Banana fruit ripening is a highly regulatory process involving various layers consisting of transcriptional regulation, epigenetic factor, and post-translational modification. Previously, we reported that MaERF11 cooperated with MaHDA1 to precisely regulate the transcription of ripening-associated genes via histone deacetylation. However, whether MaERF11 is subjected to post-translational modification during banana ripening is largely unknown. In this study, we found that MaERF11 targeted a subset of starch degradation-related genes using the DNA affinity purification sequence (DAP-Seq) approach. Electrophoresis mobility shift assay (EMSA) and dual-luciferase reporter assay (DLR) demonstrated that MaERF11 could specifically bind and repress the expression of the starch degradation-related genes , and . Further analyses of yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and Luciferase complementation imaging (LCI) assays indicated that MaERF11 interacted with the ubiquitin E3 ligase MaRFA1, and this interaction weakened the MaERF11-mediated transcriptional repression capacity. Collectively, our results suggest an additional regulatory layer in which MaERF11 regulates banana fruit ripening and expands the regulatory network in fruit ripening at the post-translational modification level.
{"title":"Interaction of MaERF11 with an E3 ubiquitin ligase MaRFA1 is involved in regulation of banana starch degradation during postharvest ripening","authors":"Mengge Jiang, Yingying Yang, Wei Wei, Chaojie Wu, Wei Shan, Jianfei Kuang, Jianye Chen, Shouxing Wei, Wangjin Lu","doi":"10.1016/j.hpj.2023.09.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.09.006","url":null,"abstract":"Banana fruit ripening is a highly regulatory process involving various layers consisting of transcriptional regulation, epigenetic factor, and post-translational modification. Previously, we reported that MaERF11 cooperated with MaHDA1 to precisely regulate the transcription of ripening-associated genes via histone deacetylation. However, whether MaERF11 is subjected to post-translational modification during banana ripening is largely unknown. In this study, we found that MaERF11 targeted a subset of starch degradation-related genes using the DNA affinity purification sequence (DAP-Seq) approach. Electrophoresis mobility shift assay (EMSA) and dual-luciferase reporter assay (DLR) demonstrated that MaERF11 could specifically bind and repress the expression of the starch degradation-related genes , and . Further analyses of yeast two-hybrid (Y2H), bimolecular fluorescence complementation (BiFC) and Luciferase complementation imaging (LCI) assays indicated that MaERF11 interacted with the ubiquitin E3 ligase MaRFA1, and this interaction weakened the MaERF11-mediated transcriptional repression capacity. Collectively, our results suggest an additional regulatory layer in which MaERF11 regulates banana fruit ripening and expands the regulatory network in fruit ripening at the post-translational modification level.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"18 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140162196","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}
Pub Date : 2024-03-16DOI: 10.1016/j.hpj.2023.08.002
Jorge Alemán-Báez, Jose Fernando Acevedo-Zamora, Johan Bucher, Chengcheng Cai, Roeland E. Voorrips, Guusje Bonnema
Cabbage ( var. ) is an economically important vegetable crop grown for its leafy head. Cabbage plants’ vegetative development goes from seedling to rosette, folding and heading stages. Leaves that form the rosette are large and mostly flat, acting as the major photosynthetic organs. In the following developmental stages, the plants produce leaves that curve inward, overlapping the shoot apex to produce the leafy head. These leaves are shielded from the light and act as sink organs. We investigated the role of miRNA-regulated genes in the transition from the rosette to the heading stage. We first phenotyped leaf formation and -expansion for two contrasting (round and pointed) heading cabbage morphotypes to define the rosette and heading developmental stages. This allowed us to collect tissue from young expanding leaves that would develop into, respectively, rosette and heading leaves for miRNA and gene expression analyses. Young leaf tissue of two time points of a non-heading collard green ( var. ) morphotype was used as a control to distinguish the transcripts (miRNAs/genes) that regulate plant age from those defining the transition from rosette to heading leaves in cabbages. For both round and pointed cabbages, we compared the miRNA and mRNA abundances between rosette and heading leaves to identify differentially expressed miRNAs (DEMs) and –genes (DEGs). After correcting for miRNAs and genes related to plant age, we identified 33 DEMs and 1,998 DEGs with roles in the transition from rosette to heading stage. We predicted the target genes of these 33 DEMs and focused on the subset that were DEGs between rosette and heading stage leaves to construct miRNA-target gene interaction networks. Our main finding is a role for miR396b-5p targeting two orthologues of () and - () in pointed cabbage head formation.
