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Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based plant Height Dynamics for Breeding

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Rice Science 2024年第05期 617-633页

作者： HONG Weiyuan LI Ziqiu FENG Xiangqian QIN Jinhua WANG Aidong JIN Shichao WANG Danying CHEN Song State Key Laboratory of Rice Biology and Breeding China National Rice Research Institute College of Computer Science and Technology Zhejiang Sci-Tech University College of Agriculture Yangtze University plant phenomics Research centre Academy for Advanced Interdisciplinary Studies Nanjing Agricultural University

Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. plant height（PH） dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle（UAV）-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading（IH） and full heading（FH）, and panicle initiation（PI）, and growth period after transplanting（GPAT） were collected during the rice growth stage. PHs were extracted using a digital surface model（DSM） and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest（RF）, support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th（R2= 0.934, RMSE = 0.056 m）. The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features（CF） and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI（R2= 0.834, RMSE = 4.344 d）, IH（R2= 0.877, RMSE = 2.721 d）, and FH（R2= 0.883, RMSE = 2.694 d）. Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.

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Estimating Key Phenological Dates of Multiple Rice Accessions Using Unmanned Aerial Vehicle-Based plant Height Dynamics for Breeding

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Rice science 2024年第5期31卷 617-628,I0066-I0070页

作者： HONG Weiyuan LI Ziqiu FENG Xiangqian QIN Jinhua WANG Aidong JIN Shichao WANG Danying CHEN Song State Key Laboratory of Rice Biology and Breeding China National Rice Research InstituteHangzhou 311400China College of Computer Science and Technology Zhejiang Sci-Tech UniversityHangzhou 310018China College of Agriculture Yangtze UniversityJingzhou 434025China plant phenomics Research centre Academy for Advanced Interdisciplinary StudiesNanjing Agricultural UniversityNanjing 210095China

Efficient and high-quality estimation of key phenological dates in rice is of great significance in breeding work. plant height(PH) dynamics are valuable for estimating phenological dates. However, research on estimating the key phenological dates of multiple rice accessions based on PH dynamics has been limited. In 2022, field traits were collected using unmanned aerial vehicle(UAV)-based images across 435 plots, including 364 rice varieties. PH, dates of initial heading(IH) and full heading(FH), and panicle initiation(PI), and growth period after transplanting(GPAT) were collected during the rice growth stage. PHs were extracted using a digital surface model(DSM) and fitted using Fourier and logistic models. Machine learning algorithms, including multiple linear regression, random forest(RF), support vector regression, least absolute shrinkage and selection operator, and elastic net regression, were employed to estimate phenological dates. Results indicated that the optimal percentile of the DSM for extracting rice PH was the 95th(R^(2) = 0.934, RMSE = 0.056 m). The Fourier model provided a better fit for PH dynamics compared with the logistic models. Additionally, curve features(CF) and GPAT were significantly associated with PI, IH, and FH. The combination of CF and GPAT outperformed the use of CF alone, with RF demonstrating the best performance among the algorithms. Specifically, the combination of CF extracted from the logistic models, GPAT, and RF yielded the best performance for estimating PI(R^(2) = 0.834, RMSE = 4.344 d), IH(R^(2) = 0.877, RMSE = 2.721 d), and FH(R^(2) = 0.883, RMSE = 2.694 d). Overall, UAV-based rice PH dynamics combined with machine learning effectively estimated the key phenological dates of multiple rice accessions, providing a novel approach for investigating key phenological dates in breeding work.

关键词： phenological date plant height unmanned aerial vehicle machine learning rice breeding

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Digital imaging approaches for phenotyping whole plant nitrogen and phosphorus response in Brachypodium distachyon

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Journal of Integrative plant Biology 2014年第8期56卷 781-796页

作者： Richard Poiré Vincent Chochois Xavier R.R.Sirault John P.Vogel Michelle Watt Robert T.Furbank CSIRO plant Industry high resolution plant phenomics centre CSIRO Plant Industry USDA-ARS Western Regional Research Center

