园艺研究(英文)最新文献

{"title":"Genomic diversity, population structure, and genome-wide association reveal genetic differentiation and trait improvements in mango.","authors":"Xiaowei Ma, Hongxia Wu, Bin Liu, Songbiao Wang, Yuehua Zhang, Muqing Su, Bin Zheng, Hongbing Pan, Bang Du, Jun Wang, Ping He, Qianfu Chen, Hong An, Wentian Xu, Xiang Luo","doi":"10.1093/hr/uhae153","DOIUrl":"10.1093/hr/uhae153","url":null,"abstract":"<p><p>Mango (<i>Mangifera indica</i> L.) has been widely cultivated as a culturally and economically significant fruit tree for roughly 4000 years. Despite its rich history, little is known about the crop's domestication, genomic variation, and the genetic loci underlying agronomic traits. This study employs the whole-genome re-sequencing of 224 mango accessions sourced from 22 countries, with an average sequencing depth of 16.37×, to explore their genomic variation and diversity. Through phylogenomic analysis, <i>M. himalis</i> J.Y. Liang, a species grown in China, was reclassified into the cultivated mango group known as <i>M. indica</i>. Moreover, our investigation of mango population structure and differentiation revealed that Chinese accessions could be divided into two distinct gene pools, indicating the presence of independent genetic diversity ecotypes. By coupling genome-wide association studies with analyses of genotype variation patterns and expression patterns, we identified several candidate loci and dominant genotypes associated with mango flowering capability, fruit weight, and volatile compound production. In conclusion, our study offers valuable insights into the genetic differentiation of mango populations, paving the way for future agronomic improvements through genomic-assisted breeding.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 7","pages":"uhae153"},"PeriodicalIF":7.6,"publicationDate":"2024-07-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11246242/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617751","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}

{"title":"Magnetofected pollen gene delivery system could generate genetically modified <i>Cucumis sativus</i>.","authors":"Chan-Woo Park, Jun-Young Choi, Ye-Jin Son, Do-Hyeon Kim, Huanjun Li, Wanqi Liang, Chanhui Lee, Ki-Hong Jung, Yu-Jin Kim","doi":"10.1093/hr/uhae179","DOIUrl":"10.1093/hr/uhae179","url":null,"abstract":"","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 8","pages":"uhae179"},"PeriodicalIF":7.6,"publicationDate":"2024-06-27","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301313/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899055","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}

{"title":"Integrated multi-omics profiling reveals a landscape of dramatic metabolic defect in <i>Artemisia annua</i>.","authors":"Wei Qin, Yongpeng Li, Hang Liu, Xin Yan, Xinyi Hu, Tiantian Chen, Saeed-Ur Rahman, Junfeng Cao, Han Zheng, Ling Li, Kexuan Tang","doi":"10.1093/hr/uhae174","DOIUrl":"10.1093/hr/uhae174","url":null,"abstract":"","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 8","pages":"uhae174"},"PeriodicalIF":7.6,"publicationDate":"2024-06-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11301311/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899054","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}

{"title":"Chemical induction of DNA demethylation by 5-Azacytidine enhances tomato fruit defense against gray mold through dicer-like protein <i>DCL2c</i>.","authors":"Xiaorong Chang, Liyao Liu, Ziwei Liu, Liping Qiao, Ruixi Shi, Laifeng Lu","doi":"10.1093/hr/uhae164","DOIUrl":"10.1093/hr/uhae164","url":null,"abstract":"<p><p>Postharvest decay, primarily caused by pathogenic fungi in ripening fruits and fresh vegetables, poses a challenge to agricultural sustainability and results in significant economic losses. The regulation of the fruit ripening by DNA methylation has been well demonstrated, while defense response of fruit underlying epigenetic regulation against postharvest decay remains uncertain. In the present study, treatment of tomato fruits with the DNA methyltransferase inhibitor 5-Azacytidine (5-Aza) notably decreased their susceptibility to gray mold. Following 5-Aza treatment, we observed a substantial increase in activities of chitinase (CHI) and glucanase (GLU) in tomato fruits, as well as an increase in the expression of the dicer-like <i>SlDCL2</i> gene family. Suppression of <i>SlDCL2c</i> through double-stranded RNA-induced RNA interference (RNAi) resulted in a decrease in the expression of chitinases <i>CHI3, CHI9, Class V chitinase</i>, and <i>endochitinase 4</i> by 71%, 29%, 55%, 64%, as well as glucanases <i>Cel1, Cel2</i>, and <i>GluB</i> by 19%, 93%, and 87%, respectively. This was accompanied by decreased activities of resistance-related enzymes, including CHI and GLU. The expression levels of genes phenylalanine ammonia-lyase <i>PAL2</i>, peroxidase <i>POD 12</i>, <i>POD P7</i>, <i>CCR1</i>, <i>CYP84A2</i>, and <i>COMT</i> in phenylpropanoid biosynthesis pathway also decreased by 33%, 53%, 18%, 50%, 30%, and 24% in <i>SlDCL2c-</i>RNAi fruit, resulting in decreased activities of PAL and POD. Consequently, the lesion diameter of gray mold in <i>SlDCL2c</i>-RNAi fruit increased by 55% compared to the control group. Overall, the present study indicated that DNA methyltransferase inhibitor 5-Aza reduces susceptibility of tomato fruit to gray mold through regulation of <i>DCL2c</i>-mediated inducible defense response.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 8","pages":"uhae164"},"PeriodicalIF":7.6,"publicationDate":"2024-06-19","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11298621/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899053","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}