{"title":"Expression changes of miRNA-regulated genes associated with the formation of the leafy head in cabbage (Brassica oleracea var. capitata).","authors":"Jorge Alemán-Báez, Jose Fernando Acevedo-Zamora, Johan Bucher, Chengcheng Cai, Roeland E. Voorrips, Guusje Bonnema","doi":"10.1016/j.hpj.2023.08.002","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.08.002","url":null,"abstract":"Cabbage ( var. ) is an economically important vegetable crop grown for its leafy head. Cabbage plants’ vegetative development goes from seedling to rosette, folding and heading stages. Leaves that form the rosette are large and mostly flat, acting as the major photosynthetic organs. In the following developmental stages, the plants produce leaves that curve inward, overlapping the shoot apex to produce the leafy head. These leaves are shielded from the light and act as sink organs. We investigated the role of miRNA-regulated genes in the transition from the rosette to the heading stage. We first phenotyped leaf formation and -expansion for two contrasting (round and pointed) heading cabbage morphotypes to define the rosette and heading developmental stages. This allowed us to collect tissue from young expanding leaves that would develop into, respectively, rosette and heading leaves for miRNA and gene expression analyses. Young leaf tissue of two time points of a non-heading collard green ( var. ) morphotype was used as a control to distinguish the transcripts (miRNAs/genes) that regulate plant age from those defining the transition from rosette to heading leaves in cabbages. For both round and pointed cabbages, we compared the miRNA and mRNA abundances between rosette and heading leaves to identify differentially expressed miRNAs (DEMs) and –genes (DEGs). After correcting for miRNAs and genes related to plant age, we identified 33 DEMs and 1,998 DEGs with roles in the transition from rosette to heading stage. We predicted the target genes of these 33 DEMs and focused on the subset that were DEGs between rosette and heading stage leaves to construct miRNA-target gene interaction networks. Our main finding is a role for miR396b-5p targeting two orthologues of () and - () in pointed cabbage head formation.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"18 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-16","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140162209","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}
Pub Date : 2024-03-09DOI: 10.1016/j.hpj.2023.11.006
Ho-Young Jeong, Yoonseo Lim, Myeong-Gyun Seo, Soon Ju Park, Chanhui Lee, Young-Joon Park, Choon-Tak Kwon
Senescence, a crucial developmental process in the life cycle of plants, involves programmed destruction of cellular components of leaves. The onset of senescence is synchronized with other developmental processes for successful reproduction since senescence eventually leads to cell death. Arabinosyltransferase FASCIATED AND BRANCHED 2 (FAB2) is known to control meristem proliferation. Here, we show that FAB2 can inhibit premature leaf senescence in tomato plants. Both chemically mutagenized and CRISPR-generated mutants exhibited excessively accelerated senescence, which resulted in sterility. Transcriptome analysis revealed that extended leaf longevity by suppressing transcription of genes highly expressed in mature leaves. Transcription of was increased in younger leaves, potentially inhibiting premature leaf senescence. The precocious senescence of mutants was in contrast to () mutants, which carried mutations in a hydroxyproline O-arabinosyltransferase gene, leading to meristem overproliferation. Our observations indicate that complex genetic hierarchy in the cascade of tomato arabinosyltransferases could control different aspects of developmental processes such as stem cell proliferation and senescence.
衰老是植物生命周期中的一个关键发育过程，涉及叶片细胞成分的程序性破坏。由于衰老最终会导致细胞死亡，因此衰老的开始要与其他发育过程同步，这样才能成功繁殖。已知阿拉伯糖基转移酶 FASCIATED AND BRANCHED 2（FAB2）能控制分生组织的增殖。在这里，我们发现 FAB2 可以抑制番茄植株叶片的过早衰老。化学诱变和 CRISPR 产生的突变体都表现出过度加速衰老，从而导致不育。转录组分析揭示，通过抑制成熟叶片中高表达基因的转录，延长了叶片的寿命。年轻叶片中的基因转录增加，可能抑制了叶片的过早衰老。突变体的过早衰老与（）突变体形成鲜明对比，后者携带羟脯氨酸 O-阿拉伯糖基转移酶基因突变，导致分生组织过度增殖。我们的观察结果表明，番茄阿拉伯糖基转移酶级联中复杂的遗传层次可控制干细胞增殖和衰老等发育过程的不同方面。
{"title":"Tomato arabinosyltransferase prevents precocious senescence","authors":"Ho-Young Jeong, Yoonseo Lim, Myeong-Gyun Seo, Soon Ju Park, Chanhui Lee, Young-Joon Park, Choon-Tak Kwon","doi":"10.1016/j.hpj.2023.11.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.11.006","url":null,"abstract":"Senescence, a crucial developmental process in the life cycle of plants, involves programmed destruction of cellular components of leaves. The onset of senescence is synchronized with other developmental processes for successful reproduction since senescence eventually leads to cell death. Arabinosyltransferase FASCIATED AND BRANCHED 2 (FAB2) is known to control meristem proliferation. Here, we show that FAB2 can inhibit premature leaf senescence in tomato plants. Both chemically mutagenized and CRISPR-generated mutants exhibited excessively accelerated senescence, which resulted in sterility. Transcriptome analysis revealed that extended leaf longevity by suppressing transcription of genes highly expressed in mature leaves. Transcription of was increased in younger leaves, potentially inhibiting premature leaf senescence. The precocious senescence of mutants was in contrast to () mutants, which carried mutations in a hydroxyproline O-arabinosyltransferase gene, leading to meristem overproliferation. Our observations indicate that complex genetic hierarchy in the cascade of tomato arabinosyltransferases could control different aspects of developmental processes such as stem cell proliferation and senescence.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"97 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-09","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140100348","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}
