Gene expression and metabolite accumulation in pear roots under alternate partial root-zone irrigation
Abstract
Aim of study: To investigate the effects of alternate partial root-zone irrigation (AI) on root growth, gene expression, and metabolite accumulation in fragrant pear (Pyrus pyrifolia (Burm. f.) Nakai ‘Yulu’), and explore the underlying mechanisms enhancing water use efficiency (WUE) and regulating the rhizosphere environment.
Area of study: The experiment was conducted in a plastic greenhouse at the Fruit Tree Institute of Shanxi Academy of Agricultural Sciences, China.
Material and methods: Three irrigation treatments —conventional irrigation (CK), fixed partial root-zone irrigation (FI), and AI— were applied. Morphological, physiological, and WUE indicators were measured. Transcriptomic and metabolomic analyses of pear roots were performed using high-throughput sequencing to identify differentially expressed genes (DEGs) and metabolites.
Main results: Alternate partial root-zone irrigation treatment significantly enhanced growth compared to CK, with shoot length, diameter, and net photosynthetic rate (Pn) increasing by 35.25%, 46.09%, and 13.41%, respectively. Significant improvements were also observed in the root-to-shoot ratio, total root length density (RLD), and root surface area density (RSAD). Additionally, WUE increased by 31.87%. Transcriptomic analysis revealed the upregulation of auxin-regulating genes (e.g., SAUR), gibberellin (GA) synthesis genes (e.g., GA20OX2), and aquaporin-related genes, which enhanced the accumulation of GA (e.g., GA44, GA24, GA5) and auxin-related metabolites (e.g., 3-indoleacetonitrile). Alternate partial root-zone irrigation also upregulated stress-responsive genes such as Cinnamoyl CoA reductase (CCR), BSK, and COI1, increasing the accumulation of metabolites like cinnamaldehyde and jasmonoyl-L-isoleucine, which enhanced root growth, plant resistance, and regulated the rhizosphere microbial community.
Research highlights: Alternate partial root-zone irrigation promotes root growth in pear trees by upregulating aquaporin genes, hormone pathway-related genes, and stress-resistance genes, while also modulating the rhizosphere environment.
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References
Abdel-Hameed AAE, Liao WB, Prasad KVSK, Reddy ASN, 2024. CAMTAs, a family of calmodulin-binding transcription factors, are versatile regulators of biotic and abiotic stress responses in plants. Crit Rev Plant Sci 43(3): 171–210. https://doi.org/10.1080/10407782.2024.2302671
Barker R, Garcia MNF, Powers SJ, Vaughan S, Bennett MJ, Phillips AL, Thomas SG, Hedden P, 2021. Mapping sites of gibberellin biosynthesis in the Arabidopsis root tip. New Phytol 229(3): 1521–1534. https://doi.org/10.1111/nph.16967
Edwards J, Santos-Medellín C, Nguyen B, Kilmer J, Liechty Z, Veliz E, Ni JD, Phillips G, Sundaresan V, 2019. Soil domestication by rice cultivation results in plant-soil feedback through shifts in soil microbiota. Genome Biol 20(1): 221. https://doi.org/10.1186/s13059-019-1825-x
Elshamly AM, Abaza A, 2024. Precise partial root-zone irrigation technique and potassium-zinc fertigation management improve maize physio-biochemical responses, yield, and water use in arid climate. BMC Plant Biol 24(1): 775. https://doi.org/10.1186/s12870-024-05467-w
Gupta A, Rico-Medina A, Cao-Delgado AI, 2020. The physiology of plant responses to drought. Science 368(6488): 266–269. https://doi.org/10.1126/science.aaz7614
Huang C, Lu Y, Du H, 2021. An Intelligent Water-Saving Irrigation System. J Water Chem Technol 42(6): 480–484. https://doi.org/10.3103/S1063455X20060041
Hose E, Steudle E, Hartung W, 2000. Abscisic acid and hydraulic conductivity of maize roots: a study using cell- and root-pressure probes. Planta 211(6): 874–882. https://doi.org/10.1007/s004250000412
