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Integrating artificial intelligence and high-throughput phenotyping for crop improvement

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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Novel Sources of Combined Resistance Against Rice Root-Knot Nematode and Brown Spot Disease in Oryza rufipogon

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Rice science 2023年第6期30卷 504-508页

作者： Anupam SEKHON Narpinderjeet Kaur DHILLON Dharminder BHATIA Jagjeet Singh LORE Harwinder Singh BUTTAR department of plant Pathology Punjab Agricultural UniversityLudhiana 141004India department of plant breeding and Genetics Punjab Agricultural UniversityLudhiana 141004India

Rice root-knot nematode(RRKN,Meloidogyne graminicola)and brown spot(BS,Drechslera oryzae)are serious constraints on the quality of rice grains,particularly under direct-seeded rice conditions in many parts of the *** rice varieties resistant to RRKN and BS will be the most effective and environmentally friendly management strategy.A total of 93 and 58 Oryza rufipogon accessions were screened against RRKN and BS,respectively,for two years under artificial inoculation *** the 93 *** accessions。

关键词： rufipogon Root Meloidogyne

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The CropGPT project:Call for a global,coordinated effort in precision design breeding driven by Al using biological big data

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Molecular plant 2024年第2期17卷 215-218页

作者： Wanchao Zhu Rui Han Xiaoyang Shang Tao Zhou Chengyong Liang Xiaomeng Qin Hong Chen Zaiwen Feng Hongwei Zhang Xingming Fan Weifu Li Lin Li National Key Laboratory of Crop Genetic Improvement Huazhong Agricultural UniversityWuhan 430070China Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region College of AgronomyNorthwest A&F UniversityYanglingShaanxi712100China College of Informatics Huazhong Agricultural UniversityWuhan 430070China State Key Laboratory of Crop Gene Resources and breeding Institute of Crop ScienceChinese Academy of Agricultural SciencesBeijing 100081China institute of Food Crops Sciences Yunnan Academy of Agricultural Sciences2238 Beijing RoadKunmingYunnan 650200China Hubei Hongshan Laboratory Wuhan 430070China Shenzhen Institute of Nutrition and Health Huazhong Agricultural UniversityWuhan 430070China Shenzhen Branch Guangdong Laboratory for Lingnan Modern AgricultureGenome Analysis Laboratory of the Ministry of AgricultureAgricultural Genomics Institute at ShenzhenChinese Academy of Agricultural SciencesShenzhen 518120China

Since the beginning of humanity,people have been seeking practical solutions to meet their most basic need:*** advent of agriculture greatly increased the food supply and led to a rapid increase in the human *** food production via agriculture can be attributed to both improved crop management practices and crop breeding through ***(crop)breeding has been categorized into four major stages based on the techniques employed(Wallace et al.,2018).

关键词： breeding seeking Wallace

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Characterization of a Novel Weak Allele of RGA1/D1 and Its Potential Application in Rice breeding

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Rice science 2022年第6期29卷 522-534,I0021,I0022页

作者： LIU Yantong LI Ting JIANG Zhishu ZENG Chuihai HE Rong QIU Jiao LIN Xiaoli PENG Limei SONG Yongping ZHOU Dahu CAI Yicong ZHU Changlan FU Junru HE Haohua XU Jie Key Laboratory of Crop Physiology Ecology and Genetic BreedingMinistry of Education/College of AgronomyJiangxi Agricultural UniversityNanchang 330045China

Semi-dwarfing improves the lodging resistance and yield of rice,and the vast majority of modern rice varieties harbor the sd1 allele to decrease plant height,resulting in reduced genetic diversity and negative agronomic ***,exploring alternative sources of dwarfism is imperative for rice ***,we identified a novel RGA1 allele,d1-w,from a local indica variety Xiaolixiang(XLX)using a map-based cloning *** with other rice varieties,RGA1 in XLX contained a unique single nucleotide polymorphism that resulted in an additional transcript and reduced functional RGA1 transcript *** RGA1 from Nipponbare was introduced into XLX to estimate the value of d1-w in rice *** with transgenic XLX plants(XLX^(D1)),XLX exhibited reduced plant height,increased stem strength,lower reactive oxygen species accumulation,delayed senescence,stronger photosynthesis,higher grain yield and quality(including external,milling and nutritional qualities),and enhanced resistance to drought and Rhizoctonia ***,we proposed that the d1-w allele has potential as an excellent dwarfism resource for rice breeding.

