Horticulture Research最新文献

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Deep learning empowers genomic selection of pest-resistant grapevine 深度学习使抗虫害葡萄藤的基因组选择成为可能
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-07 DOI: 10.1093/hr/uhaf128
Yu Gan, Zhenya Liu, Fan Zhang, Qi Xu, Xu Wang, Hui Xue, Xiangnian Su, Wenqi Ma, Qiming Long, Anqi Ma, Guizhou Huang, Wenwen Liu, Xiaodong Xu, Lei Sun, Yingchun Zhang, Yuting Liu, Xinyue Fang, Chaochao Li, Xuanwen Yang, Pengcheng Wei, Xiucai Fan, Chuan Zhang, Pengpai Zhang, Chonghuai Liu, Lianzhu Zhou, Zhiwu Zhang, Cong Tan, Yiwen Wang, Zhongjie Liu, Yongfeng Zhou
{"title":"Deep learning empowers genomic selection of pest-resistant grapevine","authors":"Yu Gan, Zhenya Liu, Fan Zhang, Qi Xu, Xu Wang, Hui Xue, Xiangnian Su, Wenqi Ma, Qiming Long, Anqi Ma, Guizhou Huang, Wenwen Liu, Xiaodong Xu, Lei Sun, Yingchun Zhang, Yuting Liu, Xinyue Fang, Chaochao Li, Xuanwen Yang, Pengcheng Wei, Xiucai Fan, Chuan Zhang, Pengpai Zhang, Chonghuai Liu, Lianzhu Zhou, Zhiwu Zhang, Cong Tan, Yiwen Wang, Zhongjie Liu, Yongfeng Zhou","doi":"10.1093/hr/uhaf128","DOIUrl":"https://doi.org/10.1093/hr/uhaf128","url":null,"abstract":"Crop pests significantly reduce crop yield and threaten global food security. Conventional pest control relies heavily on insecticides, leading to pesticide resistance and ecological concerns. However, crops and their wild relatives exhibit varied levels of pest resistance, suggesting the potential for breeding pest-resistant varieties. This study integrates deep learning (DL)/machine learning (ML) algorithms, plant phenomics, quantitative genetics and transcriptomics to conduct genomic selection (GS) of pest-resistance in grapevine. Building deep convolutional neural networks (DCNN), we accurately assess pest damage on grape leaves, achieving 95.3% classification accuracy (VGG16) and a 0.94 correlation in regression analysis (DCNN-PDS). The pest damage was phenotyped as binary and continuous traits and genome resequencing data from 231 grapevine accessions were combined in a Genome-Wide Association Studies (GWAS), which maps 69 QTLs and 139 candidate genes involved in pest resistance pathways, including jasmonic acid, salicylic acid, and ethylene. Combining this with transcriptome data, we pinpoint specific pest-resistant genes such as ACA12 and CRK3, which are crucial in herbivore responses. Machine learning-based GS demonstrates a high accuracy (95.7%) and a strong correlation (0.90) in predicting pest resistance as binary and continuous traits in grapevine, respectively. In general, our study highlights the power of DL/ML in plant phenomics and genomic selection, facilitating genomic breeding of pest-resistant grapevine.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"63 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920126","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
PagKNAT5a Promotes Plant Growth by Enhancing Xylem Cell Elongation and Secondary Wall Formation in Poplar PagKNAT5a通过增强杨树木质部细胞伸长和次生壁形成促进植物生长
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-07 DOI: 10.1093/hr/uhaf125
Li-Chao Huang, Jian-Xin Lai, Xin Tian, Yu-Yu Li, Yu-Han Chen, Yi An, Cheng Jiang, Ning-Ning Chen, Meng-Zhu Lu, Jin Zhang
{"title":"PagKNAT5a Promotes Plant Growth by Enhancing Xylem Cell Elongation and Secondary Wall Formation in Poplar","authors":"Li-Chao Huang, Jian-Xin Lai, Xin Tian, Yu-Yu Li, Yu-Han Chen, Yi An, Cheng Jiang, Ning-Ning Chen, Meng-Zhu Lu, Jin Zhang","doi":"10.1093/hr/uhaf125","DOIUrl":"https://doi.org/10.1093/hr/uhaf125","url":null,"abstract":"Investigating the regulatory mechanisms that govern plant growth is crucial for developing high-yield wood varieties. In this context, the KNOX gene family has been identified as a significant regulator of plant growth. Our study focuses on PagKNAT5a, a class II member of the KNOX gene family, which has been found to promote the growth of poplar. Transgenic plants overexpressing PagKNAT5a exhibited significant increases in both plant height and stem diameter compared to wild-type controls. Histochemical analyses revealed that these overexpression lines had elongated xylem vessels and fiber cells, which correlated with elevated auxin levels. Additionally, we observed thickened secondary cell walls and increased lignin content in the fiber