|
Alahmad S, Smith D, Katsikis C, Aldiss Z, Brunner SM, Meer SV, Meijer L, Heidariask B, Chenu K, Chapman S, Potgieter AB, Wasson A, Baraibar S, Godoy J, Moody D, Robinson H, Hickey LT (2025). Phenotyping the hidden half: combining UAV phenotyping and machine learning to predict barley root traits in the field. J Exp Bot 76, 5161-5178.
|
|
Amtmann A, Bennett MJ, Henry A (2022). Root phenotypes for the future. Plant Cell Environ 45, 595-601.
|
|
Arsenault JL, Poulcur S, Messier C, Guay R (1995). WinRHlZOTM, a root—measuring system with a unique overlap correction method . HortScience 30, 906.
|
|
Atkinson JA, Pound MP, Bennett MJ, Wells DM (2019). Uncovering the hidden half of plants using new advances in root phenotyping. Curr Opin Biotechnol 55, 1-8.
|
|
Baker DN, Selzner T, Göbbert JH, Scharr H, Riedel M, Hvannberg E Þ, Schnepf A, Zielasko D (2025). VRoot: a VR—based application for manual root system architecture reconstruction. Plant Phenomics 7, 100013.
|
|
Bates GH (1937). A device for the observation of root growth in the soil. Nature 139, 966-967.
|
|
Calderwood A, Siles L, Eastmond PJ, Kurup S, Morris RJ (2023). A causal inference and Bayesian optimisation framework for modelling multi—trait relationships: proof—of—concept using Brassica napus seed yield under controlled conditions . PLoS One 18, e0290429.
|
|
Cannon WA (1911). The Root Habits of Desert Plants. Washington: Carnegie Institution of Washington. pp. 10-11.
|
|
Cao YR, Tian DM, Tang ZX, Liu XN, Hu WJ, Zhang Z, Song SH (2024). OPIA: an open archive of plant images and related phenotypic traits. Nucleic Acids Res 52, D1530-D1537.
|
|
Changdar S, Popovic O, Wacker TS, Markussen B, Dam EB, Thorup—Kristensen K (2023). Non—invasive phenotyping for water and nitrogen uptake by deep roots explored using machine learning. Plant Soil 493, 603-616.
|
|
Chen HY, Xue L, Liu L, Zou GF, Han JX, Dong YB, Cong MZ, Liu YT, Hosseini—Nasab SM (2025). Physics—informed graph neural network for predicting fluid flow in porous media. Pet Sci 22, 4240-4253.
|
|
Chen WL, Koide RT, Adams TS, DeForest JL, Cheng L, Eissenstat DM (2016). Root morphology and mycorrhizal symbioses together shape nutrient foraging strategies of temperate trees. Proc Natl Acad Sci USA 113, 8741-8746.
|
|
Cranmer K, Brehmer J, Louppe G (2020). The frontier of simulation—based inference. Proc Natl Acad Sci USA 117, 30055-30062.
|
|
de S. Nóia—Júnior R, Ruane AC, Athanasiadis IN, Ewert F, Harrison MT, Jägermeyr J, Martre P, Müller C, Palosuo T, Salmerón M, Webber H, Maccarthy DS, Asseng S (2025). Crop models for future food systems. One Earth 8, 101487.
|
|
Dhal SB, Mahanta S, Moore JM, Kalafatis S (2024). Machine learning—based analysis of nutrient and water uptake in hydroponically grown soybeans. Sci Rep 14, 24337.
|
|
Evangelisti E, Turner C, McDowell A, Shenhav L, Yunusov T, Gavrin A, Servante EK, Quan C, Schornack S (2021). Deep learning—based quantification of arbuscular mycorrhizal fungi in plant roots. New Phytol 232, 2207-2219.
|
|
Farooq MA, Gao S, Hassan MA, Huang ZP, Rasheed A, Hearne S, Prasanna B, Li XH, Li HH (2024). Artificial intelligence in plant breeding. Trends Genet 40, 891-908.