关键词： rice weak allele RGA1 dwarf germplasm resource yield grain quality drought resistance sheath blight

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Adding Value to Crop Production Systems by Integrating Forage Cover Crop Grazing

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American Journal of plant Sciences 2024年第3期15卷 180-192页

作者： Robert B. Mitchell Daren D. Redfearn Kenneth P. Vogel Terry J. Klopfenstein Galen Erickson P. Stephen Baenziger Bruce E. Anderson Mary E. Drewnoski Jay Parsons Steven D. Masterson Marty R. Schmer Virginia L. Jin USDA-ARS Wheat Sorghum and Forage Research Unit University of Nebraska-Lincoln Lincoln NE USA department of agronomy and Horticulture University of Nebraska-Lincoln Lincoln NE USA department of Animal Science University of Nebraska-Lincoln Lincoln NE USA department of Agricultural Economics University of Nebraska-Lincoln Lincoln NE USA USDA-ARS Agroecosystem Management Research Unit University of Nebraska-Lincoln Lincoln NE USA

In addition to their value as cereal grains, wheat (Triticum aestivum L.) and triticale (× Triticosecale Wittmack) are important cool-season annual forages and cover crops. Yearling steer (Bos taurus) performance was compared in the spring following autumn establishment as for age cover crops after soybean [Glycine max (L.) Merr.] grain harvest. Replicated pastures (0.4 ha) were no-till seeded in three consecutive years into soybean stubble in autumn, fertilized, and grazed the following spring near Ithaca, NE, USA. Each pasture (n = 3) was continuously stocked in spring with four yearling steers (380 ± 38 kg) for 17, 32, and 28 d in 2005, 2006, and 2007, respectively. In 2005, average daily gain (ADG) for steers grazing triticale exceeded the ADG for wheat by 0.31 kghd-1d-1. In 2006, wheat ADG exceeded that for triticale by 0.12 kghd-1d-1. In 2007, steers grazing wheat lost weight, while steers grazing triticale gained 0.20 kghd-1d-1. Based on the 3-year average animal gains valued at $1.32 kg-1, mean net return ($ ha-1 yr-1) was $62.15 for triticale and $22.55 for wheat. Since these grazed cover crops provide ecosystem services in addition to forage, grazing could be viewed as a mechanism for recovering costs and adds additional value to the system. Based on this 3-year grazing trial, triticale was superior to wheat and likely will provide the most stable beef yearling performance across years with variable weather for the western Cornbelt USA.

关键词： Cover crops Soybean Triticale Wheat

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High-Throughput Field plant Phenotyping:A Self-Supervised Sequential CNN Method to Segment Overlapping plants

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plant Phenomics 2023年第2期5卷 285-294页

作者： Xingche Guo Yumou Qiu Dan Nettleton Patrick S.Schnable department of Statistics Iowa State UniversityAmesIAUSA plant Sciences Institute Iowa State UniversityAmesIAUSA department of agronomy Iowa State UniversityAmesIAUSA

High-throughput plant phenotyping—the use of imaging and remote sensing to record plant growth dynamics—is becoming more widely *** first step in this process is typically plant segmentation,which requires a well-labeled training dataset to enable accurate segmentation of overlapping ***,preparing such training data is both time and labor *** solve this problem,we propose a plant image processing pipeline using a self-supervised sequential convolutional neural network method for in-field phenotyping *** first step uses plant pixels from greenhouse images to segment nonoverlapping in-field plants in an early growth stage and then applies the segmentation results from those early-stage images as training data for the separation of plants at later growth *** proposed pipeline is efficient and self-supervising in the sense that no human-labeled data are *** then combine this approach with functional principal components analysis to reveal the relationship between the growth dynamics of plants and *** show that the proposed pipeline can accurately separate the pixels of foreground plants and estimate their heights when foreground and background plants overlap and can thus be used to efficiently assess the impact of treatments and genotypes on plant growth in a field environment by computer vision *** approach should be useful for answering important scientific questions in the area of high-throughput phenotyping.

