Woody bamboo (Bambusoideae) is renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, our study, based on the in vitro system combined with a high-quality reference genome, provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboo.
木竹（Bambusoideae）以其多倍体和罕见的开花而闻名。木竹（Bambusa odashimae）是竹亚科中染色体数（104）最高的竹种之一，也是迄今为止所有竹子基因组测序中杂合度最高的竹种。与其他竹类相比，它能有效地利用外源激素调节离体开花，为研究竹类开花的激素调控提供了宝贵的资料。在此，我们利用组织培养系统，在染色体数目复杂且较多的情况下，生成了单倍型解析的B. odashimae基因组组装，并补充了来自11个发育时期的33个转录组。组装的基因组可分为单倍型 I、单倍型 II 和单倍型 III，每个单倍型都包含 A、B 和 C 亚基因组。单倍型 I 可能来源于 Dendrocalamus，而单倍型 II 和 III 与簕杜鹃关系密切，这表明 B. odashimae 的起源涉及属间杂交和种间杂交。高杂合度使我们有可能检测到丰富的等位基因特异性表达（ASE），ASE基因富集于细胞分裂素相关途径，可能与细胞分裂素高效促进开花有关。值得注意的是，我们发现 CONSTANS（CO）基因可能是 B. odashimae 离体开花的关键调控因子。总之，我们的研究以离体系统为基础，结合高质量的参考基因组，为这种非单倍体竹子的起源提供了重要的见解，并将竹子的杂交和离体开花联系起来。
{"title":"Haplotype-resolved nonaploid genome provides insights into in vitro flowering in bamboo","authors":"Yu-Jiao Wang, Cen Guo, Zhao Lei, Ling Mao, Xiang-Zhou Hu, Yi-Zhou Yang, Ke-Cheng Qian, Peng-Fei Ma, Zhen-Hua Guo, De-Zhu Li","doi":"10.1093/hr/uhae250","DOIUrl":"https://doi.org/10.1093/hr/uhae250","url":null,"abstract":"Woody bamboo (Bambusoideae) is renowned for its polyploidy and rare flowering. Bambusa odashimae is one of the bamboo species with the highest chromosome count (104) in the subfamily and has the highest heterozygosity of all sequenced bamboo genomes so far. Compared with other bamboo species, it can efficiently utilize exogenous hormones to regulate in vitro flowering, providing valuable insights into the hormonal regulation of bamboo flowering. Here, we generated the haplotype-resolved genome assembly of B. odashimae, despite the complexity and high chromosome number, supplemented by thirty-three transcriptomes from eleven developmental periods using a tissue culture system. The assembled genome can be divided into Haplotype I, Haplotype II, and Haplotype III, each containing A, B, and C subgenomes. Haplotype I may be derived from Dendrocalamus whereas Haplotypes II and III are closely related to Bambusa, indicating that B. odashimae has an origin involving both intergeneric and interspecific hybridizations. The high heterozygosity renders the possibility to detect abundant allele-specific expression (ASE), with ASE genes enriched in cytokinin-related pathways, likely associated with efficient cytokinin-promoted flowering. Notably, we found that the CONSTANS (CO) genes were potentially key regulators of in vitro flowering in B. odashimae. Overall, our study, based on the in vitro system combined with a high-quality reference genome, provides critical insights into the origin of this nonaploid bamboo and links hybridization and in vitro flowering in bamboo.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142440","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}
Next-generation sequencing (NGS) library construction often requires high-quality DNA extraction, precise adjustment of DNA concentration, and restriction enzyme digestion to reduce genome complexity, which results in increased time and cost in sample preparation and processing. To address these challenges, a PCR-based method for rapid NGS library preparation, named dpMIG-seq, has been developed and proven effective for high-throughput genotyping. However, the application of dpMIG-seq has been limited to diploid and polyploid species with disomic inheritance. In this study, we obtained genome-wide single nucleotide polymorphism (SNP) markers for tetraploid blueberry to evaluate genotyping and downstream analysis outcomes. Comparison of genotyping qualities inferred across samples with different DNA concentrations and multiple bioinformatics approaches revealed high accuracy and reproducibility of dpMIG-seq-based genotyping, with Pearson’s correlation coefficients between replicates in the range of 0.91 to 0.98. Furthermore, we demonstrated that dpMIG-seq enables accurate genotyping of samples with low DNA concentrations. Subsequently, we applied dpMIG-seq to a tetraploid F1 population to examine the inheritance probability of parental alleles. Pairing configuration analysis supported the random meiotic pairing of homologous chromosomes on a genome-wide level. On the other hand, preferential pairing was observed on chr-11, suggesting that there may be an exception to the random pairing. Genotypic data suggested quadrivalent formation within the population, although the frequency of quadrivalent formation varied by chromosome and cultivar. Collectively, the results confirmed applicability of dpMIG-seq for allele dosage genotyping and are expected to catalyze the adoption of this cost-effective and rapid genotyping technology in polyploid studies.