|
|
Freschet GT, Roumet C, Comas LH, Weemstra M, Bengough AG, Rewald B, Bardgett RD, De Deyn GB, Johnson D, Klimešová J, Lukac M, McCormack ML, Meier IC, Pagès L, Poorter H, Prieto I, Wurzburger N, Zadworny M, Bagniewska—Zadworna A, Blancaflor EB, Brunner I, Gessler A, Hobbie SE, Iversen CM, Mommer L, Picon—Cochard C, Postma JA, Rose L, Ryser P, Scherer—Lorenzen M, Soudzilovskaia NA, Sun T, Valverde—Barrantes OJ, Weigelt A, York LM, Stokes A (2021). Root traits as drivers of plant and ecosystem functioning: current understanding, pitfalls and future research needs. New Phytol 232, 1123-1158.
|
|
Gaggion N, Ariel F, Daric V, Lambert É, Legendre S, Roulé T, Camoirano A, Milone DH, Crespi M, Blein T, Ferrante E (2021). ChronoRoot: high—throughput phenotyping by deep segmentation networks reveals novel temporal parameters of plant root system architecture. Gigascience 10, giab052.
|
|
Gaitan NC, Batinas BI, Ursu C, Crainiciuc FN (2025). Integrating artificial intelligence into an automated irrigation system. Sensors 25, 1199.
|
|
Ge JK, Zhang RN, He YJ, Sun ZZ, Li Q, Jin SC, Cai J, Zhou Q, Huang M, Wang X, Jiang D (2025). faCRSA: an automated pipeline for high—throughput analysis of crop root system architecture. Crop J 13, 1919-1927.
|
|
Gu HJ, Wang YZ, Peruzzo L, Li BR, Lu Y, Liu XW (2025). Linking winter wheat (Triticum aestivum L.) root traits and root water uptake with electrical resistivity tomography . Agric Water Manag 307, 109247.
|
|
Guerrero—Ramírez NR, Mommer L, Freschet GT, Iversen CM, McCormack ML, Kattge J, Poorter H, van der Plas F, Bergmann J, Kuyper TW, York LM, Bruelheide H, Laughlin DC, Meier IC, Roumet C, Semchenko M, Sweeney CJ, van Ruijven J, Valverde—Barrantes OJ, Aubin I, Catford JA, Manning P, Martin A, Milla R, Minden V, Pausas JG, Smith SW, Soudzilovskaia NA, Ammer C, Butterfield B, Craine J, Cornelissen JHC, de Vries FT, Isaac ME, Kramer K, König C, Lamb EG, Onipchenko VG, Peñuelas J, Reich PB, Rillig MC, Sack L, Shipley B, Tedersoo L, Valladares F, van Bodegom P, Weigelt P, Wright JP, Weigelt A (2021). Global root traits (GRooT) database. Glob Ecol Biogeogr 30, 25-37.
|
|
Harfouche AL, Jacobson DA, Kainer D, Romero JC, Harfouche AH, Scarascia Mugnozza G, Moshelion M, Tuskan GA, Keurentjes JJB, Altman A (2019). Accelerating climate resilient plant breeding by applying next—generation artificial intelligence. Trends Biotechnol 37, 1217-1235.
|
|
Herrero—Huerta M, Raumonen P, Gonzalez—Aguilera D (2022). 4DRoot: root phenotyping software for temporal 3D scans by X—ray computed tomography. Front Plant Sci 13, 986856.
|
|
Hodge A, Berta G, Doussan C, Merchan F, Crespi M (2009). Plant root growth, architecture and function. Plant Soil 321, 153-187.
|
|
Hruska J, Čermák J, Šustek S (1999). Mapping tree root systems with ground—penetrating radar. Tree Physiol 19, 125-130.
|
|
Jafar A, Bibi N, Naqvi RA, Sadeghi—Niaraki A, Jeong D (2024). Revolutionizing agriculture with artificial intelligence: plant disease detection methods, applications, and their limitations. Front Plant Sci 15, 1356260.
|
|
James BR, Bartlett RJ, Amadon JF (1985). A root observation and sampling chamber (rhizotron) for pot studies. Plant Soil 85, 291-293.