cells of these transgenic lines. Further protein interaction assays indicated that PagKNAT5a physically interacts with MYB46, a crucial regulator of secondary cell wall biosynthesis. This interaction activates downstream MYB-responsive elements (SMREs), leading to the upregulation of lignin biosynthesis genes driven by these cis-acting elements. Moreover, the increased photosynthetic rate observed in the overexpression lines is likely to significantly support overall plant development. Our findings suggest that PagKNAT5a facilitates the longitudinal elongation of vascular cells by modulating auxin levels, while simultaneously promoting the radial growth of xylem tissue through the activation of the MYB46-mediated lignin biosynthesis pathway. The functional analysis of PagKNAT5a highlights its potential for improving wood yield in forestry applications.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"48 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920173","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
Two aquaporins, LcPIP1;4 and LcPIP1;4a, cooperatively regulate the onset of dormancy of the terminal buds in evergreen perennial litchi (Litchi chinensis Sonn.) 两种水通道蛋白LcPIP1;4和LcPIP1;4a协同调节常绿多年生荔枝(litchi chinensis Sonn.)顶芽的休眠。
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-07 DOI: 10.1093/hr/uhaf122
Xue Tian, Zhi-Qun Zhong, Yu Qi, Meng-Meng Ma, Ming-Chao Yang, Dong-Cheng Li, Fang-Yi Zhang, Hui-Cong Wang, Ji-Yuan Shen, Ren-Fang Zeng, Xu-Ming Huang
{"title":"Two aquaporins, LcPIP1;4 and LcPIP1;4a, cooperatively regulate the onset of dormancy of the terminal buds in evergreen perennial litchi (Litchi chinensis Sonn.)","authors":"Xue Tian, Zhi-Qun Zhong, Yu Qi, Meng-Meng Ma, Ming-Chao Yang, Dong-Cheng Li, Fang-Yi Zhang, Hui-Cong Wang, Ji-Yuan Shen, Ren-Fang Zeng, Xu-Ming Huang","doi":"10.1093/hr/uhaf122","DOIUrl":"https://doi.org/10.1093/hr/uhaf122","url":null,"abstract":"Although extensively studied in various plants, the roles of aquaporin proteins in litchi remain unclear. In this study, low moisture content was observed in the dormant terminal buds of litchi. Transcriptome analysis revealed that two aquaporin genes, PLASMA MEMBRANE INTRINSIC PROTEIN 1;4 (LcPIP1;4) and LcPIP1;5, could be remarkably inhibited by exogenous ethylene (ETH), which also reduced the moisture content of litchi buds. Quantitative real-time PCR assays indicated that LcPIP1;4 expression was relatively elevated in the dormancy stage of litchi terminal buds. Inhibition of LcPIP1;4 in the buds of litchi during the growth stage delayed the onset of dormancy, resulting in a significantly reduced dormancy rate and increased moisture content. Further study indicated that LcPIP1;4 interacts with LcPIP1;4a, and they are capable of self-interaction. Silencing of LcPIP1;4a in litchi buds resulted in a phenotype consistent with silencing of LcPIP1;4. Additionally, simultaneous silencing of both LcPIP1;4 and LcPIP1;4a resulted in a more severe bud dormancy phenotype. Moreover, LcPIP1;4 was directly upregulated by LcRAP2.4. Silencing of LcRAP2.4 also delayed the onset of dormancy in litchi terminal buds, which is regulated by LcSVP2. ETH treatment at 1000 mg/L significantly downregulated the expression of LcPIP1;4 and LcRAP2.4, but had no significant effect on LcPIP1;4a. In contrast, ABA treatment at 200 mg/L significantly upregulated the expression of LcPIP1;4, LcPIP1;4a, and LcRAP2.4. Combined treatment with ETH and ABA exerted a stronger inhibitory effect on the budbreak and upregulated LcPIP1;4 and LcRAP2.4 to lower degrees than ABA alone, suggesting that ABA reversed the inhibitory effect of ETH on expression of LcPIP1;4 and LcRAP2.4. ABA treatment and combined treatment with ETH and ABA effectively reduced the moisture content of the terminal buds. These results demonstrate that LcRAP2,4, LcPIP1;4, and LcPIP1;4a play a vital role in dormancy onset of litchi terminal buds by regulating moisture levels.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"14 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-07","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920174","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
Telomere to telomere flax (Linum usitatissimum L.) genome assembly Unlocks insights beyond fatty acid metabolism pathways 端粒到端粒亚麻(Linum usitatissimum L.)基因组组装揭示了脂肪酸代谢途径之外的见解
