Integrated epigenomic and transcriptomic analyses reveal regulatory and adaptive roles of Pup1 in phosphorus deficiency tolerance in rice

Le résumé fourni par la source

Phosphorus (P) is an essential macronutrient that plays critical roles in numerous cellular/metabolic processes, including cell cycle regulation, energy metabolism, nucleic acid/membrane lipid biosynthesis, and enzyme functions. Consequently, limited P availability in soil severely constrains plant growth, developmental processes, and overall crop productivity. To investigate the regulatory/adaptive role of the Phosphorus uptake 1 ( Pup1 ) QTL, with particular emphasis on epigenetic modulations under P-deficient conditions, the P-deficiency–sensitive rice cultivar Pusa-44 and its near-isogenic line NIL-23 (harboring Pup1 ) were grown hydroponically under P-deficient (4 ppm Pi) and P-sufficient (16 ppm Pi) conditions until maturity. P-deficiency resulted in a significant reduction in root architectural traits, including root length, number, volume, and surface area, along with decreased photosynthetic activity, tiller/panicle numbers, and overall grain yield. These reductions were markedly more severe in Pusa-44 than in NIL-23. Notably, NIL-23 exhibited significantly higher levels of root-secreted acid phosphatase activity, as well as enhanced intrinsic acid phosphatase activity in roots and panicles, compared with Pusa-44 under both P-deficient and P-sufficient conditions. Genome-wide DNA methylation analysis revealed distinct tissue- and condition-specific methylation patterns between the two genotypes under both P-sufficient and P-deficient conditions, attributable to the introgression of Pup1 QTL. Integrated methylome-transcriptome analyses demonstrated hypomethylation-associated upregulation of several P stress-responsive genes in NIL-23, including those encoding purple acid phosphatases, ribonuclease T2, and protein kinases involved in phosphate scavenging, P recycling, and stress adaptation. Furthermore, enhanced expression of genes associated with carbohydrate metabolism, fatty acid biosynthesis, and phytohormone signaling likely contributed to the superior performance of NIL-23 under P-deficient conditions. Overall, this study confirms the epigenetic regulatory role of Pup1 at reproductive stage in rice. The findings provide valuable insights into epigenetic mechanisms underlying P-use efficiency and may facilitate the identification of epigenetic markers for developing P-efficient rice cultivars suitable for sustainable production in P-deficient soils.

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