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Construction of apricot variety search engine based on deep learning

Horticultural Plant Journal 2024年第2期10卷 387-397页

作者： Chen Chen Lin Wang Huimin Liu Jing Liu Wanyu Xu Mengzhen Huang Ningning Gou Chu Wang Haikun Bai Gengjie Jia Tana Wuyun state Key Laboratory of tree Genetics and Breeding Research Institute of Non-timber ForestryChinese Academy of ForestryZhengzhouHenan 450003China Shenzhen Branch Guangdong Laboratory of Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of Agriculture and Rural AffairsAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhenGuangdong 518120China Kernel-Apricot engineering and technology research center of state forestry and grassland administration ZhengzhouHenan 450003China Key Laboratory of Non-timber Forest Germplasm Enhancement and Utilization of National forestry and grassland administration ZhengzhouHenan 450003China

Apricot has a long history of cultivation and has many varieties and types. The traditional variety identification methods are timeconsuming and labor-consuming, posing grand challenges to apricot resource management. Tool development in this regard will help researchers quickly identify variety information. This study photographed apricot fruits outdoors and indoors and constructed a dataset that can precisely classify the fruits using a U-net model (F-score:99%), which helps to obtain the fruit's size, shape, and color features. Meanwhile, a variety search engine was constructed, which can search and identify variety from the database according to the above features. Besides, a mobile and web application (ApricotView) was developed, and the construction mode can be also applied to other varieties of fruit ***, we have collected four difficult-to-identify seed datasets and used the VGG16 model for training, with an accuracy of 97%, which provided an important basis for ApricotView. To address the difficulties in data collection bottlenecking apricot phenomics research, we developed the first apricot database platform of its kind (ApricotDIAP, http://***/) to accumulate, manage, and publicize scientific data of apricot.

关键词： Apricot Variety Convolutional neural network Deep learning Database platform Mobile application Image retrieval

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Indirect somatic embryogenesis and regeneration of Fraxinus mandshurica plants via callus tissue

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Journal of forestry research 2021年第4期32卷 1613-1625页

作者： Yang Liu Cheng Wei Hao Wang Xiao Ma Hailong Shen Ling Yang state Key Laboratory of tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040People’s Republic of China state forestry and grassland administration engineering technology research center of native tree species Harbin 150040People’s Republic of China

Somatic embryogenesis of Fraxinus mandshurica has the problems of low somatic embryo(SE) yield,unsynchronized SE development,and a high percentage of deformed *** aimed to improve *** SE production by synchronizing SE development,improving SE quality,and inducing root formation to obtain complete regenerated *** of immature zygotic embryos of *** were induced to form callus and then *** SE induction percentage from explants differed among 32 mother trees,and the one with the highest SE induction percentage(29.8%) was used for further *** highest callus induction percentage was94.2% on 1/2-strength Murashige and Skoog medium(MS1/2)supplemented with 0.15 mg·L^(-1) naphthalene acetic *** highest callus proliferation coefficient(240.5) was obtained on McCown's Woody Plant Medium containing 0.1 mg·L^(-1)6-benzyl adenine and 0.15 mg·L^(-1) 2,4-dichlorophenoxyacetic *** highest number of SEs(1020.5 g~(-1) fresh weight) was obtained on MS1/2 medium supplemented with1 mg·L^(-1) *** highest number of cotyledon embryos(397/g fresh weight) was obtained by incubating materials on medium containing 1 mg·L^(-1) abscisic acid and then applying a drying *** cotyledon embryos were milky white,uniformly sized(average length 4.7 mm),and 80% of them were *** SE rooting percentage on 1/2 MS medium containing 0.01 mg·L^(-1) NAA was 37.5%.Overall,the germination percentage of SEs was 26.4%,and complete regenerated plants were obtained after transplanting and *** results provide more possibilities for the preservation and breeding of ***.

关键词： Fraxinus mandshurica Somatic embryogenesis Callus induction Cell differentiation Plant regeneration

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Site index for Chinese fir plantations varies with climatic and soil factors in southern China

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Journal of forestry research 2022年第6期33卷 1765-1780页

作者： Xiaoyan Li Aiguo Duan Jianguo Zhang state Key Laboratory of tree Genetics and Breeding Key Laboratory of Tree Breeding and Cultivation of National Forestry and Grassland AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091People’s Republic of China Collaborative Innovation center of Sustainable forestry in Southern China Nanjing Forestry UniversityNanjing 210037People’s Republic of China

