Antoine Bodelot, Nicolas Dousset, Elisa Ravon, Christelle Heintz, Marie-Noelle Brisset, Alexandre Degrave, Emilie Vergne
{"title":"Inducible MdAGG lectins in apple immunity toward Fire Blight: CRISPR/Cas9 validation and their potential for intragenesis approaches","authors":"Antoine Bodelot, Nicolas Dousset, Elisa Ravon, Christelle Heintz, Marie-Noelle Brisset, Alexandre Degrave, Emilie Vergne","doi":"10.1093/hr/uhaf262","DOIUrl":"https://doi.org/10.1093/hr/uhaf262","url":null,"abstract":"Fire blight, caused by the bacterium Erwinia amylovora, represents a significant threat to apple (Malus domestica) production. Currently, only a limited number of genes effectively involved in resistance to E. amylovora have been identified. Seeking new resistance candidates, we focused on a multigene family encoding amaranthin-like lectins, which are highly upregulated following chemical elicitation by acibenzolar-S-methyl (ASM). These lectins are believed to contribute to downstream defense by promoting bacterial aggregation, which led to their designation as Malus domestica agglutinins (MdAGG). When loss-of-function editions were introduced into MdAGG genes, the plant's ability to mount a fully effective defense response against fire blight upon ASM treatment was compromised, confirming the role of MdAGGs in fire blight resistance. Next, we coupled the pPPO16 promoter, endogenous to apple and known to be rapidly induced during E. amylovora infection, with the coding sequence of MdAGG10 to create apple lines with fire blight-inducible MdAGG10 expression. Early MdAGG10 expression in these lines significantly improved resistance to fire blight, and an additional ASM treatment further enhanced this resistance. In summary, we conclude that MdAGGs act as defense genes whose timely expression can provide effective resistance against E. amylovora.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"37 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145215636","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}
Jie Zhou, Meng Ma, Qing Zhang, Shangyan Ni, Hu Zhao, Jing Wen, Jinxiong Shen, Tingdong Fu, Lun Zhao
{"title":"Genomic and Epigenomic coordination maintains subgenome transcriptional balance in Allotetraploid Brassica napus","authors":"Jie Zhou, Meng Ma, Qing Zhang, Shangyan Ni, Hu Zhao, Jing Wen, Jinxiong Shen, Tingdong Fu, Lun Zhao","doi":"10.1093/hr/uhaf266","DOIUrl":"https://doi.org/10.1093/hr/uhaf266","url":null,"abstract":"Allopolyploids have successfully overcome ‘genome shock’, yet how their subgenomes adapt to coexistence remains largely unclear. Here, we constructed high-resolution epigenomic maps for the diploids Brassica rapa (ArAr) and B. oleracea (CoCo), and examined epigenomic variation in the allotetraploid B. napus (AnAnCnCn) relative to its putative progenitors. We discovered that coordinated genomic and epigenomic reprogramming in B. napus drove convergence of sequence and epigenomic features between An and Cn, significantly reducing expression divergence in homoeologs. Convergent homoeologs were functionally enriched in pathways related to genome stability and abiotic stress responses. Notably, Cn in B. napus exhibited greater sequence conservation and epigenetic homeostasis. Furthermore, transcription factor binding sites (TFBSs) affected by genomic variation in An showed convergent regulatory changes toward Cn, indicating that allopolyploids mitigate subgenomic conflicts through multi-layered regulatory coordination. In conclusion, coordinated genomic and epigenomic convergence provides critical insights into the stability and adaptive evolution of allopolyploids.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"7 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-10-03","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145215637","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}