下一代测序（NGS）文库的构建通常需要高质量的 DNA 提取、精确的 DNA 浓度调整和限制性酶消化以降低基因组的复杂性，这就增加了样品制备和处理的时间和成本。为了应对这些挑战，一种基于 PCR 的快速 NGS 文库制备方法（名为 dpMIG-seq）已被开发出来，并被证明对高通量基因分型有效。然而，dpMIG-seq 的应用仅限于二倍体和多倍体物种，而且是非组遗传。在本研究中，我们获得了四倍体蓝莓的全基因组单核苷酸多态性（SNP）标记，以评估基因分型和下游分析结果。通过比较不同DNA浓度样本和多种生物信息学方法推断出的基因分型质量，发现基于dpMIG-seq的基因分型具有很高的准确性和可重复性，重复样本之间的皮尔逊相关系数在0.91至0.98之间。此外，我们还证明了 dpMIG-seq 能够对 DNA 浓度较低的样本进行准确的基因分型。随后，我们将 dpMIG-seq 应用于四倍体 F1 群体，研究亲本等位基因的遗传概率。配对构型分析支持同源染色体在全基因组水平上的随机减数分裂配对。另一方面，在 chr-11 上观察到了优先配对，这表明随机配对可能存在例外。基因型数据表明，虽然四价形成的频率因染色体和栽培品种而异，但在种群中仍有四价形成。总之，这些结果证实了 dpMIG-seq 在等位基因剂量基因分型方面的适用性，并有望促进这种经济高效的快速基因分型技术在多倍体研究中的应用。
{"title":"A low-cost dpMIG-seq method for elucidating complex inheritance in polysomic crops: A case study in tetraploid blueberry","authors":"Kyoka Nagasaka, Kazusa Nishimura, Ko Motoki, Keigo Yamagata, Soichiro Nishiyama, Hisayo Yamane, Ryutaro Tao, Ryohei Nakano, Tetsuya Nakazaki","doi":"10.1093/hr/uhae248","DOIUrl":"https://doi.org/10.1093/hr/uhae248","url":null,"abstract":"Next-generation sequencing (NGS) library construction often requires high-quality DNA extraction, precise adjustment of DNA concentration, and restriction enzyme digestion to reduce genome complexity, which results in increased time and cost in sample preparation and processing. To address these challenges, a PCR-based method for rapid NGS library preparation, named dpMIG-seq, has been developed and proven effective for high-throughput genotyping. However, the application of dpMIG-seq has been limited to diploid and polyploid species with disomic inheritance. In this study, we obtained genome-wide single nucleotide polymorphism (SNP) markers for tetraploid blueberry to evaluate genotyping and downstream analysis outcomes. Comparison of genotyping qualities inferred across samples with different DNA concentrations and multiple bioinformatics approaches revealed high accuracy and reproducibility of dpMIG-seq-based genotyping, with Pearson’s correlation coefficients between replicates in the range of 0.91 to 0.98. Furthermore, we demonstrated that dpMIG-seq enables accurate genotyping of samples with low DNA concentrations. Subsequently, we applied dpMIG-seq to a tetraploid F1 population to examine the inheritance probability of parental alleles. Pairing configuration analysis supported the random meiotic pairing of homologous chromosomes on a genome-wide level. On the other hand, preferential pairing was observed on chr-11, suggesting that there may be an exception to the random pairing. Genotypic data suggested quadrivalent formation within the population, although the frequency of quadrivalent formation varied by chromosome and cultivar. Collectively, the results confirmed applicability of dpMIG-seq for allele dosage genotyping and are expected to catalyze the adoption of this cost-effective and rapid genotyping technology in polyploid studies.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142441","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}
Yunpeng Cao, Jiayi Hong, Yun Zhao, Xiaoxu Li, Xiaofeng Feng, Han Wang, Lin Zhang, Mengfei Lin, Yongping Cai, Yuepeng Han
De novo genes can evolve 'from scratch' from non-coding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying de novo genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related Prunus genomes, we determined at least 178 de novo genes in P. persica ‘baifeng’. The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns. Gene ontology (GO) enrichment analysis suggested that Type I de novo genes originated from sequences related to plastid modification functions, while Type II genes were inferred to have derived from sequences related to reproductive functions. Finally, transcriptome sequencing across different tissues and developmental stages suggested that de novo genes have been evolutionarily recruited into existing regulatory networks, playing important roles in plant growth and development, which was also supported by WGCNA analysis and quantitative trait loci data. This study lays the groundwork for future research on the origins and functions of genes in Prunus and related taxa.