Chinese fir[Cunninghamia lanceolata(Lamb.)Hook.]has a large native distribution range in southern ***,we tested differences in productivity of Chinese fir plantations in different climatic regions and screened the main environmental factors affecting site productivity in each *** of a Chinese fir site index with climatic factors and the soil physiochemical properties of five soil layers were examined in a long-term positioning observation trial comprising a total of 45 permanent plots in Fujian(eastern region in the middle subtropics),Guangxi(south subtropics)and Sichuan(central region in the middle subtropics)in southern *** mixed effects models were developed to predict the site index for Chinese fir,which was found to vary significantly among different climatic *** P,total N,bulk density and total K were dominant predictors of site index in three climatic *** regional linear mixed models built using these predictors in the three climatic regions fit well(R~2=0.86–0.97).For the whole study area,the available P in the 0–20-cm soil layer and total N in the 80–100-cm soil layer were the most indicative soil *** was the most important climatic variable influencing the site *** model evaluation results showed that the fitting performance and prediction accuracy of the global site index model using the climatic region as the dummy variable and random parameters and the most important soil factors of the three climatic regions as predictors was higher than that of global site index model using the climatic variable and the most indicative soil variables of the whole study *** results will help with further evaluation of site quality of Chinese fir plantations and the selection of its appropriate sites in southern China as the climatic changes.

关键词： Site productivity Site index Climate Soil Chinese fir

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Genetic diversity and population structure of Robinia pseudoacacia from six improved variety bases in China as revealed by simple sequence repeat markers

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Journal of forestry research 2022年第2期33卷 611-621页

作者： Qi Guo Sen Cao Li Dong Xiuyu Li Jiangtao Zhang Yuanshuai Zhang Zijie Zhang Yuhan Sun Cui Long Yingming Fan Chao Han Peiyao Han Xiaodi Liu Yun Li Beijing Advanced Innovation center for tree Breeding By Molecular Design Engineering Technology Research Center of Black Locust of National Forestry and Grassland AdministrationCollege of Biological Sciences and TechnologyNational Engineering Laboratory for Tree BreedingBeijing Forestry UniversityBeijing 100083P.R.China College of Agriculture Henan University of Science and TechnologyLuoyang 471023P.R.China Henan Academy of forestry Zhengzhou 450008P.R.China Feixian County state Owned Daqingshan Forest Farm Linyi 273400P.R.China

Robinia pseudoacacia is an important afforesta-tion tree introduced to China in *** the present study,we examined the genetic diversity among 687 strains rep-resenting four improved varieties and two secondary prov-enances,comprising 641 clones and 46 ***-one simple sequence repeats(SSRs)were selected through segregation analysis and polymorphism characterization,and all sampled individuals were genotyped using well-characterized SSR *** excluding loci with non-neutral equilibrium,missing locus data and null alleles,we used 36 primer pairs to assess the genetic diversity of these germplasm resources,revealing vast genetic differentiation among the samples,with an average of 8.352 alleles per locus and a mean Shannon′s index of *** the popula-tion level,the partitioning of variability was assessed using analysis of molecular variance,which revealed 93%and 7%variation within and among collection sites,*** clusters were detected using structure analysis,indi-cating a degree of genetic differentiation among the six *** into the genetic diversity and structure of *** provide a theoretical basis for the con-servation,breeding and sustainable development in China.

关键词： Robinia pseudoacacia Genetic diversity Genetic differentiation Microsatellite Population structure Black locust

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Identifi cation and characterization of the bZIP transcription factor family in yellowhorn

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Journal of forestry research 2021年第1期32卷 273-284页

作者： Qiaoying Chang Xin Lu Zhi Liu Zhimin Zheng Song Yu state Key Laboratory of tree Genetics and Breeding School of ForestryNortheast Forestry UniversityHarbin 150040People’s Republic of China The College of Life Science Northeast Forestry UniversityHarbin 150040People’s Republic of China Shiny-Leaved Yellowhorn engineering and technology research center of National forestry and grassland administration Chifeng 024005People’s Republic of China

The basic leucine zipper(bZIP)transcription factor family is one of the largest and most diverse families in plants,regulating plant growth and development and playing an essential role in response to abiotic and biotic ***,little is known about the biological functions of bZIP proteins in yellowhorn(Xanthoceras sorbifolium).Recently,64 XsbZIP genes were identifi ed in the yellowhorn genome and found to be disproportionately distributed in linkage *** XsbZIP proteins clustered into 11 groups based on their phylogenetic relationships with AtbZIP,ZmbZIP and GmbZIP *** intron patterns in the basic and hinge regions and additional conserved motifs were defi ned,both supporting the group classifi cation and possibly contributing to their functional *** to tandem duplication,the segment duplication greatly contributed to the expansion of yellowhorn bZIP *** addition,most XsbZIP genes harbor several stress responsive cis-elements in their promoter ***,the RNA-seq and qRT-PCR data indicated XsbZIP genes were extensively involved in response to various stresses,including salt(NaCl),cold and abscisic acid,with possibly diff erent molecular *** results provide a new understanding of the biological functions of bZIP transcription factors in yellowhorn.