This work evaluates the phenotypic response of the model grass （Brachypodium distacbyon （L.） P. Beauv.） to nitrogen and phosphorus nutrition using a combination of imaging techniques and destructive harvest of shoots and roots. Reference line Bd21-3 was grown in pots using 11 phosphorus and 11 nitrogen concentrations to establish a dose-response curve. Shoot biovolume and biomass, root length and biomass, and tissue phosphorus and nitrogen concentrations increased with nutrient concentration. Shoot biovolume, estimated by imaging, was highly correlated with dry weight （R2 〉 0.92） and both biovolume and growth rate responded strongly to nutrient availability. higher nutrient supply increased nodal root length more than other root types. Photochemical efficiency was strongly reduced by low phosphorus concentrations as early as 1 week after germination, suggesting that this measurement may be suitable for high throughput screening of phosphorus response. In contrast, nitrogen concentration had little effect on photochemical efficiency. Changes in biovolume over time were used to compare growth rates of four accessions in response tonitrogen and phosphorus supply. We demonstrate that a time series image-based approach coupled with mathematical modeling provides higher resolution of genotypic response to nutrient supply than traditional destructive techniques and shows promise for high throughput screening and determina- tion of genomic regions associated with superior nutrient use efficiency.

关键词： Nutrients uptake phenomics photosynthesis root shootCitation: Poire R, Chochois V, Sirault XRR, Vogel JP, Watt M, Furbank RT(2o14) Digital imaging approaches for phenotyping whole plantnitrogen and phosphorus response in Brachypodium distachyon.

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C_4 plants as Biofuel Feedstocks: Optimising Biomass Production and Feedstock Quality from a Lignocellulosic Perspective

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Journal of Integrative plant Biology 2011年第2期53卷 120-135页

作者： Caitlin S.Byrt Christopher P.L.Grof Robert T.Furbank School of Environmental and Life Sciences University of NewcastleUniversity Drive CSIRO plant Industry and high resolution plant phenomics centre

The main feedstocks for bioethanol are sugarcane （Saccharum offic- inarum） and maize （Zea mays）, both of which are C4 grasses, highly efficient at converting solar energy into chemical energy, and both are food crops. As the systems for lignocellulosic bioethanol production become more efficient and cost effective, plant biomass from any source may be used as a feedstock for bioethanol production. Thus, a move away from using food plants to make fuel is possible, and sources of biomass such as wood from forestry and plant waste from cropping may be used. However, the bioethanol industry will need a continuous and reliable supply of biomass that can be produced at a low cost and with minimal use of water, fertilizer and arable land. As many C4 plants have high light, water and nitrogen use efficiency, as compared with C3 species, they are ideal as feedstock crops. We consider the productivity and resource use of a number of candidate plant species, and discuss biomass ＇quality＇, that is, the composition of the plant cell wall.

关键词： C4 plants as Biofuel Feedstocks Optimising Biomass Production and Feedstock Quality from a Lignocellulosic Perspective

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Simultaneously quantifying hundreds of acylcarnitines in multiple biological matrices within ten minutes using ultrahigh-performance liquid-chromatography and tandem mass spectrometry

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Journal of Pharmaceutical Analysis 2024年第1期14卷 140-148页

作者： Jingxian Zhang Qinsheng Chen Lianglong Zhang Biru Shi Men Yu Qingxia Huang Huiru Tang State Key Laboratory of Genetic Engineering School of Life SciencesHuman Phenome InstituteZhangjiang Fudan International Innovation CenterMetabonomics and Systems Biology Laboratory at Shanghai International Centre for Molecular PhenomicsZhongshan HospitalFudan UniversityShanghai200032China Wuhan Laboratory for Shanghai Metabolome Institute(SMI)Ltd. Wuhan430000China

Acylcarnitines are metabolic intermediates of fatty acids and branched-chain amino acids having vital biofunctions and pathophysiological significances. Here, we developed a high-throughput method for quantifying hundreds of acylcarnitines in one run using ultrahigh performance liquid chromatography and tandem mass spectrometry (UPLC-MS/MS). This enabled simultaneous quantification of 1136 acylcarnitines (C0–C26) within 10-min with good sensitivity (limit of detection 0.992), accuracy (relative error 0.998) for predicting retention time (tR) of acylcarnitines with no standards and built a database of their multiple reaction monitoring parameters (tR, ion-pairs, and collision energy). Furthermore, we quantified 514 acylcarnitines in human plasma and urine, mouse kidney, liver, heart, lung, and muscle. This provides a rapid method for quantifying acylcarnitines in multiple biological matrices.