{"title":"De novo gene integration into regulation networks via interaction with conserved genes in peach","authors":"Yunpeng Cao, Jiayi Hong, Yun Zhao, Xiaoxu Li, Xiaofeng Feng, Han Wang, Lin Zhang, Mengfei Lin, Yongping Cai, Yuepeng Han","doi":"10.1093/hr/uhae252","DOIUrl":"https://doi.org/10.1093/hr/uhae252","url":null,"abstract":"De novo genes can evolve 'from scratch' from non-coding sequences, acquiring novel functions in organisms and integrating into regulatory networks during evolution to drive innovations in important phenotypes and traits. However, identifying de novo genes is challenging, as it requires high-quality genomes from closely related species. According to the comparison with nine closely related Prunus genomes, we determined at least 178 de novo genes in P. persica ‘baifeng’. The distinct differences were observed between de novo and conserved genes in gene characteristics and expression patterns. Gene ontology (GO) enrichment analysis suggested that Type I de novo genes originated from sequences related to plastid modification functions, while Type II genes were inferred to have derived from sequences related to reproductive functions. Finally, transcriptome sequencing across different tissues and developmental stages suggested that de novo genes have been evolutionarily recruited into existing regulatory networks, playing important roles in plant growth and development, which was also supported by WGCNA analysis and quantitative trait loci data. This study lays the groundwork for future research on the origins and functions of genes in Prunus and related taxa.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142443","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}
Zihao Li, Lin Yang, Yanni Wu, Ran Zhang, Sen Yu, Liwen Fu
The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth, development, and stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that SlTOR inhibition transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. A widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition, which led to the accumulation of two important cryoprotective metabolites: salicylic acid (SA) and putrescine (Put). Next, we discovered SlPGH1 (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) as a direct substrate of SlTOR. Inhibiting SlTOR led to increased SlCBF1 (C-REPEAT-BINDING FACTOR 1) expression via SlPGH1, potentially triggering the activation of cold-responsive genes and subsequent metabolic alterations. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.
雷帕霉素靶蛋白激酶（TOR）是一个中心信号枢纽，在精确协调植物生长、发育和胁迫响应方面发挥着至关重要的作用。这表明 TOR 密切参与了维持植物生长和胁迫反应之间的平衡。然而，尽管观察到了这些影响，但 TOR 在这些过程中的具体作用机制仍然模糊不清。在本研究中，我们研究了番茄（Solanum lycopersicum）TOR（SlTOR）如何影响植物生长和冷反应。我们证明，抑制 SlTOR 可使冷胁迫反应转录激活，从而增强番茄的耐寒性。一项广泛的靶向代谢组学分析表明，在抑制 SlTOR 后，冷胁迫下的氨基酸代谢平衡被破坏，导致两种重要的低温保护性代谢产物：水杨酸（SA）和腐胺（Put）的积累。接着，我们发现 SlPGH1（2-PHOSPHO-D-GLYCERATE HYDRO-LYASE）是 SlTOR 的直接底物。抑制 SlTOR 会导致 SlCBF1（C-REPEAT-BINDING FACTOR 1）通过 SlPGH1 表达增加，从而可能引发冷反应基因的激活和随后的代谢改变。我们的研究提供了一个机理框架，阐明了 SlTOR 如何调节氨基酸相关代谢以提高番茄的耐寒性，从而揭示了 TOR 协调的生长和胁迫响应之间复杂的相互作用。
{"title":"TOR balances plant growth and cold tolerance by orchestrating amino acid-derived metabolism in tomato","authors":"Zihao Li, Lin Yang, Yanni Wu, Ran Zhang, Sen Yu, Liwen Fu","doi":"10.1093/hr/uhae253","DOIUrl":"https://doi.org/10.1093/hr/uhae253","url":null,"abstract":"The target of rapamycin (TOR) kinase is a central signaling hub that plays a crucial role in precisely orchestrating plant growth, development, and stress responses. This suggests that TOR is intricately involved in maintaining the balance between plant growth and stress responses. Nevertheless, despite the observed effects, the specific mechanisms through which TOR operates in these processes remain obscure. In this study, we investigated how the tomato (Solanum lycopersicum) TOR (SlTOR) affects plant growth and cold responses. We demonstrated that SlTOR inhibition transcriptionally primes cold stress responses, consequently enhancing tomato cold tolerance. A widely targeted metabolomics analysis revealed the disruption of amino acid metabolism homeostasis under cold stress upon SlTOR inhibition, which led to the accumulation of two important cryoprotective metabolites: salicylic acid (SA) and putrescine (Put). Next, we discovered SlPGH1 (2-PHOSPHO-D-GLYCERATE HYDRO-LYASE) as a direct substrate of SlTOR. Inhibiting SlTOR led to increased SlCBF1 (C-REPEAT-BINDING FACTOR 1) expression via SlPGH1, potentially triggering the activation of cold-responsive genes and subsequent metabolic alterations. Our study provides a mechanistic framework that elucidates how SlTOR modulates amino acid-related metabolism to enhance tomato cold tolerance, which sheds light on the complex interplay between growth and stress responses orchestrated by TOR.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142142442","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}