关键词： Yellowhorn(Xanthoceras sorbifolium) bZIP transcription factor Abiotic stress Gene expression pattern

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Picea species from humid continental and temperate marine climates perform better in monsoonal areas of middle latitudes of China

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Journal of forestry research 2021年第4期32卷 1395-1408页

作者： Fangqun Ouyang Jianwei Ma Junchen Wang Lisheng Kong Hanguo Zhang Mulualem Tigabu Junhui Wang state Key Laboratory of tree Genetics and Breeding Key Laboratory of Tree Breeding and Cultivation of State Forestry AdministrationResearch Institute of ForestryChinese Academy of ForestryBeijing 100091People’s Republic of China research Institute of forestry of Xiaolong Mountain Gansu Provincial Key Laboratory of Secondary Forest CultivationGansuPeople’s Republic of China Beijing Botanical Garden Beijing Floriculture Engineering Technology Research CentreBeijing Laboratory of Urban and Rural Ecological EnvironmentBeijingPeople’s Republic of China Department of Biology Centre for Forest BiologyUniversity of VictoriaVictoriaBCCanada state Key Laboratory of tree Genetics and Breeding Northeast Forestry UniversityHarbin 150040People’s Republic of China Swedish University of Agricultural Sciences Southern Swedish Forest Research CenterBox 4923053 AlnarpSweden

Picea *** a prominent component of the boreal,montane,and sub-alpine forests in the Northern Hemisphere,and have substantial economic importance due to their high quality ***,performance and wood properties of the genus have not been systematically evaluated in *** study aimed to examine genetic variations in growth traits,phenology,and wood properties of 17 Picea species,(three from North America,two from Europe,and 12 from China),in response to specific climate factors using a randomized complete block design in a monsoonal,middle latitude area of *** show that all growth traits and wood properties significantly varied among species(P species examined,*** and *** were the tallest with heights of 2.5 and 1.9 m at 9 years old,respectively,90% and 50% greater than the average *** length,number,and angles of both *** and *** were greater than those of the other *** of *** and *** were20-33% greater than the ***-growing species had high quantities of first lateral branches and large top whorl branch *** taller species exhibited greater tracheid lengths and average tracheid lengths to radial central diameter ratios(TL/R_D2),but smaller cell wall thicknesses to tracheid radial lumen diameter ratios(WT/R_D1),which is favorable for pulp *** analysis revealed that height and ring width had significant positive correlations with latitude but strongly negative correlations with *** was positively correlated with average annual rainfalls,but negative correlations with average yearly *** to the increased average annual sunshine at the China test site relative to the seed source,species such as ***,***,***,and *** from wet,humid areas performed better than native *** similar temperatures,precipitation may be the main factor affecting growth,which is beneficial for predicting the extent

关键词： Climate Growth performance Genetic variations Picea Wood properties

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A multi-modal clustering method for traditonal Chinese medicine clinical data via media convergence

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CAAI Transactions on Intelligence technology 2023年第2期8卷 390-400页

作者： Jingna Si Ziwei Tian Dongmei Li Lei Zhang Lei Yao Wenjuan Jiang Jia Liu Runshun Zhang Xiaoping Zhang state Key Laboratory of tree Genetics and Breeding College of Biological Sciences and TechnologyBeijing Forestry UniversityBeijingChina Department of Comparative Plant and Fungal Biology Wellcome Trust Millennium BuildingArdinglyUK School of Information Science and technology Beijing Forestry UniversityBeijingChina engineering research center for forestry‐oriented Intelligent Information Processing National Forestry and Grassland AdministrationBeijingChina National Data center of Traditional Chinese Medicine China Academy of Chinese Medical SciencesBeijingChina University of Wisconsin‐Milwaukee MilwaukeeWisconsinUSA Experimental research center China Academy of Chinese Medical SciencesBeijingChina Guang'anmen Hospital China Academy of Chinese Medical SciencesBeijingChina