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-06 DOI: 10.1093/hr/uhaf127
Jianyu Lu, Hanlu Wu, Fu Wang, Jinxi Li, Yifei Wang, Qian Zhao, Yingping Wang, Xiaonan Wang, Xiujuan Lei, Ruidong Sun, Jun Zhang, Aisheng Xiong, Michael K Deyholos, Jian Zhang
{"title":"Telomere to telomere flax (Linum usitatissimum L.) genome assembly Unlocks insights beyond fatty acid metabolism pathways","authors":"Jianyu Lu, Hanlu Wu, Fu Wang, Jinxi Li, Yifei Wang, Qian Zhao, Yingping Wang, Xiaonan Wang, Xiujuan Lei, Ruidong Sun, Jun Zhang, Aisheng Xiong, Michael K Deyholos, Jian Zhang","doi":"10.1093/hr/uhaf127","DOIUrl":"https://doi.org/10.1093/hr/uhaf127","url":null,"abstract":"One of China's most important resources is flax (Linum usitatissimum L.), an ancient crop with significant nutritional and therapeutic benefits. Despite its importance, existing flax reference genomes remain incomplete, with many unassembled sequences. Here, we report a gapless 482.51 Mb telomere-to-telomere (T2T) flax genome assembly, predicting 46,634 genes, of which 42,805 were functionally annotated. Repetitive sequences constitute 60.05% of the genome, and we identified 30 telomeres and 15 centromeres across the chromosomes. Whole-genome duplication (WGD) events were detected at approximately 11.5, 53.5, and 114 million years ago (MYA) based on synonymous substitution rates (Ks). The T2T assembly enabled the reconstruction of the fatty acid metabolic pathway, identifying 49 related genes, including 6 newly annotated ones. Furthermore, genomic co-localization was observed between fatty acid metabolism pathway-related genes and transposable elements, suggesting that functional differentiation of these genes in flax evolution may have occurred through transposon-mediated duplication events. Phylogenetic analysis of SAD and FAD gene families revealed that FAD genes segregate into FAD2 and FAD3/7/8 subfamilies. Gene structure and motif analyses demonstrated conserved exon-intron architectures and motif organization within each phylogenetic clade of SAD and FAD genes. Promoter region characterization identified numerous cis-acting elements responsive to phytohormones (MeJA and abscisic acid) and abiotic stresses (low temperature and anaerobic induction) in both SAD and FAD genes. Our knowledge of the evolution of the flax genome is improved by this excellent genome assembly, which also offers a strong basis for enhancing agricultural attributes and speeding up molecular breeding.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"119 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920175","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
Simulation of dry matter partitioning in cucumber fruits: reflecting gas exchange characteristics based on leaf position and cropping type 黄瓜果实干物质分配的模拟:反映叶片位置和种植类型的气体交换特征
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-06 DOI: 10.1093/hr/uhaf124
Ha Rang Shin, Yu Hyun Moon, Ha Seon Sim, Tae Yeon Lee, Soo Bin Jung, Yong Jun Kim, Na Kyoung Kim, Jin Woo Lee, Tae Hyun Kim, Seunghyun Ban, Sung Kyeom Kim
{"title":"Simulation of dry matter partitioning in cucumber fruits: reflecting gas exchange characteristics based on leaf position and cropping type","authors":"Ha Rang Shin, Yu Hyun Moon, Ha Seon Sim, Tae Yeon Lee, Soo Bin Jung, Yong Jun Kim, Na Kyoung Kim, Jin Woo Lee, Tae Hyun Kim, Seunghyun Ban, Sung Kyeom Kim","doi":"10.1093/hr/uhaf124","DOIUrl":"https://doi.org/10.1093/hr/uhaf124","url":null,"abstract":"This study aimed to predict dry matter partitioning in cucumber fruit (Cucumis sativus L.) by developing a simulation model that integrates photosynthetic characteristics based on leaf age and cropping type. Leaf gas exchange, growth, and environmental data from semi-forcing and forcing cropping types were used to calibrate models including the Farquhar-von Caemmerer-Berry (FvCB) model and other growth-related models. The FvCB model revealed reduced Vcmax and Jmax values in older leaves across all cropping types, with semi-forcing crops showing higher photosynthetic capacities than forcing crops. Simulation results showed that, in predicting dry matter partitioning to fruit, the leaf position-specific simulation model exhibited higher average R2 and lower RMSE (g m-2) compared to the leaf position-independent