关键词： Acylcarnitine UPLC-MS/MS Quantitative structure-retention relationship Molecular phenotype

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The super-pangenome of Populus unveils genomic facets for its adaptation and diversification in widespread forest trees

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Molecular plant 2024年第5期17卷 725-746页

作者： Tingting Shi Xinxin Zhang Yukang Hou Changfu Jia Xuming Dan Yulin Zhang Yuanzhong Jiang Qiang Lai Jiajun Feng Jianju Feng Tao Ma Jiali Wu Shuyu Liu Lei Zhang Zhiqin Long Liyang Chen Nathaniel R.Street Par K.Ingvarsson Jianquan Liu Tongming Yin Jing Wang Key Laboratory for Bio-Resources and Eco-Environment of Ministry of Education College of Life SciencesSichuan UniversityChengduSichuanChina College of Horticulture and Forestry Tarim UniversityAlar 843300China Umea plant Science centre Department of Plant PhysiologyUmea UniversityUmeaVasterbottenSweden Linnean centre for plant Biology Department of Plant BiologyUppsala BioCenterSwedish University of Agricultural SciencesUppsalaSweden The Key Laboratory of Tree Genetics and Biotechnology of Jiangsu Province and Education Department of China Nanjing Forestry UniversityNanjingJiangsuChina

Understanding the underlying mechanisms and links between genome evolution and adaptive innovations stands as a key goal in evolutionary ***,among the world’s most widely distributed and cultivated trees,exhibit extensive phenotypic diversity and environmental *** this study,we present a genus-level super-pangenome comprising 19 Populus genomes,revealing the likely pivotal role of private genes in facilitating local environmental and climate *** the integration of pangenomes with transcriptomes,methylomes,and chromatin accessibility mapping,we unveil that the evolutionary trajectories of pangenes and duplicated genes are closely linked to local genomic landscapes of regulatory and epigenetic architectures,notably CG methylation in gene-body *** comparative genomic analyses have enabled the identification of 142202 structural variants across species that intersect with a significant number of genes and contribute substantially to both phenotypic and adaptive *** have experimentally validated a∼180-bp presence/absence variant affecting the expression of the CUC2 gene,crucial for leaf serration ***,we developed a user-friendly web-based tool encompassing the multi-omics resources associated with the Populus super-pangenome(http://***).Together,the present pioneering super-pangenome resource in forest trees not only aids in the advancement of breeding efforts of this globally important tree genus but also offers valuable insights into potential avenues for comprehending tree biology.

关键词： Populus pangenomes whole-genome duplication structural variation genome evolution

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Integrating artificial intelligence and high-throughput phenotyping for crop improvement

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Journal of Integrative Agriculture 2024年第6期23卷 1787-1802页

作者： Mansoor Sheikh Farooq Iqra Hamadani Ambreen Kumar A Pravin Manzoor Ikra Yong Suk Chung phenomics Laboratory Department of Plant Resources and EnvironmentJeju National UniversityJeju 63234Republic of Korea Council of Scientific&Industrial Research Indian Institute of Integrative MedicinePulwamaJ&K 192301India Animal and Dairy Science University of WisconsinMadisonWI 530706United States of America Division of Fruit Science Faculty of HorticultureSher-e-Kashmir University of Agricultural Sciences and Technology of KashmirSrinagar 190025India

Crop improvement is crucial for addressing the global challenges of food security and sustainable *** advancements in high-throughput phenotyping(HTP)technologies and artificial intelligence(AI)have revolutionized the field,enabling rapid and accurate assessment of crop traits on a large *** integration of AI and machine learning algorithms with HTP data has unlocked new opportunities for crop *** algorithms can analyze and interpret large datasets,and extract meaningful patterns and correlations between phenotypic traits and genetic *** technologies have the potential to revolutionize plant breeding programs by providing breeders with efficient and accurate tools for trait selection,thereby reducing the time and cost required for variety ***,further research and collaboration are needed to overcome the existing challenges and fully unlock the power of HTP and AI in crop *** leveraging AI algorithms,researchers can efficiently analyze phenotypic data,uncover complex patterns,and establish predictive models that enable precise trait selection and crop *** aim of this review is to explore the transformative potential of integrating HTP and AI in crop *** review will encompass an in-depth analysis of recent advances and applications,highlighting the numerous benefits and challenges associated with HTP and AI.