Media convergence is a media change led by technological *** media convergence technology to the study of clustering in Chinese medicine can significantly exploit the advantages of media *** consistent and complementary information among multiple modalities through media convergence can provide technical support for *** article presents an approach based on Media Convergence and Graph convolution Encoder Clustering(MCGEC)for traditonal Chinese medicine(TCM)clinical *** feeds modal information and graph structure from media information into a multi-modal graph convolution encoder to obtain the media feature representation learnt from multiple *** captures latent information from various modalities by fusion and optimises the feature representations and network architecture with learnt clustering *** experiment is conducted on real-world multimodal TCM clinical data,including information like images and *** has improved clustering results compared to the generic single-modal clustering methods and the current more advanced multi-modal clustering *** applied to TCM clinical datasets can achieve better *** multimedia features into clustering algorithms offers significant benefits compared to single-modal clustering approaches that simply concatenate features from different *** provides practical technical support for multi-modal clustering in the TCM field incorporating multimedia features.

关键词： graph convolutional encoder media convergence multi-modal clustering traditional Chinese medicine

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Suspension Culture and Somatic Embryogenesis of Korean Pine

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Phyton-International Journal of Experimental Botany 2022年第1期91卷 223-238页

作者： Chunxue Peng Fang Gao Hao Wang Iraida Nikolaevna Tretyakova Alexander Mikhaylovich Nosov Hailong Shen Ling Yang state Key Laboratory of tree Genetics and Breeding School of ForestryNortheast Forestry UniversityHarbin150040China state forestry and grassland administration engineering technology research center of Korean Pine Harbin150040China Laboratory of Forest Genetics and Breeding Institution of the Russian Academy of SciencesV.N.Sukachev Institute of Forest Siberian Branch of RASKrasnoyarsk660036Russia Department of Cell Biology and Institute of Plant Physiology K.A.Timiryazev Russian Academy of SciencesMoscow127276Russia Department of Plant Physiology Biological FacultyLomonosov Moscow State UniversityMoscow119991Russia

Korean pine is an important afforestation tree species in Northeast China,which has a high ecological and economic *** regeneration of somatic embryogenesis using immature zygotic embryos of Korean pine as explants has been successful,it cannot be applied to automation and large-scale ***,we urgently need a method that can increase the output of somatic embryos(SEs)to meet the needs of large-scale *** used Korean pine 1-1 and 1-100 cell lines as research materials to evaluate the effects of inoculum-density,culture time,orbiting speed,vessel volume,plant growth regulator(PGR)concentration,and carbon source on the proliferation of embryogenic tissue(ET).The somatic embryogenesis ability of ET cultured in different liquid suspension media was also *** found that during liquid suspension culture of Korean pine ET,the sedimented cell volume(SCV),fresh weight(FW)and dry weight(DW)were affected by inoculumdensity,culture time,orbiting speed,2,4-D concentration,6-BA concentration and carbon source *** mg⋅mL^(−1)ET were transferred to a 200 mL Erlenmeyer flask containing 20 mL liquid medium,and cultured at 100 rpm/min for 14 days to obtain the maximum *** addition,we also found that SCV,FW and DW were higher when PGRs were reduced in the liquid suspension *** substitution of maltose for sucrose resulted in slow growth of cultures and limited SE yield(13 SEs g^(−1)FW).Although culture proliferation was high at 50 rpm,SE yield was inhibited by 48%compared with 100 rpm(50 rpm=33 SEs g^(−1)FW;100 rpm/min=70 SEs g^(−1)FW).Cultivation in low-concentration PGR(1.15μM⋅L^(−1)2,4-D,0.25μM⋅L^(−1)6-BA)and sucrose liquid medium at 100 rpm/min(80 SEs g^(−1)FW)could not only promote culture proliferation but also increase SE *** determination of the suspension culture scheme of Korean pine ET provides a reference for further expansion to bioreactor culture in the future and lays a foundation for the automatio

关键词： Pinus koraiensis Sieb.et Zucc embryogenic tissue liquid suspension medium cell proliferation

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Transcriptomic and proteomic analyses of far-red light effects in inducing shoot elongation in the presence or absence of paclobutrazol in Chinese pine

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Journal of forestry research 2022年第3期33卷 1033-1043页

作者： Yingtian Guo Shihui Niu Yousry A.El-Kassaby Wei Li National engineering Laboratory for Forest tree Breeding Beijing Advanced Innovation Center for Tree Breeding by Molecular DesignCollege of Biological Sciences and TechnologyBeijing Forestry UniversityBeijing100083People’s Republic of China Department of Forest and Conservation Sciences Faculty of ForestryUniversity of British Columbia2424 Main MallVancouverBCV6T 1Z4Canada

