Estrada Richard, Rodriguez Lila, Romero Yolanda, Arteaga Linda, Ruelas-Calloapaza Domingo, Oha-Humpiri Filiberto, Flores Nils, Coila Pedro, Arbizu Carlos I
Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Lima 15024, Peru.
Instituto de Investigación en Bioinformática y Bioestadística (BIOINFO), Lima 15024, Peru.
Genes (Basel). 2025 Mar 31;16(4):417. doi: 10.3390/genes16040417.
MicroRNAs (miRNAs) play crucial roles in regulating tissue-specific gene expression and plant development. This study explores the identification and functional characterization of miRNAs in (sacha inchi), an economically and nutritionally significant crop native to the Amazon basin, across three organs: root, stem, and leaf.
Small RNA libraries were sequenced on the Illumina Novaseq 6000 platform, yielding high-quality reads that facilitated the discovery of known and novel miRNAs using miRDeep-P.
A total of 277 miRNAs were identified, comprising 71 conserved and 206 novel miRNAs, across root, stem, and leaf tissues. In addition, differential expression analysis using DESeq2 identified distinct miRNAs exhibiting tissue-specific regulation. Notably, novel miRNAs like novel_1, novel_88, and novel_189 showed significant roles in processes such as auxin signaling, lignin biosynthesis, and stress response. Functional enrichment analysis of miRNA target genes revealed pathways related to hormonal regulation, structural reinforcement, and environmental adaptation, highlighting tissue-specific functions. The Principal Component Analysis and PERMANOVA confirmed clear segregation of miRNA expression profiles among tissues, underlining organ-specific regulation. Differential expression patterns emphasized unique regulatory roles in each organ: roots prioritized stress response and nutrient uptake, leaves focused on photosynthesis and UV protection, and stems contributed to structural integrity and nutrient transport, suggesting evolutionary adaptations in .
This study identified novel miRNA-mediated networks that regulate developmental and adaptive processes in , underscoring its molecular adaptations for resilience and productivity. By characterizing both conserved and novel miRNAs, the findings lay a foundation for genetic improvement and molecular breeding strategies aimed at enhancing agronomic traits, stress tolerance, and the production of bioactive compounds.
微小RNA（miRNA）在调节组织特异性基因表达和植物发育中起着关键作用。本研究探索了在亚马逊盆地原产的一种具有经济和营养意义的作物——印加果（sacha inchi）的根、茎和叶这三个器官中miRNA的鉴定及其功能特征。
在Illumina Novaseq 6000平台上对小RNA文库进行测序，获得高质量的 reads，使用 miRDeep-P 促进已知和新型miRNA的发现。
在根、茎和叶组织中总共鉴定出277个miRNA，包括71个保守miRNA和206个新型miRNA。此外，使用DESeq2进行的差异表达分析确定了表现出组织特异性调节的不同miRNA。值得注意的是，新型_1、新型_88和新型_189等新型miRNA在生长素信号传导、木质素生物合成和应激反应等过程中发挥着重要作用。miRNA靶基因的功能富集分析揭示了与激素调节、结构强化和环境适应相关的途径，突出了组织特异性功能。主成分分析和PERMANOVA证实了组织间miRNA表达谱的明显分离，强调了器官特异性调节。差异表达模式强调了每个器官中的独特调节作用：根优先进行应激反应和养分吸收，叶专注于光合作用和紫外线保护，茎有助于结构完整性和养分运输，表明印加果具有进化适应性。
本研究确定了调节印加果发育和适应过程的新型miRNA介导的网络，强调了其在恢复力和生产力方面的分子适应性。通过表征保守和新型miRNA，这些发现为旨在提高农艺性状、胁迫耐受性和生物活性化合物产量的遗传改良和分子育种策略奠定了基础。