{"title":"The jacktree genome and population genomics provides insights for the mechanisms of the germination obstacle and the conservation of endangered ornamental plants.","authors":"Sheng Zhu, Xue-Fen Wei, Yu-Xin Lu, Dao-Wu Zhang, Ze-Fu Wang, Jing Ge, Sheng-Lian Li, Yan-Feng Song, Yong Yang, Xian-Gui Yi, Min Zhang, Jia-Yu Xue, Yi-Fan Duan","doi":"10.1093/hr/uhae166","DOIUrl":"10.1093/hr/uhae166","url":null,"abstract":"<p><p><i>Sinojackia</i> Hu represents the first woody genus described by Chinese botanists, with all species classified as endangered ornamental plants endemic to China. Their characteristic spindle-shaped fruits confer high ornamental value to the plants, making them favored in gardens and parks. Nevertheless, the fruits likely pose a germination obstacle, contributing to the endangered status of this lineage. Here we report the chromosome-scale genome of <i>S. xylocarpa</i>, and explore the mechanisms underlying its endangered status, as well as its population dynamics throughout evolution. Population genomic analysis has indicated that <i>S. xylocarpa</i> experienced a bottleneck effect following the recent glacial period, leading to a continuous population reduction. Examination of the pericarp composition across six stages of fruit development revealed a consistent increase in the accumulation of lignin and fiber content, responsible for the sturdiness of mature fruits' pericarps. At molecular level, enhanced gene expression in the biosynthesis of lignin, cellulose and hemicellulose was detected in pericarps. Therefore, we conclude that the highly lignified and fibrotic pericarps of <i>S. xylocarpa</i>, which inhibit its seed germination, should be its threatening mechanism, thus proposing corresponding strategies for improved conservation and restoration. This study serves as a seminal contribution to conservation biology, offering valuable insights for the study of other endangered ornamental plants.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 8","pages":"uhae166"},"PeriodicalIF":7.6,"publicationDate":"2024-06-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11300842/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141899056","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}

{"title":"Retraction of: Lipidomics, transcription analysis, and hormone profiling unveil the role of <i>CsLOX6</i> in MeJA biosynthesis during black tea processing.","authors":"","doi":"10.1093/hr/uhae146","DOIUrl":"https://doi.org/10.1093/hr/uhae146","url":null,"abstract":"<p><p>[This retracts the article DOI: 10.1093/hr/uhae032.].</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 6","pages":"uhae146"},"PeriodicalIF":0.0,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11149377/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141262674","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}