{"title":"Amino Acid Transporter CsBAT Links GABA Accumulation to Flavonoid Metabolism in Camellia sinensis","authors":"Lin Feng, Panpan Liu, Yuanyuan He, Shengpeng Wang, Rui Luo, Anhui Gui, Jinjin Xue, Shiwei Gao, Pengcheng Zheng","doi":"10.1093/hr/uhaf261","DOIUrl":"https://doi.org/10.1093/hr/uhaf261","url":null,"abstract":"γ-Aminobutyric acid (GABA), a signature bioactive compound in tea, plays a crucial role in determining both flavor profile and health-promoting properties. Despite its importance, the molecular regulation of GABA accumulation in tea plants - especially its metabolic crosstalk with key quality determinants like flavonoids - remains elusive. While amino acid transporters are known to mediate source-sink allocation in plants, the functional characterization of GABA transporters in Camellia sinensis has been lacking. In this study, we identified and functionally characterized the bidirectional amino acid transporter CsBAT in tea plants. Through a comprehensive multi-platform validation system encompassing yeast heterologous expression, Arabidopsis genetic transformation, and tea transgenic system, we revealed that CsBAT shows vascular-specific expression patterns and facilitates directional amino acid transport from source (mature leaves) to sink (young shoots), thereby significantly boosting GABA accumulation in buds and young leaves. Importantly, we discovered that CsBAT functionally interacts with key flavonoid biosynthetic enzymes (LAR, 4CL, C4H) within secondary metabolic networks. Our findings provide the first mechanistic link between CsBAT-mediated amino acid transport and tea quality formation, establishing both theoretical frameworks and practical tools for molecular breeding of premium tea cultivars.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"28 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145203223","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}
Muyao Yu, Chenyi Li, Xiaoqing Wang, Dan Jiang, Xueqing Fu, Chao Chen, Guangxi Ren, Xuewei Li, Yaojie Zhang, Qi Liu, Shuyi Qian, Yang Han, Xiaoqun He, Zhenfang Bai, Badalahu Tai, Luqi Huang, Jinbao Yu, Han Zheng, Chunsheng Liu
{"title":"Integrative chromosome-level genomics and metabolomics uncover regulatory networks linking monoterpenoid biosynthesis and glandular trichome formation in Mosla chinensis","authors":"Muyao Yu, Chenyi Li, Xiaoqing Wang, Dan Jiang, Xueqing Fu, Chao Chen, Guangxi Ren, Xuewei Li, Yaojie Zhang, Qi Liu, Shuyi Qian, Yang Han, Xiaoqun He, Zhenfang Bai, Badalahu Tai, Luqi Huang, Jinbao Yu, Han Zheng, Chunsheng Liu","doi":"10.1093/hr/uhaf263","DOIUrl":"https://doi.org/10.1093/hr/uhaf263","url":null,"abstract":"Xiangru, with Mosla chinensis (Mc, 2n=18) and its considered cultivar M. chinensis ‘Jiangxiangru’ (McJ, 2n=18) as original plants, are annual herbs of the Lamiaceae family, and is widely used as medicinal and edible plant due to its spleen strengthening function. However, absence of genomic resource impedes in-depth research towards Xiangru. In this study, the morphological characteristics and volatile organic compounds (VOC) contents of Mc and McJ were analyzed, showing higher trichome density and monoterpenoids accumulation obtained in Mc, whereas McJ possessed higher biomass. We assembled high-quality Mc, McJ and their adulterant M. soochowensis (2n=18) genomes of 426.1, 408.8 and 412.8 Mb, respectively, containing the repeat sequences of 57.17%, 56.33%, and 55.83%. Comparative genomics indicating Mosla radiating ~13.3 Mya, supporting McJ initially as a natural naturally formed resource. Five monoterpene synthase genes were identified through comparative transcriptome, and were responsible for catalyzing production of diversified monoterpene skeleton, in which TPS1 mediate formation of γ-terpinene, accompanied by CYP71D179 and SDR2 leading to the final production of carvacrol and thymol. We further explore correlation between monoterpenoids biosynthesis and trichome development, indicating MIXTA and WIN1 jointly regulate both trichome formation and VOC accumulation by directly binding promotors of TPS1 and CYP71D179, respectively. Our study fills vacancy of genus Mosla genomes, improving the biosynthetic and regulatory mechanism of volatile compounds in aromatic Traditional Chinese Medicine, also offering novel targets for quality-directed breeding in Xiangru.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"114 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-10-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145203699","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}
