Sugarcane (Saccharum spp.) is a globally important crop for sugar and bioenergy production. However, genetic improvement through conventional breeding is constrained by long breeding cycles, low genetic gain, and considerable operational complexity arising from its highly allopolyploid and aneuploid genome. With the increasing global demand for sustainable food and renewable energy, sugarcane breeding programs must accelerate the development of high-yielding, stress-tolerant cultivars through the integration of advanced biotechnological tools with traditional breeding approaches. Recent advances in genetic engineering, genomic selection (GS), and high-throughput omics technologies, including genomics, transcriptomics, proteomics, metabolomics, and phenomics, have substantially enhanced the efficiency of trait improvement related to growth, development, yield, and stress resilience. The integration of multi-omics data enables the dissection of regulatory networks linking genotype to phenotype, improves predictive accuracy, and provides deeper insights into the molecular mechanisms underlying complex traits. These integrative approaches support more informed selection decisions and accelerate genetic gain in sugarcane breeding programs. This review synthesizes recent technological developments and their practical applications in sugarcane improvement. It highlights the strategic implementation of transgenic and genome-editing technologies, genomic selection, and multi-omics integration to enhance yield potential and resistance to biotic and abiotic stresses, thereby contributing to sustainable sugarcane production and global food and bioenergy security.

Transforming growth factor beta (TGF-β) is ubiquitously found in bone and plays a key role in bone turnover. Mice expressing constitutively active TGF-β receptor type I (Mx1;TβRI^CA mice) are osteopenic. Here, we identified the candidate genes involved in bone turnover in Mx1;TβRI^CA mice using RNA sequencing analysis. A total of 285 genes, including 87 upregulated and 198 downregulated genes, were differentially expressed. According to the KEGG analysis, some genes were involved in osteoclast differentiation (Fcgr4, Lilrb4a), B cell receptor signaling (Cd72, Lilrb4a), and neutrophil extracellular trap formation (Hdac7, Padi4). Lilrb4 is related to osteoclast inhibition protein, whereas Hdac7 is a Runx2 corepressor that regulates osteoblast differentiation. Silencing Lilrb4 increased the number of osteoclasts and osteoclast marker genes. The knocking down of Hdac7 increased alkaline phosphatase activity, mineralization, and osteoblast marker genes. Therefore, our present study may provide an innovative idea for potential therapeutic targets and pathways in TβRI-associated bone loss.

Background: Coding and non-coding short tandem repeats (STRs) facilitate a great diversity of phenotypic traits. The imbalance of mononucleotide A-repeats around transcription start sites (TSSs) was found in 3 mammals: H. sapiens, M. musculus, and R. norvegicus. Principal Findings: We found that the imbalance pattern originated in some vertebrates. A similar pattern was observed in mammals and birds, but not in amphibians and reptiles. We proposed that the enriched A-repeats upstream of TSSs is a novel hallmark of endotherms or warm-blooded animals. Gene ontology analysis indicates that the primary function of upstream A-repeats involves metabolism, cellular transportation, and sensory perception (smell and chemical stimulus) through housekeeping genes. Conclusions: Upstream A-repeats may play a regulatory role in the metabolic process of endothermic animals.

Aeromonas hydrophila is a major seafood-borne pathogen capable of persisting under preservative-associated stress by entering a viable but non-culturable (VBNC) state, thereby evading culture-based detection. Here, untargeted metabolomics was applied as the primary analytical approach to elucidate metabolic reprogramming during VBNC formation under seafood-relevant preservation conditions. Cells were incubated at 4 °C for 30 days in sodium benzoate-supplemented saline, comparing 0.85% NaCl (culturable condition) and 4% NaCl (VBNC-inducing condition), with sampling every 6 days. Under 4% NaCl with sodium benzoate, culturability declined from 6.18 log CFU/mL at day 0 to undetectable levels by day 30, while cell viability was retained, confirming VBNC induction. UHPLC–ESI–QTOF–MS profiling detected over 893 intracellular metabolic features, of which 518 metabolites were significantly altered between VBNC and culturable states at day 30. Principal component analysis revealed clear, time-dependent metabolic divergence, with the VBNC trajectory explaining 34.4% (PC1) and 11.5% (PC2) of total variance. Pathway enrichment analysis demonstrated significant remodeling of alanine, aspartate and glutamate metabolism (8/28 hits, FDR = 5.7 × 10⁻⁴); arginine biosynthesis (5/14 hits, FDR = 5.44 × 10⁻³); purine metabolism (10/70 hits, FDR = 8.34 × 10⁻³); and pyrimidine metabolism (7/39 hits, FDR = 1.35 × 10⁻²), indicating nitrogen conservation and metabolic downshifting. A robust biomarker panel, including depleted cyclic AMP, aminoadipic acid, hypotaurine, O6-CM-dG, and betaine, and enriched urocanic acid, pipecolic acid, proline, azelaic acid, and orcinol perfectly discriminated VBNC from culturable cells. These findings demonstrate that sodium benzoate-based preservation can induce a metabolically reprogrammed VBNC state in A. hydrophila, highlighting a hidden food safety risk beyond culture-based assessment.