Pub Date : 2024-03-08DOI: 10.1016/j.hpj.2024.01.004
Mughair Abdul Aziz, Khaled Masmoudi
Advancements in molecular approaches have been utilized to breed crops with a wide range of economically valuable traits to develop superior cultivars. This review provides a concise overview of modern breakthroughs in molecular plant production. Genotyping and high-throughput phenotyping methods for predictive plant breeding are briefly discussed. In this study, we explore contemporary molecular breeding techniques for producing desirable crop varieties. These techniques include cisgenesis, clustered regularly interspaced short palindromic repeat (CRISPR/Cas9) gene editing, haploid induction, and de novo domestication. We examine the speed breeding approach—a strategy for cultivating plants under controlled conditions. We further highlight the significance of modern breeding technologies in efficiently utilizing agricultural resources for crop production in urban areas. The deciphering of crop genomes has led to the development of extensive DNA markers, quantitative trait loci (QTLs), and pangenomes associated with various desirable crop traits. This shift to the genotypic selection of crops considerably expedites the plant breeding process. Based on the plant population used, the connection between genotypic and phenotypic data provides several genetic elements, including genes, markers, and alleles that can be used in genomic breeding and gene editing. The integration of speed breeding with genomic-assisted breeding and cutting-edge genome editing tools has made it feasible to rapidly manipulate and generate multiple crop cycles and accelerate the plant breeding process. Breakthroughs in molecular techniques have led to substantial improvements in modern breeding methods.
分子方法的进步已被用于培育具有多种经济价值性状的作物，以培育优良品种。本综述简要概述了分子植物育种的现代突破。简要讨论了用于预测性植物育种的基因分型和高通量表型方法。在本研究中，我们探讨了培育理想作物品种的现代分子育种技术。这些技术包括顺式育种、聚类规则间隔短回文重复（CRISPR/Cas9）基因编辑、单倍体诱导和从头驯化。我们研究了快速育种方法--一种在受控条件下培育植物的策略。我们进一步强调了现代育种技术在有效利用农业资源促进城市地区作物生产方面的重要意义。作物基因组的解密导致了与各种理想作物性状相关的大量 DNA 标记、数量性状位点（QTL）和泛基因组的开发。向作物基因型选择的转变大大加快了植物育种进程。根据所使用的植物群体，基因型和表型数据之间的联系提供了若干遗传要素，包括基因、标记和等位基因，可用于基因组育种和基因编辑。速度育种与基因组辅助育种和尖端基因组编辑工具的结合，使得快速操作和生成多个作物周期以及加速植物育种过程变得可行。分子技术的突破极大地改进了现代育种方法。
{"title":"Molecular Breakthroughs in Modern Plant Breeding Techniques","authors":"Mughair Abdul Aziz, Khaled Masmoudi","doi":"10.1016/j.hpj.2024.01.004","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.01.004","url":null,"abstract":"Advancements in molecular approaches have been utilized to breed crops with a wide range of economically valuable traits to develop superior cultivars. This review provides a concise overview of modern breakthroughs in molecular plant production. Genotyping and high-throughput phenotyping methods for predictive plant breeding are briefly discussed. In this study, we explore contemporary molecular breeding techniques for producing desirable crop varieties. These techniques include cisgenesis, clustered regularly interspaced short palindromic repeat (CRISPR/Cas9) gene editing, haploid induction, and de novo domestication. We examine the speed breeding approach—a strategy for cultivating plants under controlled conditions. We further highlight the significance of modern breeding technologies in efficiently utilizing agricultural resources for crop production in urban areas. The deciphering of crop genomes has led to the development of extensive DNA markers, quantitative trait loci (QTLs), and pangenomes associated with various desirable crop traits. This shift to the genotypic selection of crops considerably expedites the plant breeding process. Based on the plant population used, the connection between genotypic and phenotypic data provides several genetic elements, including genes, markers, and alleles that can be used in genomic breeding and gene editing. The integration of speed breeding with genomic-assisted breeding and cutting-edge genome editing tools has made it feasible to rapidly manipulate and generate multiple crop cycles and accelerate the plant breeding process. Breakthroughs in molecular techniques have led to substantial improvements in modern breeding methods.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"144 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140100349","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}