Li ZN, Sela A, Fridman Y, Garstka L, Höfte H, Savaldi-Goldstein S, Wolf S, 2021. Optimal BR signalling is required for adequate cell wall orientation in the Arabidopsis root meristem. Development 148(21): dev199504. https://doi.org/10.1242/dev.199504
Li P, Yang H, Wang L, Liu HJ, Huo HQ, Zhang CJ, Liu AZ, Zhu AD, Hu JY, Lin YJ, et al., 2019. Physiological and transcriptome analyses reveal short-term responses and formation of memory under drought stress in rice. Front Genet 10: 55. https://doi.org/10.3389/fgene.2019.00055
Mehari TG, Xu Y, Magwanga RO, Umer MJ, Kirungu JN, Cai X, Hou Y, Wang Y, Yu S, Wang K, et al., 2021. Genome-wide identification and characterization of light-harvesting Chloro a/b binding (LHC) genes reveals their potential role in enhancing drought tolerance in Gossypium hirsutum. J Cotton Res 4(1): 15. https://doi.org/10.1186/s42397-021-00090-8
Slamini M, Sbaa M, Arabi M, Darmous A, 2022. Review on Partial Root-zone Drying irrigation: Impact on crop yield, soil and water pollution. Agric Water Manage 271: 107807. https://doi.org/10.1016/j.agwat.2022.107807
Sonawane AV, Shrivastava PK, 2022. Partial root zone drying method of irrigation: A review. Irrig Drain 71(3): 574–588. https://doi.org/10.1002/ird.2686
Stepanova AN, Alonso JM, 2011. Bypassing transcription: a shortcut in cytokinin-auxin interactions. Dev Cell 21(4): 608–610. https://doi.org/10.1016/j.devcel.2011.09.016
Tiwari P, Srivastava D, Chauhan AS, Indoliya Y, 2021. Root system architecture, physiological analysis and dynamic transcriptomics unravel the drought-responsive traits in rice genotypes. Ecotoxicol Environ Saf 207: 111252. https://doi.org/10.1016/j.ecoenv.2020.111252
Wan X, Steudle E, Hartung W, 2004. Gating of water channels (aquaporins) in cortical cells of young corn roots by mechanical stimuli (pressure pulses): effects of ABA and of HgCl₂. J Exp Bot 55(396): 411–422. https://doi.org/10.1093/jxb/erh051
Wang CH, Shu LZ, Zhou SL, Yu HM, Zhu PF, 2019. Effects of alternate partial root-zone irrigation on the utilization and movement of nitrates in soil by tomato plants. Sci Hortic 243: 41–47. https://doi.org/10.1016/j.scienta.2018.08.006
Wei G, Zhang M, Cui B, Wei Z, Liu F, 2024. Ammonium nitrogen combined with partial root-zone drying enhanced fruit quality of tomato under elevated atmospheric CO₂. Sci Hortic 323: 112514. https://doi.org/10.1016/j.scienta.2023.112514
Wu L, Wang JL, Li XF, Guo GQ, 2021. Cytokinin-controlled gradient distribution of auxin in Arabidopsis root tip. Int J Mol Sci 22(8): 3874–3894. https://doi.org/10.3390/ijms22083874
Xu H, Jing H, Shi R, Chen M, Wang C, Xu Q, Bai J, Liu X, Kong M, 2025. Effect of Partial Root Drying Stress on Improvement in Tomato Production. Curr Issues Mol Biol 47(2): 84. https://doi.org/10.3390/cimb47020084
Yang L, You J, Li JZ, Wang YP, Chan ZL, 2021. Melatonin promotes Arabidopsis primary root growth in an IAA-dependent manner. J Exp Bot 72(15): 5599–5611. https://doi.org/10.1093/jxb/erab196
Zhalnina K, Louie KB, Hao Z, Mansoori N, Da-Rocha UN, Shi SJ, Cho HJ, Karaoz U, Loqué D, Bowen BP, et al., 2018. Dynamic root exudate chemistry and microbial substrate preferences drive patterns in rhizosphere microbial community assembly. Nat Microbiol 3(4): 470–480. https://doi.org/10.1038/s41564-018-0129-3
Zhang Y, Liu H, Gong P, He X, Wang J, Wang Z, Zhang J, 2022. Irrigation method and volume for korla fragrant pear: Impact on soil water and salinity, yield, and fruit quality. Agronomy 12(8): 1980. https://doi.org/10.3390/agronomy12081980
Zhang Y, Li X, Jia L, Ji L, Wang C, Xu W, Wang S, Zhou Y, Han H, Han K, 2024. Partial root zone irrigation and K application improves summer maize production and salt resistance in saline soil. Agric Water Manage 303: 109057. https://doi.org/10.1016/j.agwat.2024.109057
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