Orphan genes (OGs) are defined as genes having no sequence similarity with genes present in other lineages. OGs have been regarded to play a key role in the development of lineage-specific adaptations and can also serve as a constant source of evolutionary novelty. These genes have often been found related to various stress responses, species-specific traits, special expression regulation, and also participate in primary substance metabolism. The advancement in sequencing tools and genome analysis methods has made the identification and characterization of OGs comparatively easier. In the study of OG functions in plants, significant progress has been made. We review recent advances in the fast evolving characteristics, expression modulation, and functional analysis of OGs with a focus on their role in plant biology. We also emphasize current challenges, adoptable strategies and discuss possible future directions of functional study of OGs.

Orphan genes, also called lineage-specific genes (LSGs), are important for responses to biotic and abiotic stresses, and are associated with lineage-specific structures and biological functions. To date, there have been no studies investigating gene number, gene features, or gene expression patterns of orphan genes in Brassica rapa. In this study, 1540 Brassica-specific genes (BSGs) and 1824 Cruciferae-specific genes (CSGs) were identified based on the genome of Brassica rapa. The genic features analysis indicated that BSGs and CSGs possessed a lower percentage of multi-exon genes, higher GC content, and shorter gene length than evolutionary-conserved genes (ECGs). In addition, five types of BSGs were obtained and 145 out of 529 real A subgenome-specific BSGs were verified by PCR in 51 species. In silico and semi-qPCR, gene expression analysis of BSGs suggested that BSGs are expressed in various tissue and can be induced by Plasmodiophora brassicae. Moreover, an A/C subgenome-specific BSG, BSGs1, was specifically expressed during the heading stage, indicating that the gene might be associated with leafy head formation. Our results provide valuable biological information for studying the molecular function of BSGs for Brassica-specific phenotypes and biotic stress in B. rapa.

Orphan genes are essential to the emergence of species-specific traits and the process of evolution, lacking sequence similarity to any other identified genes. As they lack recognizable domains or functional motifs, however, efforts to characterize these orphan genes are often difficult. Flowering is a key trait in Brassica rapa, as premature bolting can have a pronounced adverse impact on plant quality and yield. Bolting resistance-related orphan genes, however, have yet to be characterized. In this study, an orphan gene designated BOLTING RESISTANCE 1 (BR1) was identified and found through gene structural variation analyses to be more highly conserved in Chinese cabbage than in other available accessions. The expression of BR1 was increased in bolting resistant Chinese cabbage and decreased in bolting non-resistant type, and the expression of some mark genes were consist with bolting resistance phenotype. BR1 is primarily expressed in leaves at the vegetative growth stage, and the highest BR1 expression levels during the flowering stage were observed in the flower buds and silique as compared to other tissue types. The overexpression of BR1 in Arabidopsis was associated with enhanced bolting resistance under long day (LD) conditions, with these transgenic plants exhibiting significant decreases in stem height, rosette radius, and chlorophyll content. Transcriptomic sequencing of WT and BR1OE plants showed the association of BR1 with other bolting resistance genes. Transcriptomic sequencing and qPCR revealed that six flowering integrator genes and one chlorophyll biosynthesis-related gene were downregulated following BR1 overexpression. Six key genes in photoperiodic flowering pathway exhibited downward expression trends in BR1OE plants, while the expression of floral repressor AtFLC gene was upregulated. The transcripts of these key genes were consistent with observed phenotypes in BR1OE plants, and the results indicated that BR1 may function through vernalization and photoperiodic pathway. Instead, the protein encoded by BR1 gene was subsequently found to localize to the nucleus. Taken together, we first propose that orphan gene BR1 functions as a novel regulator of flowering time, and these results suggested that BR1 may represent a promising candidate gene to support the selective breeding of Chinese cabbage cultivars with enhanced bolting resistance.