model, which applied the middle leaf FvCB model across all leaf ranks. Additionally, bias comparisons indicated greater consistency in the leaf position-specific model. This approach allows growers to optimize environmental strategies by utilizing photosynthetic data form each leaf position. However, to further improve canopy-level predictions, future models should incorporate the temperature dependence of mesophyll conductance and the effects of photoperiodicity. This study underscores the value of integrating physiological and environmental complexities into crop simulation models, providing a foundation for enhanced predictions and the development of improved crop management strategies across various cultivation scenarios.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"37 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-06","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143920172","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
CaSun1, a SUN family protein, governs the pathogenicity of Colletotrichum camelliae by recruiting CaAtg8 to promote mitophagy CaSun1是一种SUN家族蛋白,通过招募caat8促进线粒体自噬来控制茶树炭素的致病性
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-02 DOI: 10.1093/hr/uhaf121
Shuai Meng, Shufen Chao, Meng Xiong, Longjun Cheng, Yu Sun, Li Wang, Ya Chen, Sadhna Jagernath Jane, Chaoxi Luo, Jie Chen
{"title":"CaSun1, a SUN family protein, governs the pathogenicity of Colletotrichum camelliae by recruiting CaAtg8 to promote mitophagy","authors":"Shuai Meng, Shufen Chao, Meng Xiong, Longjun Cheng, Yu Sun, Li Wang, Ya Chen, Sadhna Jagernath Jane, Chaoxi Luo, Jie Chen","doi":"10.1093/hr/uhaf121","DOIUrl":"https://doi.org/10.1093/hr/uhaf121","url":null,"abstract":"Camellia oleifera, a woody oilseed plant native to China, is highly susceptible to anthracnose, a fungal disease that poses a significant threat to its yield and quality. Mitophagy, a specialized form of autophagy that specifically targets dysfunctional mitochondria, is crucial for cellular homeostasis, stress response, and pathogenesis in fungi. The proteins that potentially participate in mitophagy in Colletotrichum camelliae, were identified herein using immunoprecipitation-mass spectrometry (IP-MS) by screening for the potential protein interactors of the core autophagy-related protein, CaAtg8. Among the identified mitochondria-associated proteins, CaSun1 was selected for further investigation. Phenotypic analyses revealed that CaSun1 is a critical regulator of vegetative growth, conidiation, and pathogenicity. CaSun1 localized to the mitochondria, consistent with the conserved function of SUN family proteins. Notably, the findings revealed that CaSun1 was essential for mitophagy and co-localized with CaAtg8 during nitrogen starvation. Functional analyses demonstrated that CaSun1-mediated mitophagy is vital for the growth of invasive hyphae and pathogenicity in C. camelliae. In summary, our findings indicated that CaSun1 mediates mitophagy by facilitating the recruitment of CaAtg8 in C. camelliae, thereby contributing to the establishment of anthracnose. This study provided novel insights into the molecular mechanisms underlying the pathogenesis of fungal infections and identified a potential target for disease control.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"96 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-02","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143898295","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
Scaffold protein RhCASPL1D1 stabilizes RhPIP2 aquaporins and promotes flower recovery after dehydration in rose (Rosa hybrida) 支架蛋白RhCASPL1D1稳定RhPIP2水通道蛋白,促进玫瑰脱水后花朵恢复
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-01 DOI: 10.1093/hr/uhaf119
Kun Liu, Tao Zhang, Siqi Zhao, Jin Chen, Wentong Zhou, Siyu Chen, Yubi Su, Qinglin Liu, Junping Gao, Changqing Zhang