Soluble sugars are not only an important contributor to fruit quality, but also serve as the osmotic regulators in response to abiotic stresses. Early drought stress promotes sugar accumulation, while specific sugar transporters govern the cellular distribution of the sugars. Here, we show that apple plantlets accumulate soluble sugars in leaf tissues under drought stress. Transcriptional profiling of stressed and control plantlets revealed differential expression of several plasma membrane- or vacuolar membrane-localized sugar transporter genes. Among these, four previously identified vacuolar sugar transporter (VST) genes (MdERDL6–1, MdERDL6–2, MdTST1 and MdTST2) showed higher expression under drought, suggesting their roles in response to drought stress. Promoter cis-elements analyses, yeast one-hybrid and dual-luciferase tests confirmed that the drought-induced transcription factor MdDREB2A could promote the expression of MdERDL6–1/−2 and MdTST1/2 by binding to their promoter regions. Moreover, overexpressing of each of these four MdVSTs alone in transgenic apple or Arabidopsis plants accumulated more soluble sugars and abscisic acid, and enhanced drought resistance. Furthermore, apple plants overexpressing MdERDL6–1 also showed reduced water potential, facilitated stomatal closure and reactive oxygen species scavenging under drought condition compared to control plants. Overall, our results suggest a potential strategy to enhance drought resistance and sugar accumulation in fruits through manipulating the genes involved in vacuolar sugar transport.
{"title":"Apple vacuolar sugar transporters regulated by MdDREB2A enhance drought resistance by promoting accumulation of soluble sugars and activating ABA signaling","authors":"Lingcheng Zhu, Chunxia Zhang, Nanxiang Yang, Wenjing Cao, Yanzhen Li, Yunjing Peng, Xiaoyu Wei, Baiquan Ma, Fengwang Ma, Yong-Ling Ruan, Mingjun Li","doi":"10.1093/hr/uhae251","DOIUrl":"https://doi.org/10.1093/hr/uhae251","url":null,"abstract":"Soluble sugars are not only an important contributor to fruit quality, but also serve as the osmotic regulators in response to abiotic stresses. Early drought stress promotes sugar accumulation, while specific sugar transporters govern the cellular distribution of the sugars. Here, we show that apple plantlets accumulate soluble sugars in leaf tissues under drought stress. Transcriptional profiling of stressed and control plantlets revealed differential expression of several plasma membrane- or vacuolar membrane-localized sugar transporter genes. Among these, four previously identified vacuolar sugar transporter (VST) genes (MdERDL6–1, MdERDL6–2, MdTST1 and MdTST2) showed higher expression under drought, suggesting their roles in response to drought stress. Promoter cis-elements analyses, yeast one-hybrid and dual-luciferase tests confirmed that the drought-induced transcription factor MdDREB2A could promote the expression of MdERDL6–1/−2 and MdTST1/2 by binding to their promoter regions. Moreover, overexpressing of each of these four MdVSTs alone in transgenic apple or Arabidopsis plants accumulated more soluble sugars and abscisic acid, and enhanced drought resistance. Furthermore, apple plants overexpressing MdERDL6–1 also showed reduced water potential, facilitated stomatal closure and reactive oxygen species scavenging under drought condition compared to control plants. Overall, our results suggest a potential strategy to enhance drought resistance and sugar accumulation in fruits through manipulating the genes involved in vacuolar sugar transport.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131010","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}
Hanan Alter, Yael Sade, Archit Sood, Mira Carmeli-Weissberg, Felix Shaya, Rina Kamenetsky-Goldstein, Nirit Bernstein, Ben Spitzer-Rimon
In cannabis seedlings, the initiation of solitary flowers is photoperiod-independent. However, when cannabis reaches the adult stage, short-day photoperiod (SD) triggers branching of the shoot apex and a reduction in internode length, leading to development of a condensed inflorescence. We demonstrate that SD affects cannabis plants in two distinct phases: the first includes rapid elongation of the internodes and main stem, and occurring from day 5 to day 10 of plant cultivation under SD; in the second phase, elongation of newly developed internodes ceases, and a condensed inflorescence is formed. Exposure of plants to alternating photoperiods revealed that inflorescence onset requires at least three consecutive days of SD, and SD is consistently required throughout inflorescence maturation to support its typical condensed architecture. This photoperiod-dependent morphogenesis was associated with a decrease in gibberellin (GA4) and auxin levels in the shoot apex. Reverting the plants to a long-day photoperiod (LD) increased GA4 and auxin levels, leading to inflorescence disassembly, internode elongation and subsequent resumption of LD growth patterns. Similar developmental patterns were observed under SD following the application of exogenous GA (and not auxin), which also impeded inflorescence development. Nevertheless, additional studies will help to further evaluate auxin’s role in these developmental changes. We propose a crucial role for GA in sexual reproduction and inflorescence development in female cannabis by mediating photoperiod signaling in the inflorescence tissues.