The floral transition in Chinese cabbage (Brassica rapa ssp. pekinensis) is governed by a complex interplay of gene expression and hormonal regulation. Temporal transcriptome profiling was conducted across three developmental stages: pre-bolting (PBS), bolting (BS), and flowering stages (FS), to investigate the underlying molecular mechanisms. A total of 7092 differentially expressed genes (DEGs) were identified, exhibiting distinct expression trajectories during the transition. Moreover, functional enrichment analyses revealed strong associations with plant hormone signaling, MAPK pathways, and developmental regulation processes. Key flowering-related genes, such as BrFLM, BrAP2, BrFD, BrFT, and BrSOC1s displayed antagonistic expression patterns. Hormonal pathways involving auxin, ABA, ET, BR, GA, JA, CK, and SA showed stage-dependent modulation. Further, orphan genes (OGs), especially EARLY FLOWERING 1 (EF1), showed significant upregulation during the transition, which exhibited 1.84-fold and 1.93-fold increases at BS and FS compared to PBS, respectively (p < 0.05). Functional validation through EF1 overexpression (EF1OE) in Arabidopsis consistently promoted early flowering. The expression levels of AtFT and AtSOC1 were significantly upregulated in EF1OE lines compared to wild-type (WT) plants. The findings contribute to understanding the coordinated genetic and hormonal events driving floral development in Chinese cabbage, suggesting EF1 as a candidate for bolting resistance breeding. This work also expands the existing regulatory framework through the successful integration of OGs into the complex floral induction system of Brassica crops.

Early flowering refers to the phenomenon in which the first flower appears in fewer days than normal, regardless of the sex of the flower. It is a significant feature impacting the early maturity and economic yield of cucumbers. The early flowering trait of cucumber is influenced by several factors. Considering its heritability, technologies such as whole-genome sequencing, genetic modification, bioinformatics analysis, quantitative trait locus (QTL) mapping, molecular marker-assisted selection, and gene editing are widely used to explore the regulatory genes and molecular mechanisms of the early flowering trait in cucumbers. This review aimed to summarize the factors, QTL mapping, molecular regulation mechanisms, and omics analysis related to early flowering traits in cucumbers. This review contributes theoretical insights to support both cucumber breeding for early flowering and fundamental research on early flowering traits.

Universal Stress Protein (USP) plays crucial roles in plant stress adaptation, yet their evolutionary dynamics, regulatory mechanisms, and functional diversification in rice (Oryza sativa) remain poorly understood. This study aimed to conduct a genome-wide identification and characterization of the OsUSP gene family to elucidate its role in abiotic stress responses using integrated bioinformatics approaches. Here, we identified 46 OsUSP genes that are unevenly distributed across 11 rice chromosomes and exhibit significant divergence in protein length, molecular weight, and subcellular localization. Phylogenetic analysis classified OsUSPs into three subfamilies, with conserved motif and domain architectures within groups but distinct structural variations across subfamilies. Evolutionary analysis revealed strong collinearity between rice and other monocots, which suggests functional conservation in grasses, whereas limited synteny with dicots indicates lineage-specific divergence. Cis-regulatory element analysis showed enrichment in ABA, MeJA, drought, and hypoxia response motifs, implicating OsUSPs in hormonal and stress signaling. Expression profiling indicated tissue-specific patterns, with subfamily III genes broadly expressed, while subfamily II members were anther-enriched. Stress response profiling revealed that 24 OsUSPs were significantly induced, while LOC_Os02g54590 and LOC_Os05g37970 emerged as particularly notable due to their broad-spectrum responsiveness, being upregulated under all tested stress conditions. Protein–protein interaction (PPI) analysis indicated that OsUSP proteins potentially interact with Leo1/TPR-domain proteins and are involved in stress response and phosphorylation signaling pathways. This study yields key insights into OsUSP-mediated stress adaptation in rice and pinpoints promising candidate genes to facilitate the breeding of climate-resilient rice.