unshiu”","authors":"Shengjun Liu, Luoyun Wang, Xiang Zhang, Lifang Sun, Fuzhi Ke, Yue Huang, Lizhi Song, Haiping Ye, Jianguo Xu, Yuantao Xu, Xia Wang, Xiuxin Deng, Gaoping Liu, Qiang Xu","doi":"10.1093/hr/uhaf015","DOIUrl":"https://doi.org/10.1093/hr/uhaf015","url":null,"abstract":"Satsuma mandarin (Citrus reticulata “Unshiu”) is a global cultivar with superior fruit characteristics and ranking among the top citrus cultivars in terms of production. It is also a key contributor to citrus breeding. However, the lack of high-quality genome makes the origin of Satsuma mandarin has long been a matter of debate. Here, we assembled a gap-free, high-quality genome of Satsuma mandarin. Meanwhile, we collected and sequenced 15 indigenous citrus varieties in Zhejiang Province, 12 Satsuma mandarins, 21 citrus hybrids related to Satsuma mandarin, 10 modern citrus varieties and 7 other mandarins. Through high-resolution genome analysis we inferred that Satsuma originated from a cross between C. reticulata “Ruju” × C. reticulata “Bendiguang” and proposed that Satsuma mandarin most probably originated in East area in Zhejiang Province of China, where the two parents-like cultivars are still found in a sympatric region to date. These results provide new insights into the origin model of Satsuma mandarin. The spread of mandarin is also discussed which probably associated with the culture exchange and trade activities between Japan and China from Tang Dynasty and afterwards.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"10 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143462909","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Carotene hydroxylase DcCYP97A3 affects carotenoids metabolic flow and taproot color by influencing the conversion of α-carotene to lutein in carrot

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-18 DOI: 10.1093/hr/uhaf054

Hui-Ru Wang, Rong-Rong Zhang, Ya-Hui Wang, Jian-Hua Zhou, Miao Sun, Li-Xiang Wang, Yu-Qing Zhang, Yi Liang, Xiao-Jie Li, Zhi-Sheng Xu, Jing Ma, Hui Liu, Jian-Ping Tao, Ai-Sheng Xiong

{"title":"Carotene hydroxylase DcCYP97A3 affects carotenoids metabolic flow and taproot color by influencing the conversion of α-carotene to lutein in carrot","authors":"Hui-Ru Wang, Rong-Rong Zhang, Ya-Hui Wang, Jian-Hua Zhou, Miao Sun, Li-Xiang Wang, Yu-Qing Zhang, Yi Liang, Xiao-Jie Li, Zhi-Sheng Xu, Jing Ma, Hui Liu, Jian-Ping Tao, Ai-Sheng Xiong","doi":"10.1093/hr/uhaf054","DOIUrl":"https://doi.org/10.1093/hr/uhaf054","url":null,"abstract":"The color diversity of non-purple carrot taproots is mainly affected by carotenoid species and content. Carrot cytochrome P450 carotene β-ring hydroxylase (DcCYP97A3) may influence carotenoid accumulation in carrots, however, the roles of DcCYP97A3 in carrot remain unclear. Compared to the orange carrot ‘Kurodagosun, KRD’, the yellow carrot ‘Yellowstone, YST’ had greater relative transcript levels of DcCYP97A3. DcCYP97A3 was shown to catalyze the β-ring hydroxylation of α-carotene to create zeaxanthin when it was expressed in Escherichia coli accumulating α- and β-carotene. Expression of the DcCYP97A3 of ‘YST’ in DcCYP97A3 functionally deficient orange carrot ‘KRD’ resulted in yellow taproots, decreased α-carotene and β-carotene content, decreased α-/β-carotene ratio, and increased lutein content. In carrots overexpressing the DcCYP97A3 gene, the transcript levels of DcLCYE and DcLCYB1 were significantly up- and down-regulated, respectively. Gene editing of DcCYP97A3 in ‘YST’ resulted in DcCYP97A3 knockout mutants with significantly reduced levels of lutein and β-carotene and significantly up-regulated transcript levels of DcCHXB2 and DcCCD4. These findings advance our knowledge of the molecular mechanisms behind carrot carotenoid metabolism.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"24 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443453","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-18 DOI: 10.1093/hr/uhaf052

Dev Paudel, S Brooks Parrish, Ze Peng, Saroj Parajuli, Zhanao Deng

{"title":"A chromosome-scale and haplotype-resolved genome assembly of tetraploid blackberry (Rubus L. subgenus Rubus Watson)","authors":"Dev Paudel, S Brooks Parrish, Ze Peng, Saroj Parajuli, Zhanao Deng","doi":"10.1093/hr/uhaf052","DOIUrl":"https://doi.org/10.1093/hr/uhaf052","url":null,"abstract":"Blackberries (Rubus spp.) are globally consumed and well known for their rich anthocyanin and antioxidant content and distinct flavors. Improving blackberries has been challenging due to genetic complexity of traits and limited genomic resources. The blackberry genome has been particularly challenging to assemble due to its polyploid nature. Here, we present the first chromosome-scale and haplotype-phased assembly for the cultivated primocane-fruiting, thornless tetraploid blackberry selection BL1 (Rubus L. subgenus Rubus Watson). The genome assembly was generated using Oxford Nanopore Technology and Hi-C scaffolding, resulting in a 919 Mb genome distributed across 27 pseudochromosomes, with an N50 of 35.73 Mb. This assembly covers &gt;92% of the genome length and contains over 98% of complete BUSCOs. Approximately 58% of the assembly consists of repetitive sequences, with long terminal repeats being the most abundant class. A total of 87 968 protein-coding genes were predicted, of which, 82% were functionally annotated. Genome mining and RNA-Seq analyses identified possible candidate genes and transcription factors related to thornlessness and the key structural genes and transcription factors for anthocyanin biosynthesis. Activator genes including PAP1 and TTG1 and repressor genes such as ANL2 and MYBPA1 play an important role in the fine tuning of anthocyanin production during blackberry development. Resequencing of seven tetraploid blackberry cultivars/selections with different horticultural characteristics revealed candidate genes that could impact fruiting habit and disease resistance/susceptibility. This tetraploid reference genome should provide a valuable resource for accelerating genetic analysis of blackberries and facilitating the development of new improved cultivars with enhanced horticultural and nutritional traits.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"51 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443451","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0