{"title":"Inflorescence development in female cannabis plants is mediated by photoperiod and gibberellin","authors":"Hanan Alter, Yael Sade, Archit Sood, Mira Carmeli-Weissberg, Felix Shaya, Rina Kamenetsky-Goldstein, Nirit Bernstein, Ben Spitzer-Rimon","doi":"10.1093/hr/uhae245","DOIUrl":"https://doi.org/10.1093/hr/uhae245","url":null,"abstract":"In cannabis seedlings, the initiation of solitary flowers is photoperiod-independent. However, when cannabis reaches the adult stage, short-day photoperiod (SD) triggers branching of the shoot apex and a reduction in internode length, leading to development of a condensed inflorescence. We demonstrate that SD affects cannabis plants in two distinct phases: the first includes rapid elongation of the internodes and main stem, and occurring from day 5 to day 10 of plant cultivation under SD; in the second phase, elongation of newly developed internodes ceases, and a condensed inflorescence is formed. Exposure of plants to alternating photoperiods revealed that inflorescence onset requires at least three consecutive days of SD, and SD is consistently required throughout inflorescence maturation to support its typical condensed architecture. This photoperiod-dependent morphogenesis was associated with a decrease in gibberellin (GA4) and auxin levels in the shoot apex. Reverting the plants to a long-day photoperiod (LD) increased GA4 and auxin levels, leading to inflorescence disassembly, internode elongation and subsequent resumption of LD growth patterns. Similar developmental patterns were observed under SD following the application of exogenous GA (and not auxin), which also impeded inflorescence development. Nevertheless, additional studies will help to further evaluate auxin’s role in these developmental changes. We propose a crucial role for GA in sexual reproduction and inflorescence development in female cannabis by mediating photoperiod signaling in the inflorescence tissues.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-09-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131046","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}
Chionanthus retusus, an arbor tree of the Oleaceae family, is an ecologically and economically valuable ornamental plant for its remarkable adaptability in landscaping. During C. retusus breeding, we observed diverse floral shapes; however, no available genome for C. retusus has hindered the widespread identification of genes related to flower morphology. Thus, a de novo telomere-to-telomere (T2T) gap-free genome was generated. The assembly, incorporating high-coverage and long-read sequencing data, successfully yielded two complete haplotypes (687 and 683 Mb). The genome encompasses 42 864 predicted protein-coding genes, with all 46 telomeres and 23 centromeres in one haplotype. Whole genome duplication analysis revealed that C. retusus underwent one fewer event of whole-genome duplication after differentiation compared to other species in the Oleaceae family. Furthermore, flower vein diversity was the main reason for the differences in floral shapes. Auxin-related genes were responsible for petal shape formation on genome-based transcriptome analysis. Specifically, the removal and retention of the first intron in CrAUX/IAA20 resulted in the production of two transcripts, and the differences in the expression levels of CrAUX/IAA20 resulted in the variations of flower veins. Compared to transcripts lacking the first intron, transcripts with intron retention caused more severe decreases in the number and length of flower veins in transgenic Arabidopsis thaliana. Our findings will deepen our understanding of flower morphology development and provide important theoretical support for the cultivation of Oleaceae.