{"title":"Scaffold protein RhCASPL1D1 stabilizes RhPIP2 aquaporins and promotes flower recovery after dehydration in rose (Rosa hybrida)","authors":"Kun Liu, Tao Zhang, Siqi Zhao, Jin Chen, Wentong Zhou, Siyu Chen, Yubi Su, Qinglin Liu, Junping Gao, Changqing Zhang","doi":"10.1093/hr/uhaf119","DOIUrl":"https://doi.org/10.1093/hr/uhaf119","url":null,"abstract":"Water deficit during flowering can lead to petal wilting, necrosis, and sterility, severely limiting crop fertilization and yield. Therefore, rapid recovery of floral organs after dehydration is essential for angiosperms to achieve their full reproductive potential. Aquaporins (AQPs) are bidirectional membrane channels mediating water transmembrane transport. Plasma membrane intrinsic proteins (PIPs), one of AQP subfamily, play a key role in flower opening and dehydration responses. However, it still needs to be elucidated how PIPs are involved in flower recovery after stress. Cut rose (Rosa hybrida), a globally important ornamental flower, undergoes dehydration and rehydration during the postharvest process. Here, we show that the scaffold protein-encoding gene CASP-LIKE PROTEIN 1D1 (RhCASPL1D1), expressed during flower opening and dehydration, promotes flower recovery after dehydration. Silencing RhCASPL1D1 in rose petals and calli hindered cell recovery following dehydration and reduced the rate of water uptake, whereas RhCASPL1D1 overexpression had the opposite effect. Ethylene upregulated RhCASPL1D1 expression, and RhCASPL1D1 physically interacted with RhPIP2s at the plasma membrane. This interaction facilitated RhPIP2s retention to delay its degradation at the plasma membrane and enhanced proteins abundance under dehydration stress. Taken together, our findings reveal a potential mechanism involved in RhCASPL1D1 scaffold regulating flower recovery after dehydration stress.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"11 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143893497","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
Optimization and application of genome prediction model in rapeseed: flowering time, yield components and oil content as examples 油菜基因组预测模型的优化与应用——以花期、产量组成和含油量为例
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-01 DOI: 10.1093/hr/uhaf115
Wenkai Yu, Xinao Wang, Hui Wang, Wenxiang Wang, Hongtao Cheng, Desheng Mei, Lixi Jiang, Qiong Hu, Jia Liu
{"title":"Optimization and application of genome prediction model in rapeseed: flowering time, yield components and oil content as examples","authors":"Wenkai Yu, Xinao Wang, Hui Wang, Wenxiang Wang, Hongtao Cheng, Desheng Mei, Lixi Jiang, Qiong Hu, Jia Liu","doi":"10.1093/hr/uhaf115","DOIUrl":"https://doi.org/10.1093/hr/uhaf115","url":null,"abstract":"Rapeseed is the second-largest oilseed crop in the world with short domestication and breeding history. This study developed a batch of genomic prediction models for flowering time, oil content and yield components in rapeseed. Using worldwide 404 breeding lines, the optimal prediction model for flowering time, and five quality and yield traits was established by comparison with efficient traditional models and machine learning models. The results indicate that QTLs and significant variations identified by GWAS can significantly improve the prediction accuracy of complex traits, achieving over 90% accuracy in predicting flowering time and thousand grain weight. The GBLUP and Bayes-Lasso models provided the most accurate prediction overall, while machine learning models such as GBDT (Gradient Boosting Decision Trees) exhibited strong predictive performance. Our study provides genome selection solution for the high prediction accuracy and selection of complex traits in rapeseed breeding. The use of a diverse panel of 404 worldwide lines ensures that the findings are broadly applicable across different rapeseed breeding programs.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"46 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143893495","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
Unlocking the molecular secrets of Paeonia plants: advances in key gene mining and molecular breeding technology 揭开芍药植物的分子秘密:关键基因挖掘和分子育种技术进展
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-01 DOI: 10.1093/hr/uhaf090
Daqiu Zhao, Honglei An, Jun Tao
