Gene expression and metabolite accumulation in pear roots under alternate partial root-zone irrigation

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.