{"title":"A telomere-to-telomere gap-free reference genome of Chionanthus retusus provides insights into the molecular mechanism underlying petal shape changes","authors":"Jinnan Wang, Dong Xu, Yalin Sang, Maotong Sun, Cuishuang Liu, Muge Niu, Ying Li, Laishuo Liu, Xiaojiao Han, Jihong Li","doi":"10.1093/hr/uhae249","DOIUrl":"https://doi.org/10.1093/hr/uhae249","url":null,"abstract":"Chionanthus retusus, an arbor tree of the Oleaceae family, is an ecologically and economically valuable ornamental plant for its remarkable adaptability in landscaping. During C. retusus breeding, we observed diverse floral shapes; however, no available genome for C. retusus has hindered the widespread identification of genes related to flower morphology. Thus, a de novo telomere-to-telomere (T2T) gap-free genome was generated. The assembly, incorporating high-coverage and long-read sequencing data, successfully yielded two complete haplotypes (687 and 683 Mb). The genome encompasses 42 864 predicted protein-coding genes, with all 46 telomeres and 23 centromeres in one haplotype. Whole genome duplication analysis revealed that C. retusus underwent one fewer event of whole-genome duplication after differentiation compared to other species in the Oleaceae family. Furthermore, flower vein diversity was the main reason for the differences in floral shapes. Auxin-related genes were responsible for petal shape formation on genome-based transcriptome analysis. Specifically, the removal and retention of the first intron in CrAUX/IAA20 resulted in the production of two transcripts, and the differences in the expression levels of CrAUX/IAA20 resulted in the variations of flower veins. Compared to transcripts lacking the first intron, transcripts with intron retention caused more severe decreases in the number and length of flower veins in transgenic Arabidopsis thaliana. Our findings will deepen our understanding of flower morphology development and provide important theoretical support for the cultivation of Oleaceae.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-31","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142131012","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}
Phosphorus (P) is the macronutrients essential for the development and growth of plants, but how external inorganic phosphate (Pi) level and signaling affect tea plant growth and characteristic secondary metabolite biosynthesis are not understood. Theanine is major secondary metabolites, and its contents largely determine tea favor and nutrition qualities. Here, we found theanine contents in tea leaves and roots declined as Pi concentration increased in tea plants after Pi feeding. The transcriptome analysis of global gene expression in tea leaves under Pi feeding suggested a wide range of genes involved in Pi/N transport and responses were altered. Among them, CsSPX3 and CsPHL7 transcript levels in response to Pi feeding to tea plants, their expression patterns were generally opposite to these of major theanine biosynthesis genes, indicating possible regulatory correlations. Biochemical analyses showed that CsSPX3 interacted with CsPHL7, and CsPHL7 negatively regulated theanine biosynthesis genes CsGS1 and CsTS1. Meanwhile, VIGS and transient overexpression systems in tea plants verified the functions of CsSPX3 and CsPHL7 in mediating Pi-feeding-repressed theanine biosynthesis. This study offers fresh insights into the regulatory mechanism underlying Pi repression of theanine biosynthesis, and the CsSPX3-CsPHL7-CsGS1/CsTS1 module plays a role in high Pi-inhibition of theanine production in tea leaves. It has an instructional significance for guiding the high-quality tea production in tea garden fertilization.
磷（P）是植物生长发育所必需的宏量营养元素，但外界无机磷酸盐（Pi）水平和信号如何影响茶树生长和特征次生代谢物的生物合成尚不清楚。茶氨酸是主要的次生代谢产物，其含量在很大程度上决定了茶叶的品质和营养。在此，我们发现茶叶叶片和根中的茶氨酸含量随着茶树摄入 Pi 后 Pi 浓度的增加而下降。通过对茶叶全基因组表达的转录组分析，我们发现参与 Pi/N 转运和响应的多种基因发生了改变。其中，CsSPX3 和 CsPHL7 的转录水平在茶树摄入 Pi 后的响应中，其表达模式与主要茶氨酸生物合成基因的表达模式基本相反，表明可能存在调控相关性。生化分析表明，CsSPX3 与 CsPHL7 相互作用，CsPHL7 负调控茶氨酸生物合成基因 CsGS1 和 CsTS1。同时，在茶树中的 VIGS 和瞬时过表达系统验证了 CsSPX3 和 CsPHL7 在介导 Pi-饲料抑制的茶氨酸生物合成中的功能。该研究为Pi抑制茶氨酸生物合成的调控机制提供了新的见解，CsSPX3-CsPHL7-CsGS1/CsTS1模块在高Pi抑制茶叶茶氨酸生产中发挥了作用。这对指导茶园施肥生产优质茶叶具有指导意义。