{"title":"Unlocking the molecular secrets of Paeonia plants: advances in key gene mining and molecular breeding technology","authors":"Daqiu Zhao, Honglei An, Jun Tao","doi":"10.1093/hr/uhaf090","DOIUrl":"https://doi.org/10.1093/hr/uhaf090","url":null,"abstract":"Paeonia plants are famous for their ornamental, medicinal and oil values. Due to the popularity of seed oil and cut flowers in the market, the mechanisms underlying related traits of Paeonia plants have been fascinating, and the research work on them has increased rapidly in recent years, urging a comprehensive review of their research progress. To unlock the molecular secrets of Paeonia plants, we first summarize the latest advances in their genome research. More importantly, we emphasize the key genes involved in plant growth and development processes, such as bud dormancy, flowering regulation, seed oil formation, flower coloration, stem strength regulation, fragrance emission, as well as plant resistance to stress including drought, high-temperature, low-temperature, salt and waterlogging stresses and biotic stress. In addition, the advances in molecular breeding technology of Paeonia plants are highlighted, such as molecular marker, genetic map, localization of QTLs, tissue culture and genetic transformation system. This review covers advances in the past decades and provides valuable insights into the perspectives for the key gene mining and molecular breeding technology of Paeonia plants, which would breed new Paeonia varieties through molecular breeding technology.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"18 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143893498","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
Phenotypic dynamics and temporal heritability of tomato architectural traits using an unmanned ground vehicle-based plant phenotyping system 基于无人地面车辆植物表型系统的番茄建筑性状的表型动力学和时间遗传力
IF 8.7 1区 农林科学
Horticulture Research Pub Date : 2025-05-01 DOI: 10.1093/hr/uhaf109
Pengyao Xie, Xin Yang, Leisen Fang, Tonglin Wang, Jirong Zheng, Yu Jiang, Haiyan Cen
{"title":"Phenotypic dynamics and temporal heritability of tomato architectural traits using an unmanned ground vehicle-based plant phenotyping system","authors":"Pengyao Xie, Xin Yang, Leisen Fang, Tonglin Wang, Jirong Zheng, Yu Jiang, Haiyan Cen","doi":"10.1093/hr/uhaf109","DOIUrl":"https://doi.org/10.1093/hr/uhaf109","url":null,"abstract":"Large-scale manual measurements of plant architectural traits in tomato growth are laborious and subjective, hindering deeper understanding of temporal variations in gene expression heterogeneity. This study develops a high-throughput approach for characterizing tomato architectural traits at different growth stages and mapping temporal broad-sense heritability using an unmanned ground vehicle-based plant phenotyping system. The SegFormer with fusion of multispectral and depth imaging modalities was employed to semantically segment plant organs from the registered RGB-D and multispectral images. Organ point clouds were then generated and clustered into instances. Finally, six key architectural traits, including fruit spacing (FS), inflorescence height (IH), stem thickness (ST), leaf spacing (LS), total leaf area (TLA), and leaf inclination angle (LIA) were extracted and the temporal broad-sense heritability folds were plotted. The RMSEs of the estimated FS, IH, ST and LS were 0.014 m, 0.043 m, 0.003 m and 0.015 m. The visualizations of the estimated TLA and LIA matched the actual growth trends. The broad-sense heritability of the extracted traits exhibited different trends across the growth stages: i) ST, IH, and FS had a gradually increased broad sense heritability over time, ii) LS and LIA had a decreasing trend, and iii) TLA showed fluctuations (i.e., an M-shaped pattern) of the broad sense heritability throughout the growth period. The developed system and analytical approach are promising tools for accurate and rapid characterization of spatiotemporal changes of tomato plant architecture in controlled environments, laying the foundation for efficient crop breeding and precision production management in the future.","PeriodicalId":13179,"journal":{"name":"Horticulture Research","volume":"34 1","pages":""},"PeriodicalIF":8.7,"publicationDate":"2025-05-01","publicationTypes":"Journal Article","fieldsOfStudy":null,"isOpenAccess":false,"openAccessPdf":"","citationCount":null,"resultStr":null,"platform":"Semanticscholar","paperid":"143893496","PeriodicalName":null,"FirstCategoryId":null,"ListUrlMain":null,"RegionNum":1,"RegionCategory":"农林科学","ArticlePicture":[],"TitleCN":null,"AbstractTextCN":null,"PMCID":"","EPubDate":null,"PubModel":null,"JCR":null,"JCRName":null,"Score":null,"Total":0}
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