关键词： artificial intelligence crop improvement data analysis high-throughput phenotyping machine learning precision agriculture trait selection

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Chloroplast immunity: A cornerstone of plant defense

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Molecular plant 2024年第5期17卷 686-688页

作者： Jie Liu Pan Gong Ruobin Lu Rosa Lozano-Duran Xueping Zhou Fangfang Li State Key Laboratory for Biology of plant Diseases and Insect Pests Institute of Plant ProtectionChinese Academy of Agricultural SciencesBeijing 100081China State Key Laboratory of Rice Biology Institute of BiotechnologyZhejiang UniversityHangzhouZhejiang 310058China Department of plant Biochemistry Centre for Plant Molecular Biology(ZMBP)Eberhard Karls UniversityTubingen 72076Germany

Increasing evidence supports the notion that pattern-recognition-receptor-mediated immunity goes beyond plasma membrane-to-nucleus *** the findings of the pathways linking plasma membrane and chloroplasts and the functions of stromules and perinuclear chloroplast clustering(PCC)in plant defense,chloroplast immunity has emerged as a cornerstone of plant defense and a target of plant pathogens.

关键词： plant immunity corners

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The genetic basis and process of inbreeding depression in an elite hybrid rice

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Science China(Life Sciences) 2024年第8期67卷 1727-1738页

作者： Xiaodong Xu Yawen Xu Jian Che Xu Han Zhengji Wang Xianmeng Wang Qinghua Zhang Xu Li Qinglu Zhang Jinghua Xiao Xianghua Li Qifa Zhang Yidan Ouyang National Key Laboratory of Crop Genetic Improvement and National centre of plant Gene Research(Wuhan) Hubei Hongshan LaboratoryHuazhong Agricultural UniversityWuhan 430070China

Inbreeding depression refers to the reduced performance arising from increased homozygosity,a phenomenon that is the reverse of heterosis and exists among plants and *** a natural self-pollinated crop with strong heterosis,the mechanism of inbreeding depression in rice is largely *** understand the genetic basis of inbreeding depression,we constructed a successive inbreeding population from the F_(2)to F_(4)generation and observed inbreeding depression of all heterotic traits in the progeny along with the decay of heterozygosity in each *** expected depression effect was largely explained by 13 QTLs showing dominant effects for spikelets per panicle,11 for primary branches,and 12 for secondary branches,and these loci constitute the main correlation between heterosis and inbreeding ***,the genetic basis of inbreeding depression is also distinct from that of heterosis,such that a biased transmission ratio of alleles for QTLs with either dominant or additive effects in four segregation distortion regions would result in minor effects in expected ***,two-locus interactions may change the extent and direction of the depression effects of the target loci,and overall interactions would promote inbreeding depression among *** an F_(2:3)variation population,the actual performance of the loci showing expected depression was evaluated considering the heterozygosity decay in the background after *** found inconsistent or various degrees of background depression from the F_(2)to F_(3)generation assuming different genotypes of the target locus,which may affect the actual depression effect of the locus due to *** results suggest that the genetic architecture of inbreeding depression and heterosis is closely linked but also differs in their intrinsic mechanisms,which expand our understanding of the whole-genome architecture of inbreeding depression.

关键词： rice inbreeding depression spikelet development dominance segregation distortion epistasis

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The combined effects of farm yard manure and boron application on growth,and oil quality of Canola grown under newly reclaimed soils

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Oil Crop Science 2024年第1期9卷 53-59页

作者： Farid Hellal Saied El Sayed Amany Abdel Mohsen Ramadan Doaa M.Abobasha plant Nutrition Department National Research Centre33 El-Behouth St12622DokkiCairoEgypt Botany Department National Research Centre33 El-Behouth St12622DokkiCairoEgypt

Two field experiments were conducted during the main seasons of 2021/2022 at the Research and Production Station of National Research centre in Egypt to investigate the effects of farmyard manure(FYM)and boron on Canola growth,yield,oil yield,and *** results unequivocally demonstrated that the combined application of FYM at a rate of 14.4 ton ha^(-1)with a foliar spray of boron at 100 ppm positively influenced plant characteristics,leading to enhanced growth rates and higher yields compared to the control ***,this integrated approach significantly improved nutrient content by enhancing levels of oil content,carbohydrates,proteins,phenolics,flavonoids,and total soluble *** findings provide compelling evidence that utilizing farm manure along with boron can effectively enhance Canola properties in newly reclaimed soils while promoting sustainable agricultural practices.

关键词： Oil quality Farmyard manure Phytochemical content Canola Yield production

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