|
|
Kamil H, Soulaïmani A, Beljadid A (2025). Physics—informed neural operators for efficient modeling of infiltration in porous media. J Comput Phys 538, 114156.
|
|
Khaliq A, Khan A, Jan S, Umair M, Gulshair A, Ali A, Ali Shah U (2025). AI—driven smart agriculture: an integrated approach for soil analysis, irrigation, and crop—fertilizer recommendations. IEEE Access 13, 141124-141138.
|
|
Khan MA, Gemenet DC, Villordon A (2016). Root system architecture and abiotic stress tolerance: current knowledge in root and tuber crops. Front Plant Sci 7, 1584.
|
|
Klepper B, Kaspar TC (1994). Rhizotrons: their development and use in agricultural research. Agron J 86, 745-753.
|
|
Köckenberger W, Pope JM, Xia Y, Jeffrey KR, Komor E, Callaghan PT (1997). A non—invasive measurement of phloem and xylem water flow in castor bean seedlings by nuclear magnetic resonance microimaging. Planta 201, 53-63.
|
|
Li AC (2023). Image Segmentation and Phenotypic Analysis of In Situ Root Systems in Crops . PhD dissertation. Baoding: Hebei Agricultural University. pp. 1-103. (in Chinese with English abstract)
|
|
李安昌 (2023). 作物原位根系图像分割及表型分析技术研究. 博士论文. 保定: 河北农业大学. pp. 1-103.
|
|
Li GJ (2024). AI4R: the fifth scientific research paradigm. Bull Chin Acad Sci 39, 1-9. (in Chinese with English abstract)
|
|
李国杰 (2024). 智能化科研(AI4R): 第五科研范式. 中国科学院院刊 39, 1-9.
|
|
Li X, Yu HC (2024). A new paradigm of life science research driven by artificial intelligence. Bull Chin Acad Sci 39, 50-58. (in Chinese with English abstract)
|
|
李鑫, 于汉超 (2024). 人工智能驱动的生命科学研究新范式. 中国科学院院刊 39, 50-58.
|
|
Liu YQ, Wang AW, Li B, Šimůnek J, Liao RK (2024). Combining mathematical models and machine learning algorithms to predict the future regional—scale actual transpiration by maize. Agric Water Manag 303, 109056.
|
|
Lopez G, Ahmadi SH, Amelung W, Athmann M, Ewert F, Gaiser T, Gocke MI, Kautz T, Postma J, Rachmilevitch S, Schaaf G, Schnepf A, Stoschus A, Watt M, Yu P, Seidel SJ (2023). Nutrient deficiency effects on root architecture and root—to—shoot ratio in arable crops. Front Plant Sci 13, 1067498.
|
|
Lynch J (1995). Root architecture and plant productivity. Plant Physiol 109, 7-13.
|
|
Lynch JP (2013). Steep, cheap and deep: an ideotype to optimize water and N acquisition by maize root systems. Ann Bot 112, 347-357.
|
|
Lynch JP (2019). Root phenotypes for improved nutrient capture: an underexploited opportunity for global agriculture. New Phytol 223, 548-564.
|
|
Lynch JP (2022). Harnessing root architecture to address global challenges. Plant J 109, 415-431.
|
|
Macha P (2023). Root2Graph: a Graph—based Semantic Segmentation Architecture for Plant Roots. Master’s thesis. Saskatoon: University of Saskatchewan. pp. 1-77.
|
|
McCormack ML, Guo DL, Iversen CM, Chen WL, Eissenstat DM, Fernandez CW, Li L, Ma CG, Ma ZQ, Poorter H, Reich PB, Zadworny M, Zanne A (2017). Building a better foundation: improving root—trait measurements to understand and model plant and ecosystem processes. New Phytol 215, 27-37.
|
|
McDougall WB (1916). The growth of forest tree roots. Am J Bot 3, 384-392.
|
|
Micikevicius P, Narang S, Alben J, Diamos G, Elsen E, Garcia D, Ginsburg B, Houston M, Kuchaiev O, Venkatesh G, Wu H (2018). Mixed precision training. arXiv.
