Integrated Multiomics and an Optimized Hairy Root Transformation System Reveal a Candidate miR319-TCP3 Module Regulating Peanut Root Responses to Nitrate.

Authors

Kong Xiangjun, Li Hengbin, Li Junhui, Li Fei, Li Zengqiang, Zhang Nina, Li Lijie, Bai Na, Zheng Shuaichao, Dai Haifang, Zhang Zhiyong, Jia Peipei

Published in

Physiologia plantarum. Volume 178. Issue 6.

Abstract

Root system architecture is tightly linked to nitrogen use efficiency and crop yield. Nitrate (NO₃ ^-) acts as both a key nutrient and signal governing root development, in which microRNAs (miRNAs) play essential regulatory roles. However, NO₃ ^--responsive miRNA-mediated regulatory networks in peanut roots remain largely unclear, and efficient functional verification tools are lacking. Therefore, we performed small RNA sequencing to identify NO₃ ^--responsive miRNAs in peanut roots under low-nitrogen (LN) and high-nitrogen (HN) conditions. Nine and 99 t-test-derived differentially expressed candidate miRNAs (DEMs) were identified after 5 and 10 days of treatment, respectively. Complementary differential expression analysis was further conducted using edgeR with FDR correction to obtain edgeR FDR-significant DEMs. Integrated analysis with previous transcriptome and degradome data uncovered 114 negatively correlated miRNA-mRNA pairs, with 9 candidate miRNA-mRNA modules involved in signal transduction, plant hormone signaling, transcription factor regulation, and cell wall biogenesis as potential regulators of peanut root development in response to NO₃ ^-. Furthermore, a highly efficient cut-dipping hairy root transformation system (CDHRTS) for peanut was established with a maximum transformation efficiency of 82.22%. Using this system, we functionally verified that silencing gma-miR319f-R+1 (miR319) significantly promoted root elongation under HN but not LN conditions. Consistent with multiomics and qRT-PCR evidence supporting TCP3 as a candidate target of miR319, we hypothesize that miR319 may negatively regulate NO₃ ^--dependent root development putatively by repressing TCP3. Collectively, this study reveals critical miRNA-mRNA regulatory networks underlying peanut root response to NO₃ ^- and provides a reliable technical platform for gene function verification in peanut roots.

PMID:
43031383
Bibliographic data and abstract were imported from PubMed on 14 Nov 2026.

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