Molecular Horticulture最新文献_第3页

Super pan-genome reveals extensive genomic variations associated with phenotypic divergence in Actinidia.

IF 10.6

Molecular Horticulture Pub Date : 2025-01-24 DOI: 10.1186/s43897-024-00123-1

Xiaofen Yu, Minghao Qu, Pan Wu, Miao Zhou, Enhui Lai, Huan Liu, Sumin Guo, Shan Li, Xiaohong Yao, Lei Gao

{"title":"Super pan-genome reveals extensive genomic variations associated with phenotypic divergence in Actinidia.","authors":"Xiaofen Yu, Minghao Qu, Pan Wu, Miao Zhou, Enhui Lai, Huan Liu, Sumin Guo, Shan Li, Xiaohong Yao, Lei Gao","doi":"10.1186/s43897-024-00123-1","DOIUrl":"10.1186/s43897-024-00123-1","url":null,"abstract":"Kiwifruit is an economically and nutritionally important horticultural fruit crop worldwide. The genomic data of several kiwifruit species have been released, providing an unprecedented opportunity for pan-genome analysis to comprehensively investigate the inter- and intra-species genetic diversity and facilitate utilization for kiwifruit breeding. Here, we generated a kiwifruit super pan-genome using 15 high-quality assemblies of eight Actinidia species. For gene-based pan-genome, a total of 61,465 gene families were identified, and the softcore and dispensable genes were enriched in biological processes like response to endogenous stimulus, response to hormone and cell wall organization or biogenesis. Then, structural variations (SVs) against A. chinensis 'Donghong' were identified and then used to construct a graph-based genome. Further population-scale SVs based on resequencing data from 112 individuals of 20 species revealed extensive SVs which probably contributed to the phenotypic diversity among the Actinidia species. SV hotspot regions were found contributed to environmental adaptation. Furthermore, we systematically identified resistance gene analogs (RGAs) in the 15 assemblies and generated a pan-RGA dataset to reveal the diversity of genes potentially involved in disease resistance in Actinidia. The pan-genomic data obtained here is useful for evolutionary and functional genomic studies in Actinidia, and facilitates breeding design.","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"5 1","pages":"4"},"PeriodicalIF":10.6,"publicationDate":"2025-01-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11758757/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143030002","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Peptide hormones in plants.

IF 10.6

Molecular Horticulture Pub Date : 2025-01-23 DOI: 10.1186/s43897-024-00134-y

Zhenbiao Zhang, Huibin Han, Junxiang Zhao, Zhiwen Liu, Lei Deng, Liuji Wu, Junpeng Niu, Yongfeng Guo, Guodong Wang, Xiaoping Gou, Chao Li, Chuanyou Li, Chun-Ming Liu

{"title":"Peptide hormones in plants.","authors":"Zhenbiao Zhang, Huibin Han, Junxiang Zhao, Zhiwen Liu, Lei Deng, Liuji Wu, Junpeng Niu, Yongfeng Guo, Guodong Wang, Xiaoping Gou, Chao Li, Chuanyou Li, Chun-Ming Liu","doi":"10.1186/s43897-024-00134-y","DOIUrl":"10.1186/s43897-024-00134-y","url":null,"abstract":"Peptide hormones are defined as small secreted polypeptide-based intercellular communication signal molecules. Such peptide hormones are encoded by nuclear genes, and often go through proteolytic processing of preproproteins and post-translational modifications. Most peptide hormones are secreted out of the cell to interact with membrane-associated receptors in neighboring cells, and subsequently activate signal transductions, leading to changes in gene expression and cellular responses. Since the discovery of the first plant peptide hormone, systemin, in tomato in 1991, putative peptide hormones have continuously been identified in different plant species, showing their importance in both short- and long-range signal transductions. The roles of peptide hormones are implicated in, but not limited to, processes such as self-incompatibility, pollination, fertilization, embryogenesis, endosperm development, stem cell regulation, plant architecture, tissue differentiation, organogenesis, dehiscence, senescence, plant-pathogen and plant-insect interactions, and stress responses. This article, collectively written by researchers in this field, aims to provide a general overview for the discoveries, functions, chemical natures, transcriptional regulations, and post-translational modifications of peptide hormones in plants. We also updated recent discoveries in receptor kinases underlying the peptide hormone sensing and down-stream signal pathways. Future prospective and challenges will also be discussed at the end of the article.","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"5 1","pages":"7"},"PeriodicalIF":10.6,"publicationDate":"2025-01-23","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11756074/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143029965","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Allelic variation in an expansin, MdEXP-A1, contributes to flesh firmness at harvest in apples. 膨胀蛋白MdEXP-A1的等位基因变异有助于苹果收获时果肉的硬度。