In angiosperms, low red (R)/far-red (FR) ratio light increases gibberellin (GA) levels. GA signaling in conifer seedlings requires FR to promote shoot elongation and reduce the inhibition of shoot elongation induced by paclobutrazol (PAC), yet the effects of far-red light in inducing shoot elongation in the presence or absence of PAC is poorly understood. In this study, transcriptomic and proteomic analyses was used to examine the molecular mechanism of FR regulation of shoot elongation in Chinese pine (Pinus tabuliformis Carr.) seedlings in the presence of PAC. Four treatments were compared: white light + water (WW), FR + water (RW), white light + PAC (WP), and FR + PAC (RP), and 1436 differentially expressed genes (DEGs) and 450 differentially expressed proteins (DEPs) were identified in RW_WW (RW contrast WW), and 1862 DEGs and 481 DEPs in RP_WP (RP contrast WP). Metabolic and signal transduction pathway analyses of DEGs and DEPs in RW_WW and RP_WP, indicated that the former required more energy than the latter. Moreover, gibberellic acid, auxin, and brassinolide are equally important in RW_WW and RP_WP for shoot elongation, except for the ethylene pathway. Amino acid metabolism and cell wall organization were significantly enriched in RW_WW and RP_WP, respectively. In summary, RW_WW and RP_WP had different effects in secondary metabolism, energy metabolism, amino acid metabolism, cell wall organization, and hormone response. These results provide an important theoretical and reference basis for studying the regulatory effect of low R/FR and PAC in conifer shoot elongation.

关键词： Low R/FR ratio Pinus tabuliformis Paclobutrazol Proteome Shoot elongation Transcriptome

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Intraspecific leaf morphological variation in Quercus dentata Thunb.:a comparison of traditional and geometric morphometric methods,a pilot study

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Journal of forestry research 2022年第6期33卷 1751-1764页

作者： Kaiyu Yang Jianghao Wu Xinman Li Xinbo Pang Yangchen Yuan Guohui Qi Minsheng Yang College of forestry Hebei Agricultural UniversityBaoding 071000HebeiPeople’s Republic of China Hebei Key Laboratory for tree Genetic Resources and Forest Protection Baoding 071000HebeiPeople’s Republic of China administration Bureau of Hongyashan state Owned Forest Farm in Yixian County Yixian 074200HebeiPeople’s Republic of China research center for Walnut engineering and technology of Hebei Lincheng 054300HebeiPeople’s Republic of China Institute of Walnut Industry technology of Hebei Province(Xingtai) Lincheng 054300HebeiPeople’s Republic of China

To compare the application of traditional morphometric methods(TMMs)and geometric morphometric methods(GMMs)in the study of intraspecific leaf morphological characters of Quercus dentata,fifteen linear measurement indices and thirteen landmarks of leaves were used to study leaf morphology of three provenances(H1,H2,and H3).In TMMs,principal component analysis(PCA)showed that leaf size–related indices played an important role in population *** least square(PLS)analysis showed that the main morphological characters affecting leaf size were the average depth of the lobes and the length–width ***,the important indices to distinguish the provenances were circularity,leaf width,and length–width *** results of discriminant analysis(DA)showed that 74.0%of H1,68.0%of H2,and 74.0%of H3 were correctly *** analysis showed that the Mahalanobis distances between H1 and H2,H1 and H3,and H2 and H3 were 4.3761,11.4629,and 10.2067,*** GMMs,PCA based on symmetrical components showed that the difference in leaf morphology was mainly due to the changing trend of the leaf apex and base,petiole length,and degree of leaf *** analysis showed that there was a significant covariation between the leaf symmetrical components and size:as the leaf enlarged,the widest part gradually moved up,and the shape changed from nearly oval to *** results showed that 86.0%and 78.0%of H1 and H2,70.0%and 80.0%of H1 and H3,and 82.0%and 76.0%of H2 and H3 were correctly *** variate analysis results showed that the Mahalanobis distances between H1 and H2,H1 and H3,and H2 and H3 were 1.7238,1.5380,and 1.6329,*** GMMs and TMMs showed significant differences in morphology among the three *** provenances,but GMMs had higher classification accuracy and could provide more information about leaf shape,whereas TMMs could provide more information about leaf *** on our results,GMMs are promising in t

关键词： Traditional morphometrics Geometric morphometrics Leaf morphology variation Quercus dentata Intraspecific

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