In grapevine, previous studies have suggested that, gibberellin (GA) inhibits bud break before dormancy release while enhanced after dormancy release; the capacity of GA accumulation shows a trend of first inhibition and then upregulation. However, the regulatory mechanism of GA metabolism genes expression is as yet unclear during the process of dormancy release. In this study, we further validated the effect of GA and hydrogen cyanamide (HC) on bud break of ‘Red globe’ grape, confirmed inhibition and promotion effect, respectively. Restricted GA biosynthetic genes’ expression and enhanced GA catabolic gene’s expression were observed in the early stage after HC treatment, while opposite expression trend showed in the late stage. , a MADS-box transcription factor gene, was downregulated in the late stage, which might play an important role in regulating GA metabolism genes’ expression. It was shown that, VvSVP1 could bind to the promoter regions of GA biosynthetic gene and catabolic gene , negatively and positively regulated the corresponding genes’ expression, respectively; the contents of GAs related to GA20ox were significantly reduced in the grape callus overexpressed , while the ratio of GAs related to GA2ox were significantly increased. Taken together, VvSVP1 can regulate the endogenous GAs level by manipulating the expression of GA metabolism genes before dormant bud break induced by HC. Our findings may provide some new theoretical insights for the study of bud dormancy regulation in the perennial woody fruit trees.
以往的研究表明，赤霉素（GA）在葡萄休眠解除前对花芽分化有抑制作用，而在休眠解除后对花芽分化有促进作用；GA的积累能力呈现先抑后扬的趋势。然而，休眠解除过程中 GA 代谢基因表达的调控机制尚不清楚。本研究进一步验证了GA和氢氰酸酰胺（HC）对'红地球'葡萄花芽分化的影响，分别证实了抑制和促进作用。HC处理后，早期GA生物合成基因表达受限，GA分解代谢基因表达增强，而后期则表现出相反的表达趋势。在后期，MADS-box 转录因子基因Ⅴ表达下调，这可能在调控 GA 代谢基因的表达中起着重要作用。研究表明，VvSVP1能与GA生物合成基因和分解代谢基因的启动子区域结合，分别对相应基因的表达产生负调控和正调控作用；在过表达VvSVP1的葡萄胼胝体中，与GA20ox相关的GA含量显著降低，而与GA2ox相关的GA比例显著增加。综上所述，VvSVP1可在HC诱导的休眠芽断裂前通过调控GA代谢基因的表达来调节内源GA水平。我们的研究结果可为多年生木本果树花芽休眠调控的研究提供一些新的理论依据。
{"title":"VvSVP1 negatively regulates gibberellin accumulation before the dormant bud break of grapevine triggered by hydrogen cyanamide","authors":"Jingyi Li, Pinqi Sun, Anni Chen, Jilong Xu, Peiyong Xin, Jinfang Chu, Chuanlin Zheng","doi":"10.1016/j.hpj.2023.12.002","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.12.002","url":null,"abstract":"In grapevine, previous studies have suggested that, gibberellin (GA) inhibits bud break before dormancy release while enhanced after dormancy release; the capacity of GA accumulation shows a trend of first inhibition and then upregulation. However, the regulatory mechanism of GA metabolism genes expression is as yet unclear during the process of dormancy release. In this study, we further validated the effect of GA and hydrogen cyanamide (HC) on bud break of ‘Red globe’ grape, confirmed inhibition and promotion effect, respectively. Restricted GA biosynthetic genes’ expression and enhanced GA catabolic gene’s expression were observed in the early stage after HC treatment, while opposite expression trend showed in the late stage. , a MADS-box transcription factor gene, was downregulated in the late stage, which might play an important role in regulating GA metabolism genes’ expression. It was shown that, VvSVP1 could bind to the promoter regions of GA biosynthetic gene and catabolic gene , negatively and positively regulated the corresponding genes’ expression, respectively; the contents of GAs related to GA20ox were significantly reduced in the grape callus overexpressed , while the ratio of GAs related to GA2ox were significantly increased. Taken together, VvSVP1 can regulate the endogenous GAs level by manipulating the expression of GA metabolism genes before dormant bud break induced by HC. Our findings may provide some new theoretical insights for the study of bud dormancy regulation in the perennial woody fruit trees.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"38 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140100352","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}
N-methyladenosine (mA) RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms. Despite its significance, a comprehensive analysis of mA-related genes in non-model plants, such as kiwifruit, is lacking. Here, we identified 36 mA-related genes in the kiwifruit genome according to homology and phylogenetic inference. We performed bioinformatics and evolutionary analyses of the writer, eraser, and reader families of mA modification. Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most mA-related genes were remarkably expressed under different conditions. Through construction of gene co-expression networks, we found significant correlations between several mA-related genes and transcription factors (TFs) as well as receptor-like genes during the development and ripening of kiwifruit. Furthermore, we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of mA-related genes. We identified 10 common open chromatin regions that were present in at least two tissues, and these regions might serve as potential binding sites for MADS protein, C2H2 protein, and other predicted TFs. Our study offers comprehensive insights into the gene family of mA-related components in kiwifruit, which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.