IF 10.6

Molecular Horticulture Pub Date : 2025-01-20 DOI: 10.1186/s43897-024-00121-3

Qiufang Su, Yifeng Feng, Xianglu Li, Zidun Wang, Yuanwen Zhong, Zhengyang Zhao, Huijuan Yang

{"title":"Allelic variation in an expansin, MdEXP-A1, contributes to flesh firmness at harvest in apples.","authors":"Qiufang Su, Yifeng Feng, Xianglu Li, Zidun Wang, Yuanwen Zhong, Zhengyang Zhao, Huijuan Yang","doi":"10.1186/s43897-024-00121-3","DOIUrl":"10.1186/s43897-024-00121-3","url":null,"abstract":"Flesh firmness is a core quality trait in apple breeding because of its correlation with ripening and storage. Quantitative trait loci (QTLs) were analyzed through bulked segregant analysis sequence (BSA-seq) and comparative transcriptome analysis (RNA-seq) to explore the genetic basis of firmness formation. In this study, phenotypic data were collected at harvest from 251 F1 hybrids derived from 'Ruiyang' and 'Scilate', the phenotype values of flesh firmness at harvest were extensively segregated for two consecutive years. A total of 11 candidate intervals were identified on chromosomes 03, 05, 06, 07, 13, and 16 via BSA-seq analysis. We characterized a major QTL on chromosome 16 and selected a candidate gene encoding expansin MdEXP-A1 by combining RNA-seq analysis. Furthermore, the genotype of Del-1166 (homozygous deletion) in the MdEXP-A1 promoter was closely associated with the super-hard phenotype of F1 hybrids, which could be used as a functional marker for marker-assisted selection (MAS) in apple. Functional identification revealed that MdEXP-A1 positively expedited fruit softening in both apple fruits and tomatoes that overexpressed MdEXP-A1. Moreover, the promoter sequence of TE-1166 was experimentally validated containing two binding motifs of MdNAC1, and the absence of the MdEXP-A1 promoter fragment reduced its transcription activity. MdNAC1 also promotes the expression of MdEXP-A1, indicating its potential modulatory role in quality breeding. These findings provide novel insight into the genetic control of flesh firmness by MdEXP-A1.","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"5 1","pages":"3"},"PeriodicalIF":10.6,"publicationDate":"2025-01-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11744834/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143013044","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Transcriptional regulation of miR528-PPO module by miR156 targeted SPLs orchestrates chilling response in banana. miR156靶向SPLs对miR528-PPO模块的转录调控调控了香蕉的低温反应。

IF 10.6

Molecular Horticulture Pub Date : 2025-01-10 DOI: 10.1186/s43897-024-00115-1

Xiangjin Kong, Kuan Peng, Youxia Shan, Ze Yun, Tamas Dalmay, Xuewu Duan, Yueming Jiang, Hongxia Qu, Hong Zhu