{"title":"A novel tomato interspecific (<i>Solanum lycopersicum</i> var. <i>cerasiforme</i> and <i>Solanum pimpinellifolium</i>) MAGIC population facilitates trait association and candidate gene discovery in untapped exotic germplasm.","authors":"Andrea Arrones, Oussama Antar, Leandro Pereira-Dias, Andrea Solana, Paola Ferrante, Giuseppe Aprea, Mariola Plazas, Jaime Prohens, María José Díez, Giovanni Giuliano, Pietro Gramazio, Santiago Vilanova","doi":"10.1093/hr/uhae154","DOIUrl":"10.1093/hr/uhae154","url":null,"abstract":"<p><p>We developed a novel eight-way tomato multiparental advanced generation intercross (MAGIC) population to improve the accessibility of tomato relatives genetic resources to geneticists and breeders. The interspecific tomato MAGIC population (ToMAGIC) was obtained by intercrossing four accessions each of <i>Solanum lycopersicum</i> var. <i>cerasiforme</i> and <i>Solanum pimpinellifolium</i>, which are the weedy relative and the ancestor of cultivated tomato, respectively. The eight exotic ToMAGIC founders were selected based on a representation of the genetic diversity and geographical distribution of the two taxa. The resulting MAGIC population comprises 354 lines, which were genotyped using a new 12k tomato single primer enrichment technology panel and yielded 6488 high-quality single-nucleotide polymorphism (SNPs). The genotyping data revealed a high degree of homozygosity, an absence of genetic structure, and a balanced representation of the founder genomes. To evaluate the potential of the ToMAGIC population, a proof of concept was conducted by phenotyping it for fruit size, plant pigmentation, leaf morphology, and earliness. Genome-wide association studies identified strong associations for the studied traits, pinpointing both previously identified and novel candidate genes near or within the linkage disequilibrium blocks. Domesticated alleles for fruit size were recessive and were found, at low frequencies, in wild/ancestral populations. Our findings demonstrate that the newly developed ToMAGIC population is a valuable resource for genetic research in tomato, offering significant potential for identifying new genes that govern key traits in tomato. ToMAGIC lines displaying a pyramiding of traits of interest could have direct applicability for integration into breeding pipelines providing untapped variation for tomato breeding.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 7","pages":"uhae154"},"PeriodicalIF":7.6,"publicationDate":"2024-06-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11246243/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141617750","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}

{"title":"Genome assembly and resequencing shed light on evolution, population selection, and sex identification in <i>Vernicia montana</i>.","authors":"Wenying Li, Xiang Dong, Xingtan Zhang, Jie Cao, Meilan Liu, Xu Zhou, Hongxu Long, Heping Cao, Hai Lin, Lin Zhang","doi":"10.1093/hr/uhae141","DOIUrl":"10.1093/hr/uhae141","url":null,"abstract":"<p><p><i>Vernicia montana</i> is a dioecious plant widely cultivated for high-quality tung oil production and ornamental purposes in the Euphorbiaceae family. The lack of genomic information has severely hindered molecular breeding for genetic improvement and early sex identification in <i>V. montana</i>. Here, we present a chromosome-level reference genome of a male <i>V. montana</i> with a total size of 1.29 Gb and a contig N50 of 3.69 Mb. Genome analysis revealed that different repeat lineages drove the expansion of genome size. The model of chromosome evolution in the Euphorbiaceae family suggests that polyploidization-induced genomic structural variation reshaped the chromosome structure, giving rise to the diverse modern chromosomes. Based on whole-genome resequencing data and analyses of selective sweep and genetic diversity, several genes associated with stress resistance and flavonoid synthesis such as CYP450 genes and members of the LRR-RLK family, were identified and presumed to have been selected during the evolutionary process. Genome-wide association studies were conducted and a putative sex-linked insertion and deletion (InDel) (Chr 2: 102 799 917-102 799 933 bp) was identified and developed as a polymorphic molecular marker capable of effectively detecting the gender of <i>V. montana</i>. This InDel is located in the second intron of <i>VmBASS4</i>, suggesting a possible role of <i>VmBASS4</i> in sex determination in <i>V. montana.</i> This study sheds light on the genome evolution and sex identification of <i>V. montana</i>, which will facilitate research on the development of agronomically important traits and genomics-assisted breeding.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 7","pages":"uhae141"},"PeriodicalIF":7.6,"publicationDate":"2024-05-18","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11233859/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141581685","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}