{"title":"PpSnRK1α-PpNAC6/PpNAC36 module mediates nitrogen-regulated biosynthesis of γ-decalactone in peach fruit","authors":"Jiahui Liang, Xin Zheng, Xuelian Wu, Zhe Wang, Zixuan Li, Yuansong Xiao, Jian Guo, Qiuju Chen, Jingjing Luo, Huaifeng Gao, Yangyang Gao, Futian Peng","doi":"10.1093/hr/uhaf256","DOIUrl":"https://doi.org/10.1093/hr/uhaf256","url":null,"abstract":"Flavor-related compounds, particularly γ-decalactone—the key contributor to the characteristic ‘peach-like’ aroma—serve as essential indicators of peach fruit quality and strongly influence consumer purchasing decisions. However, excessive application of N fertilizers has led to a significant decline in the flavor quality of peaches, posing a major obstacle to the sustainable development of the peach industry. Although this remains a critical challenge, the molecular mechanisms linking N to flavor compound biosynthesis are still not well characterized. In this study, we discovered that excessive N application reduced the biosynthesis of γ-decalactone in peach, based on multi-year field observations. Correlation analysis and expression profiling under N treatments revealed that two NAC (NAM-ATAF1/2-CUC2) transcription factors (TFs), PpNAC6 and PpNAC36, were involved in regulating γ-decalactone biosynthesis in response to N signaling. Genetic analyses indicated that PpNAC6 and PpNAC36 positively regulated the accumulation of γ-decalactone. Both yeast one-hybrid (Y1H) assays and dual-luciferase reporter assays consistently showed that PpNAC6 and PpNAC36 directly interact with the promoter regions of γ-decalactone biosynthesis-related genes (PpAAT2, PpAAT3, PpLOX1, PpLOX6, and PpFAD3) and significantly enhance their transcriptional activity. Furthermore, transgene verification demonstrated that the α subunit of peach SNF-related Kinase 1 (PpSnRK1α) suppresses γ-decalactone biosynthesis. Notably, we found that PpSnRK1α interacts with PpNAC6/PpNAC36 and selectively phosphorylates PpNAC36 in response to N, thus regulating γ-decalactone production. Our study uncovers the transcriptional regulatory network involved in PpSnRK1α-mediated phosphorylation of PpNAC6/PpNAC36, linking N signaling to γ-decalactone synthesis in peach, and provides insights for molecular breeding and precision fertilization to enhance peach flavor.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"39 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-09-30","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145195281","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}
{"title":"Single-nucleus transcriptomics reveals the cellular immune responses to Candidatus Liberibacter asiaticus in rough lemon","authors":"Xu-Bin Tian, Jinhuan Zhou, Jiaxin Li, Yayu Li, Changyong Zhou, Zhen Song","doi":"10.1093/hr/uhaf265","DOIUrl":"https://doi.org/10.1093/hr/uhaf265","url":null,"abstract":"Citrus Huanglongbing (HLB) is the most destructive disease in citriculture, mainly caused by Candidatus Liberibacter asiaticus (CLas). However, the immune response of citrus to CLas at the cellular level remains to be elucidated. In this study, the first single-cell atlas of rough lemon (Citrus jambhiri Lush.) root apexes were generated using single-nucleus RNA sequencing at 20 weeks post-inoculation with CLas. According to gene expression patterns, the single-cell atlas was partitioned into 20 transcriptionally distinct clusters, and five cell types were identified within these clusters. A significant number of defense-related genes were co-upregulated across the five cell types following CLas infection, whereas genes involved in signal transduction pathways, such as tubulin beta-6 chain (TUBB1) and the phospholipase D alpha 1 (PLD1), were concurrently downregulated. Based on pseudotime trajectory analysis, the key pathways and genes involved in the coordination of cell differentiation and resistance in citrus under CLas infection were characterized. Following CLas infection, the development of phloem cells was significantly delayed, and the differentiation of cambium cells into xylem cells was evident. The expression of genes associated with lignin synthesis was significantly upregulated in these cells. The reduction in phloem cell differentiation and the enhanced differentiation of cambium cells into defense-related xylem cells may represent the primary vascular immune mechanisms exhibited by citrus plants in response to CLas infection. Additionally, DNA-binding one zinc finger transcription factor DOF2.4 was found to potentially serve dual roles in regulating vascular cell development and inducing plant resistance against CLas. In conclusion, this study collectively provides insights into the cellular innate immunity responses of citrus to CLas infection. These findings hold significant implications for the sustainable development of citriculture amidst the ongoing global HLB epidemic, and offer novel insights into vascular immunity and plant defense responses.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"1 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-09-28","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145195282","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}