|
|
Morandage S, Laloy E, Schnepf A, Vereecken H, Vanderborght J (2021). Bayesian inference of root architectural model parameters from synthetic field data. Plant Soil 467, 67-89.
|
|
Mungoli N (2023). Scalable, distributed AI frameworks: leveraging cloud computing for enhanced deep learning performance and efficiency. arXiv.
|
|
Murmu S, Sinha D, Chaurasia H, Sharma S, Das R, Jha GK, Archak S (2024). A review of artificial intelligence—assisted omics techniques in plant defense: current trends and future directions. Front Plant Sci 15, 1292054.
|
|
Nabwire S, Suh HK, Kim MS, Baek I, Cho BK (2021). Review: application of artificial intelligence in phenomics. Sensors 21, 4363.
|
|
Nigar N, Muhammad Faisal H, Umer M, Oki O, Manappattukunnel Lukose J (2024). Improving plant disease classification with deep—learning—based prediction model using explainable artificial intelligence. IEEE Access 12, 100005-100014.
|
|
Persson H (1978). Root dynamics in a young Scots pine stand in central Sweden. Oikos 30, 508-519.
|
|
Petrovic AM, Siebert JE, Rieke PE (1982). Soil bulk density analysis in three dimensions by computed tomographic scanning. Soil Sci Soc Am J 46, 445-450.
|
|
Pierz LD, Heslinga DR, Buell CR, Haus MJ (2023). An image—based technique for automated root disease severity assessment using PlantCV. Appl Plant Sci 11, e11507.
|
|
Postma JA, Lynch JP (2012). Complementarity in root architecture for nutrient uptake in ancient maize/bean and maize/bean/squash polycultures. Ann Bot 110, 521-534.
|
|
Pound MP, Atkinson JA, Townsend AJ, Wilson MH, Griffiths M, Jackson AS, Bulat A, Tzimiropoulos G, Wells DM, Murchie EH, Pridmore TP, French AP (2017). Deep machine learning provides state—of—the—art performance in image—based plant phenotyping. Gigascience 6, gix083.
|
|
Rahman MA, Chakraborty NR, Sufiun A, Banshal SK, Tajnin FR (2024). An AIoT—based hydroponic system for crop recommendation and nutrient parameter monitorization. Smart Agric Technol 8, 100472.
|
|
Raza S, Pandey BK, Hawkesford MJ, Griffiths S, Bennett MJ, Mooney SJ (2025). Future crop breeding needs to consider future soils. Nat Plants 11, 939-941.
|
|
Rellán—Álvarez R, Lobet G, Lindner H, Pradier PL, Sebastian J, Yee MC, Geng Y, Trontin C, LaRue T, Schrager—Lavelle A, Haney CH, Nieu R, Maloof J, Vogel JP, Dinneny JR (2015). GLO—Roots: an imaging platform enabling multidimensional characterization of soil—grown root systems. eLife 4, e07597.
|
|
Shahhosseini M, Hu G, Huber I, Archontoulis SV (2021). Coupling machine learning and crop modeling improves crop yield prediction in the US Corn Belt. Sci Rep 11, 1606.
|
|
Sheikh M, Iqra F, Ambreen H, Pravin KA, Ikra M, Chung YS (2024). Integrating artificial intelligence and high—throughput phenotyping for crop improvement. J Integr Agric 23, 1787-1802.
|
|
Shi JW, Xie SY, Li WK, Wang X, Wang JL, Chen YY, Chang YY, Lou QJ, Yang WN (2025). RPT: an integrated root phenotyping toolbox for segmenting and quantifying root system architecture. Plant Biotechnol J 23, 2095-2109.
|
|
Shi WS, Cao J, Zhang Q, Li YHZ, Xu LY (2016). Edge computing: vision and challenges. IEEE Internet Things J 3, 637-646.
|
|
Smith AG, Petersen J, Selvan R, Rasmussen CR (2020). Segmentation of roots in soil with U—Net. Plant Methods 16, 13.