{"title":"Coping with alpine habitats: genomic insights into the adaptation strategies of <i>Triplostegia glandulifera</i> (Caprifoliaceae).","authors":"Jian Zhang, Kai-Lin Dong, Miao-Zhen Ren, Zhi-Wen Wang, Jian-Hua Li, Wen-Jing Sun, Xiang Zhao, Xin-Xing Fu, Jian-Fei Ye, Bing Liu, Da-Ming Zhang, Mo-Zhu Wang, Gang Zeng, Yan-Ting Niu, Li-Min Lu, Jun-Xia Su, Zhong-Jian Liu, Pamela S Soltis, Douglas E Soltis, Zhi-Duan Chen","doi":"10.1093/hr/uhae077","DOIUrl":"10.1093/hr/uhae077","url":null,"abstract":"<p><p>How plants find a way to thrive in alpine habitats remains largely unknown. Here we present a chromosome-level genome assembly for an alpine medicinal herb, <i>Triplostegia glandulifera</i> (Caprifoliaceae), and 13 transcriptomes from other species of Dipsacales. We detected a whole-genome duplication event in <i>T. glandulifera</i> that occurred prior to the diversification of Dipsacales. Preferential gene retention after whole-genome duplication was found to contribute to increasing cold-related genes in <i>T. glandulifera</i>. A series of genes putatively associated with alpine adaptation (e.g. <i>CBF</i>s, <i>ERF-VII</i>s, and <i>RAD51C</i>) exhibited higher expression levels in <i>T. glandulifera</i> than in its low-elevation relative, <i>Lonicera japonica</i>. Comparative genomic analysis among five pairs of high- vs low-elevation species, including a comparison of <i>T. glandulifera</i> and <i>L. japonica</i>, indicated that the gene families related to disease resistance experienced a significantly convergent contraction in alpine plants compared with their lowland relatives. The reduction in gene repertory size was largely concentrated in clades of genes for pathogen recognition (e.g. <i>CNL</i>s, <i>prRLP</i>s, and XII <i>RLK</i>s), while the clades for signal transduction and development remained nearly unchanged. This finding reflects an energy-saving strategy for survival in hostile alpine areas, where there is a tradeoff with less challenge from pathogens and limited resources for growth. We also identified candidate genes for alpine adaptation (e.g. <i>RAD1</i>, <i>DMC1</i>, and <i>MSH3</i>) that were under convergent positive selection or that exhibited a convergent acceleration in evolutionary rate in the investigated alpine plants. Overall, our study provides novel insights into the high-elevation adaptation strategies of this and other alpine plants.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 5","pages":"uhae077"},"PeriodicalIF":0.0,"publicationDate":"2024-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11109519/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141082470","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}

{"title":"Transposable elements in Rosaceae: insights into genome evolution, expression dynamics, and syntenic gene regulation.","authors":"Ze Yu, Jiale Li, Hanyu Wang, Boya Ping, Xinchu Li, Zhiguang Liu, Bocheng Guo, Qiaoming Yu, Yangjun Zou, Yaqiang Sun, Fengwang Ma, Tao Zhao","doi":"10.1093/hr/uhae118","DOIUrl":"10.1093/hr/uhae118","url":null,"abstract":"<p><p>Transposable elements (TEs) exert significant influence on plant genomic structure and gene expression. Here, we explored TE-related aspects across 14 Rosaceae genomes, investigating genomic distribution, transposition activity, expression patterns, and nearby differentially expressed genes (DEGs). Analyses unveiled distinct long terminal repeat retrotransposon (LTR-RT) evolutionary patterns, reflecting varied genome size changes among nine species over the past million years. In the past 2.5 million years, <i>Rubus idaeus</i> showed a transposition rate twice as fast as <i>Fragaria vesca</i>, while <i>Pyrus bretschneideri</i> displayed significantly faster transposition compared with <i>Crataegus pinnatifida</i>. Genes adjacent to recent TE insertions were linked to adversity resistance, while those near previous insertions were functionally enriched in morphogenesis, enzyme activity, and metabolic processes. Expression analysis revealed diverse responses of LTR-RTs to internal or external conditions. Furthermore, we identified 3695 pairs of syntenic DEGs proximal to TEs in <i>Malus domestica</i> cv. 'Gala' and <i>M. domestica</i> (GDDH13), suggesting TE insertions may contribute to varietal trait differences in these apple varieties. Our study across representative Rosaceae species underscores the pivotal role of TEs in plant genome evolution within this diverse family. It elucidates how these elements regulate syntenic DEGs on a genome-wide scale, offering insights into Rosaceae-specific genomic evolution.</p>","PeriodicalId":57479,"journal":{"name":"园艺研究(英文)","volume":"11 6","pages":"uhae118"},"PeriodicalIF":7.6,"publicationDate":"2024-04-26","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"https://www.ncbi.nlm.nih.gov/pmc/articles/PMC11197308/pdf/","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"141452301","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}