Guotao Huo, Haibin Wei, Shuping He, Guojun Ge, Lei Wang, Guangliu Xu, Yan Huang, Yiwen Zhou, Xiao Yang, Zhenzhen Li, Yingyan Han, Shiwei Wei, Lijun Luo
{"title":"From genetic diversity to genomic design breeding: a lettuce core collection of 811 accessions catalyzes anthocyanin-enriched cultivar development","authors":"Guotao Huo, Haibin Wei, Shuping He, Guojun Ge, Lei Wang, Guangliu Xu, Yan Huang, Yiwen Zhou, Xiao Yang, Zhenzhen Li, Yingyan Han, Shiwei Wei, Lijun Luo","doi":"10.1093/hr/uhaf258","DOIUrl":"https://doi.org/10.1093/hr/uhaf258","url":null,"abstract":"Lettuce (Lactuca sativa) is a globally cultivated vegetable crop prized for its leafy morphology, which critically influences consumer preference and market value. Despite the agronomic importance of leaf traits, the genetic basis underlying their diversity remains poorly characterized. To address this, we performed whole-genome resequencing to characterize ~800 lettuce accessions collected from major lettuce production areas as well as the relative wild species, and developed a publicly accessible core collection of 268 accessions that represents at least 99.4% of the genetic variation. Sixteen leaf morphological traits were systematically evaluated over two growing seasons. Population structure analysis revealed frequent introgression events from looseleaf type into domesticated varieties (butterhead, crisphead, romaine, and stem lettuce), highlighting dynamic gene flow during breeding. Trait correlation analyses identified significant associations: plant width exhibited negative correlations with anthocyanin content, leaf tip shape, and leaf lobes of margin (P < 0.001), while apical margin incision of leaf blade positively correlated with multiple leaf architecture traits. Genome-wide association studies (GWAS) pinpointed 13 quantitative trait loci (QTLs) and candidate genes regulating leaf morphology, including a validated anthocyanin biosynthesis regulator (ANS). Notably, we pinpointed the causal gene genotypes responsible for leaf anthocyanin coloration. Leveraging these insights, we engineered a high-anthocyanin cultivar binfen5 with optimized leaf shape through genomic design breeding. This study provides a comprehensive genetic resource and actionable targets for precision breeding to enhance lettuce quality.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"95 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133579","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}
Zhu Chen, Faheem Afzal Shah, Xiaoyu Lu, Lu Zhu, Guo Wei, Xin Meng, Qiuyue Ma, Jie Ren
{"title":"The ApWRKY26/ApERF4-ApMYB2 module regulates anthocyanin accumulation for the seasonal leaf color transition in Acer palmatum","authors":"Zhu Chen, Faheem Afzal Shah, Xiaoyu Lu, Lu Zhu, Guo Wei, Xin Meng, Qiuyue Ma, Jie Ren","doi":"10.1093/hr/uhaf257","DOIUrl":"https://doi.org/10.1093/hr/uhaf257","url":null,"abstract":"Acer palmatum 'Duocai' is an excellent ornamental cultivar maintained through asexual propagation. In spring and autumn, it exhibits red leaves, and in summer, it displays green leaves. To investigate the genetic and epigenetic regulation underlying these seasonal pigmentation shifts, we implemented a comprehensive multi-omics approach. Metabolomic profiling identified cyanidin-3-O-glucoside as the predominant biochemical factor governing seasonal leaf color transitions. RNA-seq, ATAC-seq, Hi-C, and WGBS were utilized to examine transcriptomic and chromatin remodeling dynamics. Multi-omics regulatory network analysis identified ApMYB2 as a key transcription factor affecting anthocyanin accumulation by regulating ApF3'H2 expression. Functional analyses demonstrated that the transcription factor ApWRKY26 positively modulates ApMYB2 expression, while ApERF4 exerts an inhibitory effect on its expression. These regulatory interactions were corroborated by seasonal RNA-seq-based correlation analyses. Genetic manipulation experiments, including overexpression and silencing of these genes in A. palmatum, provided empirical evidence supporting their functional roles in the anthocyanin biosynthetic pathway. Together, our study elucidates the molecular mechanism by which ApWRKY26 and ApERF4 coordinate the activity of ApMYB2 to govern seasonal anthocyanin synthesis in A. palmatum foliage.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"18 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133576","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}