{"title":"CsSPX3-CsPHL7-CsGS1/CsTS1 module mediated pi-regulated negatively theanine biosynthesis in tea (Camellia sinensis)","authors":"Zhouzhuoer Chen, Zhixun Yu, TingTing Liu, Xinzhuan Yao, Shiyu Zhang, Yilan Hu, Mingyuan Luo, Yue Wan, Litang Lu","doi":"10.1093/hr/uhae242","DOIUrl":"https://doi.org/10.1093/hr/uhae242","url":null,"abstract":"Phosphorus (P) is the macronutrients essential for the development and growth of plants, but how external inorganic phosphate (Pi) level and signaling affect tea plant growth and characteristic secondary metabolite biosynthesis are not understood. Theanine is major secondary metabolites, and its contents largely determine tea favor and nutrition qualities. Here, we found theanine contents in tea leaves and roots declined as Pi concentration increased in tea plants after Pi feeding. The transcriptome analysis of global gene expression in tea leaves under Pi feeding suggested a wide range of genes involved in Pi/N transport and responses were altered. Among them, CsSPX3 and CsPHL7 transcript levels in response to Pi feeding to tea plants, their expression patterns were generally opposite to these of major theanine biosynthesis genes, indicating possible regulatory correlations. Biochemical analyses showed that CsSPX3 interacted with CsPHL7, and CsPHL7 negatively regulated theanine biosynthesis genes CsGS1 and CsTS1. Meanwhile, VIGS and transient overexpression systems in tea plants verified the functions of CsSPX3 and CsPHL7 in mediating Pi-feeding-repressed theanine biosynthesis. This study offers fresh insights into the regulatory mechanism underlying Pi repression of theanine biosynthesis, and the CsSPX3-CsPHL7-CsGS1/CsTS1 module plays a role in high Pi-inhibition of theanine production in tea leaves. It has an instructional significance for guiding the high-quality tea production in tea garden fertilization.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100863","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}
Qiao Wang, Baoquan Du, Yujing Bai, Yan Chen, Feng Li, Jinzhe Du, Xiuwen Wu, Liping Yan, Yue Bai, Guohua Chai
Rose (Rosa rugosa) petals are rich in diverse secondary metabolites, which have important physiological functions as well as great economic values. Currently, it remains unclear how saline and/or alkaline stress(es) influence the accumulation of secondary metabolites in rose. In this study, we analyzed the transcriptome and metabolite profiles of rose petals under aline-alkali stress and uncovered the induction mechanism underlying major metabolites. Dramatic changes were observed in the expression of 1363 genes and the abundances of 196 metabolites in petals in response to saline-alkali stress. These differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) are mainly associated with flavonoid and terpenoid metabolism and the reconstruction of cell walls. Of them, TERPENE SYNTHASE 31 (TPS31) overexpression in tobacco leaves driven by its own promoter resulted in significant alterations in the levels of various terpenoids, which were differentially influenced by saline-alkali stress. An integrated analysis of metabolomic and transcriptomic data revealed a high correlation between the abundances of flavonoids/terpenoids and the expression of the transcription factor MYB5. MYB5 may orchestrate the biosynthesis of sesquiterpenoids and proanthocyanidins through direct regulation of TPS31 and ANR expression under aline-alkali stress. Our finding facilitates improving the bioactive substance accumulation of rose petals by metabolic engineering.
{"title":"Saline-alkali stress affects the accumulation of proanthocyanidins and sesquiterpenoids via the MYB5-ANR/TPS31 cascades in the rose petals","authors":"Qiao Wang, Baoquan Du, Yujing Bai, Yan Chen, Feng Li, Jinzhe Du, Xiuwen Wu, Liping Yan, Yue Bai, Guohua Chai","doi":"10.1093/hr/uhae243","DOIUrl":"https://doi.org/10.1093/hr/uhae243","url":null,"abstract":"Rose (Rosa rugosa) petals are rich in diverse secondary metabolites, which have important physiological functions as well as great economic values. Currently, it remains unclear how saline and/or alkaline stress(es) influence the accumulation of secondary metabolites in rose. In this study, we analyzed the transcriptome and metabolite profiles of rose petals under aline-alkali stress and uncovered the induction mechanism underlying major metabolites. Dramatic changes were observed in the expression of 1363 genes and the abundances of 196 metabolites in petals in response to saline-alkali stress. These differentially expressed genes (DEGs) and differentially accumulated metabolites (DAMs) are mainly associated with flavonoid and terpenoid metabolism and the reconstruction of cell walls. Of them, TERPENE SYNTHASE 31 (TPS31) overexpression in tobacco leaves driven by its own promoter resulted in significant alterations in the levels of various terpenoids, which were differentially influenced by saline-alkali stress. An integrated analysis of metabolomic and transcriptomic data revealed a high correlation between the abundances of flavonoids/terpenoids and the expression of the transcription factor MYB5. MYB5 may orchestrate the biosynthesis of sesquiterpenoids and proanthocyanidins through direct regulation of TPS31 and ANR expression under aline-alkali stress. Our finding facilitates improving the bioactive substance accumulation of rose petals by metabolic engineering.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100592","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}