N-甲基腺苷（mA）RNA修饰是一种调节真核生物中RNA命运的保守机制。尽管其意义重大，但目前还缺乏对猕猴桃等非模式植物中 mA 相关基因的全面分析。在此，我们根据同源性和系统发育推断在猕猴桃基因组中鉴定了 36 个 mA 相关基因。我们对mA修饰的书写器、橡皮擦和阅读器家族进行了生物信息学和进化分析。对从各种生物和非生物胁迫下的样本中收集的公开 RNA-seq 数据进行的再分析表明，大多数 mA 相关基因在不同条件下都有显著表达。通过构建基因共表达网络，我们发现在猕猴桃的发育和成熟过程中，多个 mA 相关基因与转录因子（TFs）以及受体类基因之间存在显著的相关性。此外，我们还对不同的猕猴桃组织进行了 ATAC-seq 分析，以研究 mA 相关基因的调控机制。我们发现了 10 个共同的开放染色质区域，它们至少存在于两个组织中，这些区域可能是 MADS 蛋白、C2H2 蛋白和其他预测的 TFs 的潜在结合位点。我们的研究全面揭示了猕猴桃中 mA 相关成分的基因家族，这将为探索猕猴桃发育和适应过程中的转录后调控机制奠定基础。
{"title":"Identification and characterization of genes related to m6A modification in kiwifruit using RNA-seq and ATAC-seq","authors":"Xiaoli Hu, Tong Li, Changbin Xu, Yanna Xu, Congjun You, Xinyi Li, Jinli Gong, Xiaolong Li, Xuepeng Sun","doi":"10.1016/j.hpj.2024.02.001","DOIUrl":"https://doi.org/10.1016/j.hpj.2024.02.001","url":null,"abstract":"N-methyladenosine (mA) RNA modification is a conserved mechanism that regulates the fate of RNA across eukaryotic organisms. Despite its significance, a comprehensive analysis of mA-related genes in non-model plants, such as kiwifruit, is lacking. Here, we identified 36 mA-related genes in the kiwifruit genome according to homology and phylogenetic inference. We performed bioinformatics and evolutionary analyses of the writer, eraser, and reader families of mA modification. Reanalysis of public RNA-seq data collected from samples under various biotic and abiotic stresses indicated that most mA-related genes were remarkably expressed under different conditions. Through construction of gene co-expression networks, we found significant correlations between several mA-related genes and transcription factors (TFs) as well as receptor-like genes during the development and ripening of kiwifruit. Furthermore, we performed ATAC-seq assays on diverse kiwifruit tissues to investigate the regulatory mechanisms of mA-related genes. We identified 10 common open chromatin regions that were present in at least two tissues, and these regions might serve as potential binding sites for MADS protein, C2H2 protein, and other predicted TFs. Our study offers comprehensive insights into the gene family of mA-related components in kiwifruit, which will lay foundation for exploring mechanisms of post-transcriptional regulation involved in development and adaptation of kiwifruit.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"30 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-05","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140100350","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}
The preharvest internal browning of Nane plum fruit, with no visible effects on the appearance of the fruit, has become a serious problem in recent years in its production area in Guangdong Province, China. This study investigated the effects of environmental factors, including temperature, on Nane plum internal browning. Plum orchards at different elevations with different incidences of internal browning were selected. Using fruits with different internal browning incidence levels, the internal browning mechanism was analyzed with transcriptome and metabolome analyses. The results revealed decreased internal browning at high altitudes. Shading treatment significantly reduced internal browning, whereas bagging and insect-proof net-covering treatments significantly increased internal browning. Because bagging and net coverings increase the local ambient temperature, the findings suggest that high temperature is an important factor influencing the internal browning of Nane plum. The metabolome experiments showed that with increased internal browning, the levels of phenolic hydroxyls such as catechol increased, with simultaneous increases in hydrogen peroxide content and oxidase activity. It can be speculated that the oxidation of phenolic hydroxyl substances is the main cause of the preharvest browning of Nane plum. Transcriptome analysis revealed the increased expression of calcium signaling-related and downstream effector genes and indicated an important role of calcium in internal browning, possibly due to its increased content in the fruit. Further, with increasingly serious internal browning, genes related to photosynthesis were down-regulated, while genes related to senescence were up-regulated, thus suggesting the up-regulation of the process of cell senescence during internal browning. In conclusion, heat stress should be eliminated to reduce preharvest internal browning in Nane plum.
