Horticulture Research最新文献_第4页

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

IF 8.7 1区农林科学

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

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

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

引用次数: 0

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

IF 8.7 1区农林科学

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

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

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

引用次数: 0

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

IF 8.7 1区农林科学

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

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

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

引用次数: 0

Genomic origin of Citrus reticulata “Unshiu”

IF 8.7 1区农林科学

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

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

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

引用次数: 0

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

IF 8.7 1区农林科学

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

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

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

引用次数: 0

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

IF 8.7 1区农林科学

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

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

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

引用次数: 0

Tea polyphenol mediated CsMYB77 regulation of CsPOD44 to promote tea plant (Camellia sinensis) root drought resistance

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-18 DOI: 10.1093/hr/uhaf048

Rong Xu, Chenyu Shao, Yuqi Luo, Biao Zhou, Qian Zhu, Shuqi Qiu, Zhonghua Liu, Shuoqian Liu, Chengwen Shen

{"title":"Tea polyphenol mediated CsMYB77 regulation of CsPOD44 to promote tea plant (Camellia sinensis) root drought resistance","authors":"Rong Xu, Chenyu Shao, Yuqi Luo, Biao Zhou, Qian Zhu, Shuqi Qiu, Zhonghua Liu, Shuoqian Liu, Chengwen Shen","doi":"10.1093/hr/uhaf048","DOIUrl":"https://doi.org/10.1093/hr/uhaf048","url":null,"abstract":"Drought stress significantly alters the metabolic homeostasis of tea plants; however, few studies have examined the role of specific metabolites, particularly tea polyphenols, in drought resistance. This study reveals that the tea polyphenol content in drought-tolerant tea cultivars tends to increase under drought conditions. Notably, in environments characterized by staged and repeated drought, changes in tea polyphenol are significantly positively correlated with drought resistance. To investigate this further, we irrigated the roots with exogenous tea polyphenols before subjecting the plants to drought. Our findings indicated that the absorptive roots of the experimental group exhibited enhanced development, improved cellular integrity, and a significant increase in peroxidase activity. A comprehensive analysis of the transcriptome and metabolome revealed that tea polyphenols are closely associated with the phenylpropanoid metabolism pathway. Notably, CsMYB77 and CsPOD44 genes were identified as highly correlated with this pathway. Overexpression experiments in Arabidopsis thaliana demonstrated that CsMYB77 promotes the expression of phenylpropanoid pathway genes, thereby enhancing drought resistance. Conversely, antisense oligonucleotide silencing of CsMYB77 decreased drought resistance in tea plants. Additional experiments, including yeast one-hybrid assays, luciferase complementation imaging, dual-luciferase assays, and electrophoretic mobility shift assays, confirmed that CsMYB77 positively regulates the expression of CsPOD44. In summary, our findings indicate that the differences in drought tolerance among tea cultivars are closely linked to phenylpropanoid metabolism. Specifically, tea polyphenols may mediate the regulatory network involving CsMYB77 and CsPOD44, thereby enhancing stress resistance by promoting root development. This study offers new insights into the breeding of drought-resistant tea cultivars.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443452","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

The UDP-glycosyltransferase PpUGT74F2 is involved in fruit immunity via modulating salicylic acid metabolism

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-18 DOI: 10.1093/hr/uhaf049

Dan Jiang, Siyin Lin, Linfeng Xie, Miaojing Chen, Yanna Shi, Kunsong Chen, Xian Li, Boping Wu, Bo Zhang

{"title":"The UDP-glycosyltransferase PpUGT74F2 is involved in fruit immunity via modulating salicylic acid metabolism","authors":"Dan Jiang, Siyin Lin, Linfeng Xie, Miaojing Chen, Yanna Shi, Kunsong Chen, Xian Li, Boping Wu, Bo Zhang","doi":"10.1093/hr/uhaf049","DOIUrl":"https://doi.org/10.1093/hr/uhaf049","url":null,"abstract":"Flesh fruits are essential for human health, but pathogen infection poses a threat to fruit production and postharvest storage. The hormone salicylic acid (SA) and its metabolites, such as sugar conjugates and methyl salicylate MeSA, play a crucial role in regulating plant immune responses. However, the UDP-glycosyltransferases (UGTs) responsible for modulating SA metabolism in fruit have yet to be identified, and further investigation is needed to elucidate its involvement in fruit immune response. Here, we identified PpUGT74F2 as an enzyme with the highest transcription level in peach fruit, responsible for catalyzing the biosynthesis of SA glucoside (SAG), but not for MeSAG formation in fruit. Furthermore, infection of peach fruit with Monilinia fructicola, which causes brown rot disease, led to reduced expression of PpUGT74F2 resulting in significant decrease in SAG content and an increase in MeSA levels. Transgenic tomatoes expressing heterologous PpUGT74F2 increased susceptibility to gray mold. Interestingly, overexpressing PpUGT74F2 did not affect SA levels but dramatically reduced MeSA levels in response to pathogen infection, accompanied by significantly reduced expression of pathogen related (PR) genes in transgenic tomatoes. This study highlights that PpUGT74F2 acts as a negative regulatory factor for fruit immunity through a distinct mechanism not previously reported in plants.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"14 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143443450","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