关键词： computer preparing plant

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Estimation of alfalfa fall dormancy using spaced plant and sward trials across multiple environments

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Grassland Research 2023年第1期2卷 15-21页

作者： Scott A.Newell Daniel J.Undersander Donald Viands Julie Hansen Steve Orloff Daniel H.Putnam E.Charles Brummer department of plant Sciences University of CaliforniaDavisDavisCaliforniaUSA department of agronomy University of WisconsinMadisonMadisonWisconsinUSA plant breeding&Genetics Section School of Integrated Plant SciencesCornell UniversityIthacaNew YorkUSA Univeristy of California Cooperative Extension YrekaCaliforniaUSA

Background:Alfalfa is a globally important forage *** are characterized by fall dormancy(FD).FD affects biomass yield and winter survival and is used to identify appropriate growing regions of *** has historically been assessed by measuring the natural height of regrowth in autumn of spaced plants in the *** commercial alfalfa is normally grown as a solid planted sward,FD could be different if plants were grown under real production *** objective of this experiment was to assess whether FD ratings obtained from swards were similar to those obtained on spaced ***:We evaluated 20 alfalfa cultivars in field trials established in 2015 at five locations in the United *** harvested the trials in early autumn and measured regrowth plant height approximately 3 weeks later in 2015 and ***:Autumn plant height responded as expected for the established check cultivars in all *** dormancy ratings for cultivars under both management systems were highly ***:Estimating FD from spaced plant height measurements in autumn is very robust,and using height data from sward plots gives equivalent results to that measured in spaced plant *** finding has many practical advantages.

关键词： alfalfa fall dormancy lucerne Medicago sativa plant height

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The OsWRKY72-OsAAT30/OsGSTU26 module mediates reactive oxygen species scavenging to drive heterosis for salt tolerance in hybrid rice

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Journal of Integrative plant Biology 2024年第4期66卷 709-730页

作者： Citao Liu Bigang Mao Yanxia Zhang Lei tian Biao Ma Zhuo Chen Zhongwei Wei Aifu Li Ye Shao Gongye Cheng Lingling Li Wenyu Li Di Zhang Xiaoping Ding Jiangxiang Peng Yulin Peng Jiwai He Nenghui Ye Dingyang Yuan Chengcai Chu Meijuan Duan Hunan Provincial Key Laboratory of Stress Biology College of AgricultureHunan Agricultural UniversityChangsha 410128China State Key Laboratory of Hybrid Rice Hunan Hybrid Rice Research CenterChangsha 410125China College of Agriculture South China Agricultural UniversityGuangzhou 510642China State Key Laboratory of Wheat and Maize Crop Science Center for Crop Genome EngineeringCollege of AgronomyHenan Agricultural UniversityZhengzhou 450002China College of Horticulture Fujian Agriculture and Forestry UniversityFuzhou 350002China department of Computational Medicine and Bioinformatics University of MichiganAnn ArborMI 48109 USA Biobin Data Science Co. Ltd.Changsha 410221China

Hybrid rice(Oryza sativa)generally outperforms its inbred parents in yield and stress tolerance,a phenomenon termed heterosis,but the underlying mechanism is not completely ***,we combined transcriptome,proteome,physiological,and heterosis analyses to examine the salt response of super hybrid rice Chaoyou1000(CY1000).In addition to surpassing the mean values for its two parents(mid-parent heterosis),CY1000 exhibited a higher reactive oxygen species scavenging ability than both its parents(over-parent heterosis or heterobeltiosis).Nonadditive expression and allele-specific gene expression assays showed that the glutathione S-transferase gene OsGSTU26 and the amino acid transporter gene OsAAT30 may have major roles in heterosis for salt tolerance,acting in an overdominant fashion in ***,we identified OsWRKY72 as a common transcription factor that binds and regulates OsGSTU26 and *** salt-sensitive phenotypes were associated with the OsWRKY72^(paternal)genotype or the OsAAT30^(maternal)genotype in core rice germplasm ***72^(paternal)specifically repressed the expression of OsGSTU26 under salt stress,leading to salinity sensitivity,while OsWRKY72^(maternal)specifically repressed OsAAT30,resulting in salinity *** results suggest that the OsWRKY72-OsAAT30/OsGSTU26 module may play an important role in heterosis for salt tolerance in an overdominant fashion in CY1000 hybrid rice,providing valuable clues to elucidate the mechanism of heterosis for salinity tolerance in hybrid rice.