{"title":"Transcriptome and metabolome analysis of preharvest internal browning in Nane plum fruit caused by high temperatures","authors":"Cheng Peng, Linping Deng, Hejun Tan, Wancong Meng, Jianliang Luo, Zengwen Zhang, Huiqiong Chen, Jishui Qiu, Xiaoxiao Chang, Yusheng Lu","doi":"10.1016/j.hpj.2023.10.004","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.10.004","url":null,"abstract":"The preharvest internal browning of Nane plum fruit, with no visible effects on the appearance of the fruit, has become a serious problem in recent years in its production area in Guangdong Province, China. This study investigated the effects of environmental factors, including temperature, on Nane plum internal browning. Plum orchards at different elevations with different incidences of internal browning were selected. Using fruits with different internal browning incidence levels, the internal browning mechanism was analyzed with transcriptome and metabolome analyses. The results revealed decreased internal browning at high altitudes. Shading treatment significantly reduced internal browning, whereas bagging and insect-proof net-covering treatments significantly increased internal browning. Because bagging and net coverings increase the local ambient temperature, the findings suggest that high temperature is an important factor influencing the internal browning of Nane plum. The metabolome experiments showed that with increased internal browning, the levels of phenolic hydroxyls such as catechol increased, with simultaneous increases in hydrogen peroxide content and oxidase activity. It can be speculated that the oxidation of phenolic hydroxyl substances is the main cause of the preharvest browning of Nane plum. Transcriptome analysis revealed the increased expression of calcium signaling-related and downstream effector genes and indicated an important role of calcium in internal browning, possibly due to its increased content in the fruit. Further, with increasingly serious internal browning, genes related to photosynthesis were down-regulated, while genes related to senescence were up-regulated, thus suggesting the up-regulation of the process of cell senescence during internal browning. In conclusion, heat stress should be eliminated to reduce preharvest internal browning in Nane plum.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"87 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140038116","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}
Inducing adventitious root (AR) formation in mature walnut species ( L.) is challenging. However, the AR formation of mature trees can be improved by rejuvenation. In rejuvenated cuttings, exogenous indole-3-butyric acid (IBA) is essential for AR formation, and the underlying mechanism is still not well understood. Therefore, we utilized transcriptome sequencing to investigate the mechanism of IBA-induced AR formation. Our results revealed that, in comparison to the control group, IBA treatment (9 mM) significantly increased the endogenous indole-3-acetic acid (IAA) content, leading to an enhanced rooting rate. We performed RNA sequencing to identify differentially expressed genes (DEGs) between the IBA-treated and control (CK) groups at 1, 2, 3, and 5 days after cutting (DAC). The results showed that, compared to the control cuttings, there were 1 539, 889, 785, and 984 up-regulated genes and 2 791, 2 936, 3 017, and 1 752 down-regulated genes, at 1, 2, 3, and 5 DAC, respectively. Analysis of RNA-seq data revealed that (/) and (), associated with IBA transport, were down-regulated in the rejuvenation cuttings. In contrast, () and (), associated with auxin efflux, were up-regulated. We identified 49 ()-encoding genes, including , , , , , , , , and , which were up-regulated at 1–5 DAC in the rejuvenated cuttings. This study highlights that the overexpression of in poplar significantly enhance AR growth, as evidenced by increased root length, surface area, volume, and quantity. Moreover, the co-expression network analysis involving and in walnut cuttings elucidates complex genetic interactions, underscoring their pivotal role in the formation of AR. Our data supported the following molecular mechanism of IBA-induced adventitious root formation. Firstly, IBA is converted to free IAA in peroxisomes. Then, the highly concentrated IAA in the procambium and parenchyma cells induces
{"title":"Transcriptome profiling of Indole-3-Butyric Acid-Induced Adventitious Root Formation in softwood Cuttings of walnut","authors":"Xiaobo Song, Ruimin Huang, Hao Liu, Zhang Junpei, Yingying Chang, Dong Pei","doi":"10.1016/j.hpj.2023.04.013","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.04.013","url":null,"abstract":"Inducing adventitious root (AR) formation in mature walnut species ( L.) is challenging. However, the AR formation of mature trees can be improved by rejuvenation. In rejuvenated cuttings, exogenous indole-3-butyric acid (IBA) is essential for AR formation, and the underlying mechanism is still not well understood. Therefore, we utilized transcriptome sequencing to investigate the mechanism of IBA-induced AR formation. Our results revealed that, in comparison to the control group, IBA treatment (9 mM) significantly increased the endogenous indole-3-acetic acid (IAA) content, leading to an enhanced rooting rate. We performed RNA sequencing to identify differentially expressed genes (DEGs) between the IBA-treated and control (CK) groups at 1, 2, 3, and 5 days after cutting (DAC). The results showed that, compared to the control cuttings, there were 1 539, 889, 785, and 984 up-regulated genes and 2 791, 2 936, 3 017, and 1 752 down-regulated genes, at 1, 2, 3, and 5 DAC, respectively. Analysis of RNA-seq data revealed that (/) and (), associated with IBA transport, were down-regulated in the rejuvenation cuttings. In contrast, () and (), associated with auxin efflux, were up-regulated. We identified 49 ()-encoding genes, including , , , , , , , , and , which were up-regulated at 1–5 DAC in the rejuvenated cuttings. This study highlights that the overexpression of in poplar significantly enhance AR growth, as evidenced by increased root length, surface area, volume, and quantity. Moreover, the co-expression network analysis involving and in walnut cuttings elucidates complex genetic interactions, underscoring their pivotal role in the formation of AR. Our data supported the following molecular mechanism of IBA-induced adventitious root formation. Firstly, IBA is converted to free IAA in peroxisomes. Then, the highly concentrated IAA in the procambium and parenchyma cells induces","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"12 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-03-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140038123","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}
Pub Date : 2024-02-29DOI: 10.1016/j.hpj.2023.06.006
Esther Gimeno-Páez, Jaime Prohens, María Moreno-Cerveró, Ana de Luis-Margarit, María José Díez, Pietro Gramazio
Unlike other major crops, little research has been performed on tomato to reduce the generation time for speed breeding. We evaluated several agronomic treatments to reduce the generation time of tomato in the ‘M82’ (determinate) and ‘Moneymaker’ (indeterminate) varieties and evaluated the best combination in conjunction with embryo rescue. Five container sizes with volumes of 0.2 L (XS), 0.45 L (S), 0.8 L (M), 1.3 L (L), and 6 L (XL), were evaluated in the first experiment under the autumn cycle. We found that plants grown in XL containers exhibited better development and required less time from sowing to anthesis (DSA) and from anthesis to fruit ripening (DAR). In the second experiment, using XL containers in the autumn–winter cycle, we evaluated the effects of cold priming at the cotyledonary stage, water stress, P supplementation, and K supplementation on generation time. Compared to the control, we found that cold priming significantly reduced the number of leaves, plant height to first the inflorescence, and DSA (2.7 d), whereas K supplementation reduced the DAR (8.8 d). In contrast, water stress and P supplementation did not significantly affect any of the measured traits like DAR, DSA or fruit set. To validate these data, in a third experiment with XL containers in the spring-summer cycle, the combination of cold priming and K supplementation was tested, confirming the significant effect of this combination on the reduction of generation time (2.9 d for DSA and 3.9 d for DAR) compared to the control. Embryo rescue during the cell expansion cycle (average of 22.0 d and 23.3 d after anthesis for ‘M82’ and ‘Moneymaker’, respectively) allowed the shortening of the generation time by 8.7 d in ‘M82’ and 11.6 d in ‘Moneymaker’ compared to the fruit ripening. The combination of agronomic treatments with embryo rescue can effectively increase the number of generations per year from three to four for speed breeding of tomato.
{"title":"Agronomic treatments combined with embryo rescue for rapid generation advancement in tomato speed breeding","authors":"Esther Gimeno-Páez, Jaime Prohens, María Moreno-Cerveró, Ana de Luis-Margarit, María José Díez, Pietro Gramazio","doi":"10.1016/j.hpj.2023.06.006","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.06.006","url":null,"abstract":"Unlike other major crops, little research has been performed on tomato to reduce the generation time for speed breeding. We evaluated several agronomic treatments to reduce the generation time of tomato in the ‘M82’ (determinate) and ‘Moneymaker’ (indeterminate) varieties and evaluated the best combination in conjunction with embryo rescue. Five container sizes with volumes of 0.2 L (XS), 0.45 L (S), 0.8 L (M), 1.3 L (L), and 6 L (XL), were evaluated in the first experiment under the autumn cycle. We found that plants grown in XL containers exhibited better development and required less time from sowing to anthesis (DSA) and from anthesis to fruit ripening (DAR). In the second experiment, using XL containers in the autumn–winter cycle, we evaluated the effects of cold priming at the cotyledonary stage, water stress, P supplementation, and K supplementation on generation time. Compared to the control, we found that cold priming significantly reduced the number of leaves, plant height to first the inflorescence, and DSA (2.7 d), whereas K supplementation reduced the DAR (8.8 d). In contrast, water stress and P supplementation did not significantly affect any of the measured traits like DAR, DSA or fruit set. To validate these data, in a third experiment with XL containers in the spring-summer cycle, the combination of cold priming and K supplementation was tested, confirming the significant effect of this combination on the reduction of generation time (2.9 d for DSA and 3.9 d for DAR) compared to the control. Embryo rescue during the cell expansion cycle (average of 22.0 d and 23.3 d after anthesis for ‘M82’ and ‘Moneymaker’, respectively) allowed the shortening of the generation time by 8.7 d in ‘M82’ and 11.6 d in ‘Moneymaker’ compared to the fruit ripening. The combination of agronomic treatments with embryo rescue can effectively increase the number of generations per year from three to four for speed breeding of tomato.