{"title":"Chromosome-level genome assembly of Cornus officinalis reveals the evolution of loganin biosynthesis","authors":"Xiang Zhang, Jiangbo Xie, Jiadong Wu, Haoyu Zhang, Zhelun Jin, Qing Liu, Deqiang Zhang","doi":"10.1093/hr/uhaf259","DOIUrl":"https://doi.org/10.1093/hr/uhaf259","url":null,"abstract":"Cornus officinalis is a traditional medicinal plant known for producing loganin, a bioactive iridoid glycoside with potential anticancer properties. However, the absence of a high-quality reference genome has limited insights into its biosynthetic pathways. Here, we present a chromosome-level genome assembly of C. officinalis with a size of 2.85 Gb. Comparative genomic analysis revealed that the genome expansion and longer gene structures, relative to other Cornales species, are primarily due to a recent expansion of transposable elements (TEs). In this study, we identified unique biosynthetic gene clusters (BGCs) coding multiple core enzymes, including loganin acid O-methyltransferase (LAMT), secologanin synthase (SLS), and cytochrome P450, all of which catalyze sequential steps leading to loganin formation. LAMT enzymes from C. officinalis capable of catalyzing the C-9 hydroxylation of loganin acid were identified, whereas the homolog (CoLMAT) was not found to possess this activity. Additionally, molecular docking studies revealed critical residues in CoLAMT that govern substrate positioning, providing insights into the mechanism of C-9 regioselective hydroxylation. Further characterization of 7-deoxyloganicacid hydroxylase (7-DLH), LAMT, and SLS enzymes allowed us to elucidate the complete biosynthetic pathway of major loganin derivatives in the medicinal plant C. officinalis. Finally, we introduced CoLAMT and its upstream genes into Nicotiana benthamiana and successfully achieved the de novo biosynthesis of a series of loganin derivatives. This work reveals key evolutionary and molecular mechanisms in loganin biosynthesis, providing insights into biotechnological applications in anticancer drug development.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"12 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133578","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}
{"title":"Integrative Genomics for Mango Genetics and Breeding","authors":"Bilal Ahmad, Ying Su, Rida Arshad, Tayyaba Razzaq, Yi Zhang, Ting Hou, Chaochao Li, Zhongxin Jin, Chengjie Chen, Peng Wang, Melanie J Wilkinson, Yibo Bai, Yeyuan Chen, Yu Zhang, Zhiguo Dang, Yongfeng Zhou, Xinmin Tian, Jianfeng Huang","doi":"10.1093/hr/uhaf260","DOIUrl":"https://doi.org/10.1093/hr/uhaf260","url":null,"abstract":"Mango is the second most important tropical fruit crop. Due to ever-changing environmental conditions, world mango production is facing challenges such as diseases (anthracnose and mango malformation), physiological disorders (alternate bearing), low fruit setting, poor fruit quality, short shelf life, and climate change adaptation. Breeding efforts are hindered by the long juvenile period, outdated breeding system, and high heterozygosity, resulting in a slow pace of mango improvement programs. However, over the last decade, significant advances in high-quality genome assemblies, pangenomics, genetic mapping, multi-omics data, and phenomics of large populations have accelerated crop genetics and breeding. Here, we summarize recent progress on the origin and domestication of mango, advancements in genome assemblies, development of genetic maps, functional and comparative genomics, evolutionary insights, and assessments of global phenotypic and genotypic diversity, including species at risk. We also discuss the integration of multi-omics approaches with quantitative genetics for crop improvement. Further, we highlight the key research gaps that limit breeding efficiency and propose integrative strategies combining pangenomics, multi-omics, and machine learning with improved transformation protocols and multi-environment testing to accelerate the development of climate-resilient, high-quality mango cultivars.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"59 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-09-24","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"145133580","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}