Richard Tegtmeier, Anže Švara, Dilyara Gritsenko, Awais Khan
Apples are one of the most valued tree fruit crops around the world. Currently, a few highly popular and economically successful apple cultivars dominate the commercial production and serve as main genetic contributors to the development of new apple cultivars. This limited level of genetic diversity, grown as a clonally propagated monoculture renders the apple industry vulnerable to the wide range of weather events, pests, and pathogens. Wild apple species are an excellent source of beneficial alleles for the wide range of biotic and abiotic stressors challenging apple production. However, the biological barriers of breeding with small-fruited wild apples greatly limit their use. Using a closely related wild species of apple such as Malus sieversii can improve the efficiency of breeding efforts and broaden the base of available genetics. M. sieversii is the main progenitor of the domesticated apple, native to Central Asia. The similarity of fruit morphology to domesticated apples and resistances to abiotic and biotic stresses makes it appealing for apple breeding programs. However, this important species is under threat of extinction in its native range. Preserving the wild apple forests in Central Asia is vital for ensuring the sustainable protection of this important genetic resource. The insufficient awareness about the complete range of challenges and opportunities associated with M. sieversii hinders the maximization of its potential benefits. This review aims to provide comprehensive information on the cultural and historical context of M. sieversii, current genetic knowledge for breeding, and the conservation challenges of wild apple forests.
苹果是全世界最有价值的木本水果作物之一。目前，在商业生产中，少数几个非常受欢迎且在经济上非常成功的苹果栽培品种占主导地位，它们也是开发新苹果栽培品种的主要遗传贡献者。这种以克隆繁殖的单一栽培方式种植的遗传多样性水平有限，使得苹果产业很容易受到各种天气事件、虫害和病原体的影响。对于苹果生产所面临的各种生物和非生物压力，野生苹果物种是有益等位基因的极佳来源。然而，利用小果型野生苹果进行育种的生物障碍极大地限制了它们的使用。利用苹果的近缘野生种（如 Malus sieversii）可以提高育种工作的效率，扩大可用遗传基础。M. sieversii 是原产于中亚的驯化苹果的主要祖先。其果实形态与驯化苹果相似，并能抵抗非生物和生物胁迫，因此对苹果育种计划很有吸引力。然而，这一重要物种在其原产地正面临灭绝的威胁。保护中亚的野生苹果林对于确保这一重要遗传资源的可持续保护至关重要。由于对与 M. sieversii 相关的一系列挑战和机遇认识不足，阻碍了其潜在效益的最大化。本综述旨在提供有关 M. sieversii 的文化和历史背景、当前用于育种的遗传知识以及野生苹果林保护挑战的全面信息。
{"title":"Malus sieversii: a historical, genetic, and conservational perspective of the primary progenitor species of domesticated apples","authors":"Richard Tegtmeier, Anže Švara, Dilyara Gritsenko, Awais Khan","doi":"10.1093/hr/uhae244","DOIUrl":"https://doi.org/10.1093/hr/uhae244","url":null,"abstract":"Apples are one of the most valued tree fruit crops around the world. Currently, a few highly popular and economically successful apple cultivars dominate the commercial production and serve as main genetic contributors to the development of new apple cultivars. This limited level of genetic diversity, grown as a clonally propagated monoculture renders the apple industry vulnerable to the wide range of weather events, pests, and pathogens. Wild apple species are an excellent source of beneficial alleles for the wide range of biotic and abiotic stressors challenging apple production. However, the biological barriers of breeding with small-fruited wild apples greatly limit their use. Using a closely related wild species of apple such as Malus sieversii can improve the efficiency of breeding efforts and broaden the base of available genetics. M. sieversii is the main progenitor of the domesticated apple, native to Central Asia. The similarity of fruit morphology to domesticated apples and resistances to abiotic and biotic stresses makes it appealing for apple breeding programs. However, this important species is under threat of extinction in its native range. Preserving the wild apple forests in Central Asia is vital for ensuring the sustainable protection of this important genetic resource. The insufficient awareness about the complete range of challenges and opportunities associated with M. sieversii hinders the maximization of its potential benefits. This review aims to provide comprehensive information on the cultural and historical context of M. sieversii, current genetic knowledge for breeding, and the conservation challenges of wild apple forests.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":null,"pages":null},"PeriodicalIF":8.7,"publicationDate":"2024-08-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142100862","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}
京公网安备 11010802042870号
京ICP备2023020795号-1
扫码关注我们
求助内容：
应助结果提醒方式：