Background: Tuberous root formation and development is a complex process in sweet potato, which is regulated by multiple genes and environmental factors. However, the regulatory mechanism of tuberous root development is unclear.Results: In this study, the transcriptome of fibrous roots (R0) and tuberous roots in three developmental stages (Rl, R2, R3) were analyzed in two sweet potato varieties, GJS-8 and XGH. A total of 22,914 and 24,446 differentially expressed genes (DEGs) were identified in GJS-8 and XGH respectively, 15,920 differential genes were shared by GJS-8 and XGH. KEGG pathway enrichment analysis showed that the DEGs shared by GJS-8 and XGH were mainly involved in “plant hormone signal transduction” “starch and sucrose metabolism” and “MAPK signal transduction”. Trihelix transcription factor (Tai6.25300) was found to be closely related to tuberous root enlargement by the comprehensive analysis of these DEGs and weighted gene co-expression network analysis (WGCNA).Conclusion: A hypothetical model of genetic regulatory network for tuberous root development of sweet potato is proposed, which emphasizes that some specific signal transduction pathways like “plant hormone signal transduction” “Ca²⁺signal” “MAPK signal transduction” and metabolic processes including “starch and sucrose metabolism” and “cell cycle and cell wall metabolism” are related to tuberous root development in sweet potato. These results provide new insights into the molecular mechanism of tuberous root development in sweet potato.

Peanut is one of the most important oil crops in the world. In China, the peanut is highly produced in its southern part, in which the arable land is dominated by acid soil. At present, miRNAs have been identified in stress response, but their roles and mechanisms are not clear, and no miRNA studies have been found related to aluminum (Al)-induced programmed cell death (PCD). In the present study, transcriptomics, sRNAs, and degradome analysis in the root tips of two peanut cultivars ZH2 (Al-sensitive, S) and 99-1507 (Al-tolerant, T) were carried out. Here, we generated a comprehensive resource focused on identifying key regulatory miRNA-target circuits that regulate PCD under Al stress. Through deep sequencing, 2284 miRNAs were identified and 147 miRNAs were differentially expressed under Al stress. Furthermore, 19237 target genes of 749 miRNAs were validated by degradome sequencing. GO and KEGG analyses of differential miRNA targets showed that the pathways of synthesis and degradation of ketone bodies, citrate cycle (TCA cycle), and peroxisome were responded to Al stress. The combined analysis of the degradome data sets revealed 89 miRNA-mRNA interactions that may regulate PCD under Al stress. Ubiquitination may be involved in Al-induced PCD in peanut. The regulatory networks were constructed based on the differentially expressed miRNAs and their targets related to PCD. Our results will provide a useful platform to research on PCD induced by Al and new insights into the genetic engineering for plant stress response.

Peanut is among the most important oil crops in the world. In the southern part of China, peanut is highly produced; however, the arable land is acidic. In acidic soils, aluminum (Al) inhibits plant growth and development by changing the properties of the cell wall and causing the disorder of the intracellular metabolic process. Circadian rhythm is an internal mechanism that occurs about every 24 h and enables plants to maintain internal biological processes with a daily cycle. To investigate the effect of photoperiod and Al stress on the Al-induced programmed cell death (PCD), two peanut varieties were treated with 100 μM AlCl₃ under three photoperiodic conditions (8/16, SD; 12/12, ND; 16/8 h, LD). The results show that Al toxicity was higher in ZH2 than in 99-1507 and higher under LD than under SD. Root length decreased by 30, 37.5, and 50% in ZH2 and decreased by 26.08, 34.78, and 47.82% in 99-1507 under SD, ND, and LD, respectively, under Al stress. Photoperiod and Al induced cell death and ROS production. MDA content, PME activity, and LOX activity increased under SD, ND, and LD, respectively, under Al stress both in ZH2 and 99-1507. APX, SOD, CAT, and POD activities were higher under SD, ND, and LD, respectively. Al stress increased the level of AhLHY expression under SD and ND but decreased it under LD in both ZH2 and 99-1507. Contrastingly, AhSTS expression levels increased exponentially and were higher under SD, LD, and ND, respectively, under Al stress. Our results will be a useful platform to research PCD induced by Al and gain new insights into the genetic manipulation of the circadian clock for plant stress response.

Thioredoxins (Trx) are small multifunctional redox proteins that contain thioredoxin conserved domain and active site WCXXC. The Trx family has an important role in multiple processes, including electron transport, seed germination, redox regu...

The circadian clock is an endogenous timekeeping system that coordinates plant growth, development, metabolism, and responses to environmental stimuli. Although circadian regulation has been implicated in multiple abiotic stress responses, its potential involvement in aluminum (Al) stress adaptation in peanut (Arachis hypogaea L.) remains poorly understood. A genome-wide analysis was performed to identify and characterize circadian clock genes in peanut and investigate their transcriptional responses to Al stress. A total of 74 circadian clock genes from Arabidopsis thaliana were used as reference sequences to identify homologous genes in the peanut genome. A total of 71 encoding circadian clock proteins were identified and comprehensively characterized through analyses of chromosomal distribution, conserved domains, motif composition, transmembrane regions, subcellular localization, phylogenetic relationships, functional annotation, and protein interaction networks. Transcriptome data (RNA-seq accession PRJNA525247) from Al-sensitive ZH2 (Zhonghua 2) and Al-tolerant 99-1507 peanut cultivars were further analyzed to evaluate gene expression patterns under Al stress. The identified genes were unevenly distributed across all 20 peanut chromosomes and exhibited diverse structural features and predicted biological functions. Phylogenetic analysis demonstrated a high degree of evolutionary conservation between peanut and Arabidopsis circadian clock genes. Functional annotation indicated that many identified genes are associated with transcriptional regulation, light perception, signal transduction, phytohormone signaling, and stress-responsive pathways. Comparative transcriptome analysis revealed distinct expression profiles between the Al-sensitive and Al-tolerant cultivars, with several genes, including homologs of XAP5, PIF3, GIGANTEA (GI), FLOWERING LOCUS T (FT), and AGL15, displaying cultivar-dependent responses to Al treatment, where these were upregulated in ZH2 but downregulated in 99-1507. These findings provide the first comprehensive overview of the circadian clock genes in peanut and suggest that circadian regulatory pathways may contribute to transcriptional responses associated with Al stress adaptation. This study establishes a valuable genomic resource for future functional characterization of circadian clock genes and supports molecular breeding efforts for rhythmic traits for Al tolerance in cultivated peanuts.