{"title":"Transcriptional regulation of miR528-PPO module by miR156 targeted SPLs orchestrates chilling response in banana.","authors":"Xiangjin Kong, Kuan Peng, Youxia Shan, Ze Yun, Tamas Dalmay, Xuewu Duan, Yueming Jiang, Hongxia Qu, Hong Zhu","doi":"10.1186/s43897-024-00115-1","DOIUrl":"10.1186/s43897-024-00115-1","url":null,"abstract":"Banana is sensitive to cold stress and often suffers from chilling injury with browning peel and failure to normal ripening. We have previously reported that banana chilling injury is accompanied by a reduction of miR528 accumulation, alleviating the degradation of its target gene MaPPO and raising ROS levels that cause peel browning. Here, we further revealed that the miR528-MaPPO cold-responsive module was regulated by miR156-targeted SPL transcription factors, and the miR156c-MaSPL4 module was also responsive to cold stress in banana. Transient overexpression of miR156c resulted in a more severe chilling phenotype by decreasing the expression of MaSPL4 and miR528. Conversely, the browning was alleviated in STTM-miR156c silencing and OE-MaSPL4 samples. Furthermore, DNA affinity purification sequencing and MaSPL4-overexpressing transcriptome jointly revealed that MaSPL4 may mediate the transcription of genes related to lipid metabolism and antioxidation, in addition to the miR528-MaPPO module, demonstrating MaSPL4 as a master regulator in the fruit cold response network. In summary, our results suggest that the miR156c-MaSPL4 module can mediate the chilling response in banana by regulating the miR528-MaPPO module and multiple other pathways, which provides evidence for the crosstalk between TFs and miRNAs that can be used for the molecular breeding of fruit cold tolerance.","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"5 1","pages":"2"},"PeriodicalIF":10.6,"publicationDate":"2025-01-10","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11720309/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142956037","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Population sequencing of cherry accessions unravels the evolution of Cerasus species and the selection of genetic characteristics in edible cherries. 樱桃种群测序揭示了樱桃物种的进化和食用樱桃遗传特征的选择。

IF 10.6

Molecular Horticulture Pub Date : 2025-01-08 DOI: 10.1186/s43897-024-00120-4

Yahui Lei, Songtao Jiu, Yan Xu, Baozheng Chen, Xiao Dong, Zhengxin Lv, Anthony Bernard, Xunju Liu, Lei Wang, Li Wang, Jiyuan Wang, Zhuo Zhang, Yuliang Cai, Wei Zheng, Xu Zhang, Fangdong Li, Hongwen Li, Congli Liu, Ming Li, Jing Wang, Jijun Zhu, Lei Peng, Teresa Barreneche, Fei Yu, Shiping Wang, Yang Dong, Dirlewanger Elisabeth, Shengchang Duan, Caixi Zhang

{"title":"Population sequencing of cherry accessions unravels the evolution of Cerasus species and the selection of genetic characteristics in edible cherries.","authors":"Yahui Lei, Songtao Jiu, Yan Xu, Baozheng Chen, Xiao Dong, Zhengxin Lv, Anthony Bernard, Xunju Liu, Lei Wang, Li Wang, Jiyuan Wang, Zhuo Zhang, Yuliang Cai, Wei Zheng, Xu Zhang, Fangdong Li, Hongwen Li, Congli Liu, Ming Li, Jing Wang, Jijun Zhu, Lei Peng, Teresa Barreneche, Fei Yu, Shiping Wang, Yang Dong, Dirlewanger Elisabeth, Shengchang Duan, Caixi Zhang","doi":"10.1186/s43897-024-00120-4","DOIUrl":"10.1186/s43897-024-00120-4","url":null,"abstract":"Cerasus is a subgenus of Prunus in the family Rosaceae that is popular owing to its ornamental, edible, and medicinal properties. Understanding the evolution of the Cerasus subgenus and identifying selective trait loci in edible cherries are crucial for the improvement of cherry cultivars to meet producer and consumer demands. In this study, we performed a de novo assembly of a chromosome-scale genome for the sweet cherry (Prunus avium L.) cultivar 'Burlat', covering 297.55 Mb and consisting of eight chromosomes with 33,756 protein-coding genes. The resequencing and population structural analysis of 384 Cerasus representative accessions revealed that they could be divided into four groups (Group 1, Group 2, Group 3, and Group 4). We inferred that Group 1 was the oldest population and Groups 2, 3, and 4 were clades derived from it. In addition, we found selective sweeps for fruit flavor and improved stress resistance in different varieties of edible cherries (P. avium, P. cerasus, and P. pseudocerasus). Transcriptome analysis revealed significant differential expression of genes associated with key pathways, such as sucrose starch and sucrose metabolism, fructose and mannose metabolism, and the pentose phosphate pathway, between the leaves and fruits of P. avium. This study enhances the understanding of the evolutionary processes of the Cerasus subgenus and provides resources for functional genomics research and the improvement of edible cherries.","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"5 1","pages":"6"},"PeriodicalIF":10.6,"publicationDate":"2025-01-08","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11708008/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142956036","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Advances in the molecular mechanism of grapevine resistance to fungal diseases. 葡萄抗真菌病害分子机制研究进展。