|
|
Soltaninejad M, Sturrock CJ, Griffiths M, Pridmore TP, Pound MP (2020). Three dimensional root CT segmentation using multi—resolution encoder—decoder networks. IEEE Trans Image Process 29, 6667-6679.
|
|
Song H, Panjvani K, Liu ZG, Amar H, Kochian L, Ye SJ, Yang X, Feurtado JA, Chavda K, Chimbo Huatatoca KA, Eramian M (2023). Plant root occlusion inpainting with generative adversarial network. 2023 IEEE/CVF International Conference on Computer Vision Workshops (ICCVW). Paris: IEEE. pp. 531-539.
|
|
Sordo Z, Andeer P, Sethian J, Northen T, Ushizima D (2024). RhizoNet segments plant roots to assess biomass and growth for enabling self—driving labs. Sci Rep 14, 12907.
|
|
Sun BR, Gao YZ, Wu X, Ma HM, Zheng CC, Wang XY, Zhang HL, Li ZJ, Yang HJ (2020). The relative contributions of pH, organic anions, and phosphatase to rhizosphere soil phosphorus mobilization and crop phosphorus uptake in maize/alfalfa polyculture. Plant Soil 447, 117-133.
|
|
Taccari ML, Nuttall J, Chen XH, Wang H, Minnema B, Jimack PK (2022). Attention U—Net as a surrogate model for groundwater prediction. Adv Water Resour 163, 104-169.
|
|
Tennant D (1975). A test of a modified line intersect method of estimating root length. J Ecol 63, 995-1001.
|
|
Teramoto S, Uga Y (2024). Convolutional neural networks combined with conventional filtering to semantically segment plant roots in rapidly scanned X—ray computed tomography volumes with high noise levels. Plant Methods 20, 73.
|
|
Thesma V, Velni JM (2022). Plant root phenotyping using deep conditional GANs and binary semantic segmentation. Sensors 23, 309.
|
|
Trachsel S, Kaeppler SM, Brown KM, Lynch JP (2011). Shovelomics: high throughput phenotyping of maize (Zea mays L.) root architecture in the field . Plant Soil 341, 75-87.
|
|
Weihs BJ, Heuschele DJ, Tang Z, York LM, Zhang ZW, Xu ZY (2024a). The state of the art in root system architecture image analysis using artificial intelligence: a review. Plant Phenomics 6, 0178.
|
|
Weihs BJ, Tang Z, Tian ZZ, Heuschele DJ, Siddique A, Terrill TH, Zhang Z, York LM, Zhang ZW, Xu ZY (2024b). Phenotyping alfalfa (Medicago sativa L.) root structure architecture via integrating confident machine learning with ResNet—18 . Plant Phenomics 6, 0251.
|
|
Wójcik—Gront E, Zieniuk B, Pawełkowicz M (2024). Harnessing AI—powered genomic research for sustainable crop improvement. Agriculture 14, 2299.
|
|
Xing YY, Wang XK (2024). Precise application of water and fertilizer to crops: challenges and opportunities. Front Plant Sci 15, 1444560.
|
|
Yang XK, Xu YY, Chen L, Wang WB, Gao Y, Tian JD, Yu K, Jin YH, Mei H (2024). AI for Science: AI enabled scientific facility transforms fundamental research. Bull Chin Acad Sci 39, 59-69. (in Chinese with English abstract)
|
|
杨小康, 许岩岩, 陈露, 王韫博, 高岳, 田济东, 俞凯, 金耀辉, 梅宏 (2024). AI for Science: 智能化科学设施变革基础研究. 中国科学院院刊 39, 59-69.
|
|
Yu P, He XM, Baer M, Beirinckx S, Tian T, Moya YAT, Zhang XC, Deichmann M, Frey FP, Bresgen V, Li CJ, Razavi BS, Schaaf G, von Wirén N, Su Z, Bucher M, Tsuda K, Goormachtig S, Chen XP, Hochholdinger F (2021). Plant flavones enrich rhizosphere Oxalobacteraceae to improve maize performance under nitrogen deprivation. Nat Plants 7, 481-499.
|