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"119 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140038143","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}
Pub Date : 2024-02-29DOI: 10.1016/j.hpj.2023.07.008
Jinita Sthapit Kandel, Ivan Simko, Ryan J. Hayes, Beiquan Mou
Fresh-cut lettuce is widely used in ready-to-eat salads sold in modified atmosphere packages (MAP). Even in MAP, fresh-cut lettuce has short shelf life that results in loss of nutrients. Lettuce cultivars exhibit genetic variation for shelf life in MAP, but their variation for nutrient retention is not known. Fifty accessions were evaluated for initial content of ascorbic acid (AsA), carotenoids, and sugars and their retention in storage. Accessions with high content and/or good retention of one or more nutrients were identified. The romaine accession ‘Floricos’ had high levels of all the three nutrients. Accessions with relatively high retention of all the three nutrients were ‘Salinas 88’, ‘Siskiyou’, ‘Solar’, SM09A, ‘Romance’, and ‘Green Towers’. Romaine cultivars, ‘Balady Barrage’, ‘Green Towers’, and ‘Darkland’ had relatively high initial levels of all tested nutrients and good rate of their retention. There was no clear correlation between initial AsA/carotene concentrations and their retention rates, suggesting that besides content, retention of nutrients should also be a breeding target in a lettuce nutritional improvement program. Statistical analyses with the Pearson’s correlation coefficient determined a negative relationship between tissue deterioration (AUDePS) and retention of all tested nutrients [ of -0.52 ( < 0.0001) for AsA, -0.27 ( < 0.01) for total carotene, and -0.59 ( < 0.0001) for total sugars], suggesting that an increase in tissue deterioration intensifies nutrient decay. Broad-sense heritability () across the experiments was 0.15 for AsA, 0.23 for total carotene, and 0.50 for total sugars. Identification of germplasm with high nutrient content, extended shelf life and good nutrient retention provides valuable information for the lettuce industry and associated breeding programs.
{"title":"Concentration and retention of ascorbic acid, carotenoids, and sugars in fresh-cut lettuce in modified atmosphere packaging","authors":"Jinita Sthapit Kandel, Ivan Simko, Ryan J. Hayes, Beiquan Mou","doi":"10.1016/j.hpj.2023.07.008","DOIUrl":"https://doi.org/10.1016/j.hpj.2023.07.008","url":null,"abstract":"Fresh-cut lettuce is widely used in ready-to-eat salads sold in modified atmosphere packages (MAP). Even in MAP, fresh-cut lettuce has short shelf life that results in loss of nutrients. Lettuce cultivars exhibit genetic variation for shelf life in MAP, but their variation for nutrient retention is not known. Fifty accessions were evaluated for initial content of ascorbic acid (AsA), carotenoids, and sugars and their retention in storage. Accessions with high content and/or good retention of one or more nutrients were identified. The romaine accession ‘Floricos’ had high levels of all the three nutrients. Accessions with relatively high retention of all the three nutrients were ‘Salinas 88’, ‘Siskiyou’, ‘Solar’, SM09A, ‘Romance’, and ‘Green Towers’. Romaine cultivars, ‘Balady Barrage’, ‘Green Towers’, and ‘Darkland’ had relatively high initial levels of all tested nutrients and good rate of their retention. There was no clear correlation between initial AsA/carotene concentrations and their retention rates, suggesting that besides content, retention of nutrients should also be a breeding target in a lettuce nutritional improvement program. Statistical analyses with the Pearson’s correlation coefficient determined a negative relationship between tissue deterioration (AUDePS) and retention of all tested nutrients [ of -0.52 ( < 0.0001) for AsA, -0.27 ( < 0.01) for total carotene, and -0.59 ( < 0.0001) for total sugars], suggesting that an increase in tissue deterioration intensifies nutrient decay. Broad-sense heritability () across the experiments was 0.15 for AsA, 0.23 for total carotene, and 0.50 for total sugars. Identification of germplasm with high nutrient content, extended shelf life and good nutrient retention provides valuable information for the lettuce industry and associated breeding programs.","PeriodicalId":13178,"journal":{"name":"Horticultural Plant Journal","volume":"29 1","pages":""},"PeriodicalIF":5.7,"publicationDate":"2024-02-29","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"140038119","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}
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