Genomic insights into the domestication and genetic basis of yield in papaya

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-17 DOI: 10.1093/hr/uhaf045

Min Yang, Xiangdong Kong, Chenping Zhou, Ruibin Kuang, Xiaming Wu, Chuanhe Liu, Han He, Ze Xu, Yuerong Wei

{"title":"Genomic insights into the domestication and genetic basis of yield in papaya","authors":"Min Yang, Xiangdong Kong, Chenping Zhou, Ruibin Kuang, Xiaming Wu, Chuanhe Liu, Han He, Ze Xu, Yuerong Wei","doi":"10.1093/hr/uhaf045","DOIUrl":"https://doi.org/10.1093/hr/uhaf045","url":null,"abstract":"Papaya (Carica papaya L.) is an important tropical and subtropical fruit crop, and understanding its genome is essential for breeding. In this study, we assembled a high-quality genome of 344.17 Mb for the newly cultivated papaya ‘Zihui,’ which contains 22 250 protein-coding genes. By integrating 201 resequenced papaya genomes, we identified four distinct papaya groups and a 34 Mb genomic region with strong domestication selection signals. Within these regions, two key genes associated with papaya yield were discovered: Cp_zihui06549, encoding a leucine-rich receptor-like protein kinase, and Cp_zihui06768, encoding the accumulation of photosystem one 1 (APO1) protein. Heterologous expression of Cp_zihui06549 in tomato confirmed that the total number of fruits in transgenic lines more than doubled compared to wild-type plants, resulting in a significant yield increase. Furthermore, we constructed a pan-genome of papaya and obtained a 77.41 Mb non-reference sequence containing 1543 genes. Within this pan-genome, 2483 variable genes we detected, including four genes annotated as the ‘terpene synthase activity’ Gene Ontology term, which were lost in cultivars during domestication. Finally, gene retention analyses were performed using gene presence and absence variation (PAV) data and differentially expressed genes across various tissues and organs. This study provides valuable insights into the genes and loci associated with phenotypes and domestication processes, laying a solid foundation for future papaya breeding efforts.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"13 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435153","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0

A chromosome-scale genome assembly and Epigenomic profiling reveal temperature-dependent histone methylation in iridoid biosynthesis regulation in Scrophularia ningpoensis

IF 8.7 1区农林科学

Horticulture Research Pub Date : 2025-02-17 DOI: 10.1093/hr/uhae328

Qing Xu, Chang Liu, Bin Li, Kewei Tian, Lei You, Li Xie, Huang Wang, Meide Zhang, Wuxian Zhou, Yonghong Zhang, Chao Zhou

{"title":"A chromosome-scale genome assembly and Epigenomic profiling reveal temperature-dependent histone methylation in iridoid biosynthesis regulation in Scrophularia ningpoensis","authors":"Qing Xu, Chang Liu, Bin Li, Kewei Tian, Lei You, Li Xie, Huang Wang, Meide Zhang, Wuxian Zhou, Yonghong Zhang, Chao Zhou","doi":"10.1093/hr/uhae328","DOIUrl":"https://doi.org/10.1093/hr/uhae328","url":null,"abstract":"Understanding how medicinal plants adapt to global warming, particularly through epigenetic mechanisms that modify phenotypes without changing DNA sequences is crucial. Scrophularia ningpoensis Hemsl., a traditional Chinese Medicine (TCM), produces bioactive compounds that are influenced by environmental temperatures, making it an ideal model for studying the biological basis of TCM geoherbalism. However, the adaptive potential of epigenetic marks in S. ningpoensis under varying temperatures remains understudied, partly due to the absence of a reference genome. Here, it was demonstrated that mild warm temperatures contribute to the metabolic accumulation and the cultivated migration of S. ningpoensis using a global dataset. A high-quality chromosome-level genome was assembled, and an atlas of epigenetic, metabolic, and transcriptomic profiles across different tissues. Transcriptome analysis identified 3,401 allele-specific expressed genes (ASEGs) across nine tissues by comparing two haplotypes. ChIP-seq and BS-seq data from leaf and root tissues revealed that ASEGs are associated with distinct epigenetic patterns, particularly the active mark H3K36me3, which functions differently in these tissues. Notably, genes marked with H3K36me3 in iridoid synthesis pathway predominantly expressed in roots. Additionally, the histone methyltransferase SnSDG8 was identified to regulate ectopic H3K36me3 in iridoid biosynthesis in response to warming temperatures. Our results highlight the epigenetic mechanisms of global warming on herb-derived products, significant for medicinal plant breeding under temperature stress.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"88 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-02-17","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143435208","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}

引用次数: 0