关键词： allele-specific gene expression(ASE) heterosis hybrid rice nonadditive effect(NAE) salt tolerance transcriptome and proteome

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Potential of plant growth-promoting rhizobacteria-plant interactions in mitigating salt stress for sustainable agriculture:A review

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Pedosphere 2022年第2期32卷 223-245页

作者： Kailash Chand KUMAWAT Sharon NAGPAL Poonam SHARMA department of Microbiology Punjab Agricultural UniversityLudhianaPunjab 141004India department of plant breeding and Genetics Punjab Agricultural UniversityLudhianaPunjab 141004India

Soil salinization affecting different crops is one of the serious threats to global food *** salinity affects 20%and 33%of the total cultivated and irrigated agricultural lands,respectively,and has been reported to caused a global crop production loss of 27.3 billion *** conventional approaches,such as using salt-tolerant varieties,saline soil scrapping,flushing,leaching,and adding supplements (e.g.,gypsum and lime),often fail to alleviate *** this context,developing diverse arrays of microbes enhancing crop productivity under saline soil conditions without harming soil health is *** advanced omics approaches have enabled gaining new insights into the structure and metabolic functions of plant-associated beneficial *** genera of salt-tolerating rhizobacteria ameliorating biotic and abiotic stresses have been isolated from different legumes,cereals,vegetables,and oil seeds under extreme alkaline and saline soil *** progress in rhizosphere microbiome research has revived the belief that plants may be more benefited from their association with interacting diverse microbial communities as compared with individual members in a *** the last decade,several salt-tolerating plant growth-promoting rhizobacteria (PGPR) that improve crop production under salt stress have been exploited for the reclamation of saline *** review highlights that the interaction of salt-tolerating microbes with plants improves crop productivity under salinity stress along with potential salt tolerance mechanisms involved and will open new avenues for capitalizing on cultivable diverse microbial communities to strengthen plant salt tolerance and,thus,to refine agricultural practices and production under saline conditions.

关键词： antagonistic activities antioxidant enzymes benefical microbes osmotolerance rhizosphere microbiome salt tolerance sustainable agriculture

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Nucleic Acid Metabolism, Proline Concentration and Antioxidants Enzyme Activity in Canola (Brassica nupus L.) Under Salinity Stress

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Agricultural Sciences in China 2010年第4期9卷 504-511页

作者： Mostafa Heidari department of agronomy and plant breeding University of ZabolZabol P.O. Box 98615-538 Iran

Seedling of five canola genotypes, Hyola 308, Hyola 401, Hyola 60, Option 50 and RGS003, were grown in Hoagland nutrient solution containing S1 = 0, S2 = 100, S3 = 200 and S4 = 300 mmol L-1 NaCl in controlled environment. Proline, antioxidant activities like catalase （CAT）, ascobrate peroxidase （APX） and guaiacol peroxidase （GPX） and some enzyme activities of nucleic acid metabolism were determined in shoot and root 20 days after induction of salinity stress. Results showed application of stress significantly affected plant growth components such as fresh （FW） and dry weight （DW） of canola genotypes. Among the genotypes, RGS003 had the highest reduction of FW and DW in S3 treatment. By increasing NaCl levels from 0 to 300 mmol L-1, the activity of two antioxidant enzymes （APX and CAT） in shoot and root increased but GPX in all of genotypes decreased. The increase in salinity stress, increased proline concentration in both root and shoot tissues of canola genotypes. Hyola 401 genotype had the maximum concentration of proline in root and shoot in S3 treatment. Along with increased salinity stress in all of the studied plants, salinity significantly increased the level of the total nucleic acid and the activity of DNase I in all of salinity treatments and at the S3 level, RGS003 had the maximum concentration of nucleolytic enzyme.

关键词： antioxidant activity proline salinity nucleolytic enzyme canola

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