IF 10.6

Molecular Horticulture Pub Date : 2025-01-02 DOI: 10.1186/s43897-024-00119-x

Zhi Li, Ronghui Wu, Fangying Guo, Yuejin Wang, Peter Nick, Xiping Wang

引用次数: 0

Correction: Efficient genome editing in grapevine using CRISPR/LbCas12a system. 更正：利用CRISPR/LbCas12a系统对葡萄藤进行高效基因组编辑。

IF 10.6

Molecular Horticulture Pub Date : 2024-12-13 DOI: 10.1186/s43897-024-00133-z

Chong Ren, Elias Kirabi Gathunga, Xue Li, Huayang Li, Junhua Kong, Zhanwu Dai, Zhenchang Liang

引用次数: 0

Potato steroidal glycoalkaloids: properties, biosynthesis, regulation and genetic manipulation. 马铃薯甾体糖生物碱：性质、生物合成、调控和基因操作。

IF 10.6

Molecular Horticulture Pub Date : 2024-12-13 DOI: 10.1186/s43897-024-00118-y

Yongming Liu, Xiaowei Liu, Yingge Li, Yanfei Pei, Abdul Jaleel, Maozhi Ren

引用次数: 0

Recent advances and future directions in banana molecular biology and breeding. 香蕉分子生物学与育种研究进展与展望。

IF 10.6

Molecular Horticulture Pub Date : 2024-12-02 DOI: 10.1186/s43897-024-00122-2

Chunzhen Cheng, Shuofan Wu, Guiming Deng, Ou Sheng, Ganjun Yi, Qiaosong Yang

引用次数: 0

Horizontal transfer of plasmid-like extrachromosomal circular DNAs across graft junctions in Solanaceae. 茄科植物中类似质粒的染色体外环状 DNA 跨嫁接接头的水平转移。

IF 10.6

Molecular Horticulture Pub Date : 2024-11-20 DOI: 10.1186/s43897-024-00124-0

Aijun Zhang, Tingjin Wang, Lu Yuan, Yuxin Shen, Ke Liu, Bin Liu, Kexin Xu, Mohamed A Elsadek, Yiting Wang, Liang Wu, Zhenyu Qi, Jingquan Yu, Mingfang Zhang, Liping Chen

{"title":"Horizontal transfer of plasmid-like extrachromosomal circular DNAs across graft junctions in Solanaceae.","authors":"Aijun Zhang, Tingjin Wang, Lu Yuan, Yuxin Shen, Ke Liu, Bin Liu, Kexin Xu, Mohamed A Elsadek, Yiting Wang, Liang Wu, Zhenyu Qi, Jingquan Yu, Mingfang Zhang, Liping Chen","doi":"10.1186/s43897-024-00124-0","DOIUrl":"10.1186/s43897-024-00124-0","url":null,"abstract":"The transfer of genetic material between stocks and scions of grafted plants has been extensively studied; however, the nature and frequency of the transferred material remain elusive. Here, we report a grafting system involving woody goji as the stock and herbaceous tomato as the scion, which was developed using in vitro and in vivo approaches; the results confirmed horizontal transfer of multiple nuclear DNA fragments from donor goji cells to recipient tomato cells. Tomato tissues containing goji donor DNA fragments at or near the grafting junctions had a perennial-biased anatomical structure, from which roots or shoots were regenerated. Most of the fragments were plasmid-like extrachromosomal circular DNAs (eccDNAs) present in the regenerants derived from the cells and in their asexual offspring. Plants with transferred eccDNAs in regenerated roots or shoots (designated \"Go-tomato\") were grown perennially and showed excellent agronomic performance. The present study provides new insights into the replication, expression, and potential function of eccDNAs in the pleiotropic traits of Go-tomato. Mobile eccDNAs offer evidence of stock-to-scion horizontal DNA transfer beyond chromosomes and organelles, thereby contributing to the molecular understanding of graft-induced genetic variation, evolution, and breeding.","PeriodicalId":29970,"journal":{"name":"Molecular Horticulture","volume":"4 1","pages":"41"},"PeriodicalIF":10.6,"publicationDate":"2024-11-20","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11577957/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"142677231","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":0,"RegionCategory":"","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"OA","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0