Plant flavor diversity arises from genomic variation across species and cultivars, yet the mechanisms linking natural genomic variation to flavor-related phenotypes remain insufficiently integrated. Here, we systematically review how diverse forms of genomic variation reshape the biosynthesis, transport, and accumulation of flavor-related metabolites, thereby driving diversification in sweetness, acidity, bitterness, piquancy, astringency, and aroma. We further integrate evidence from genomics, transcriptomics, metabolomics, and functional validation to outline a mechanistic framework linking genomic variation to the molecular and metabolic basis of flavor phenotypes. We then examine how artificial intelligence-assisted breeding and precision gene editing can accelerate the identification of causal variants and enable targeted improvement of flavor-related traits. This framework establishes plant flavor as a mechanism-based target for plant improvement, with broad implications for quality, nutrition, and sustainability.

Over the past two decades, omics and big data have shifted plant molecular biology from single-gene, hypothesis-driven studies to systems-level, data-driven discovery. As datasets expand in scale and diversity, bioinformatics software has become essential for routine analysis and interpretation. However, the efficiency of data exploration and evidence integration has not kept pace with data growth, leaving many datasets underutilized and only slowly translated into biological insight. A central bottleneck is the widening gap between the limited data analysis skills of many experimental biologists and the increasing complexity of biological data. TBtools was developed to narrow this gap by providing low-barrier, interactive functions for common plant omics tasks, and it has been broadly adopted. Here, we use TBtools as a decade-long case study to discuss why certain local tools achieve broad adoption in plant omics research, distill eight actionable design recommendations, and propose four capacity pillars for next-generation local workbenches: project-level data management, reproducible workflow construction, elastic remote computing, and AI-assisted navigation and automation. Together, these lessons provide a practical roadmap for accelerating the translation of omics data into biological insights.

The purpose of this study was to evaluate the effects of Eucommia ulmoides leaf extract (ELE) on growth performance, liver and gut health, gut microbiota profile and disease resistance of largemouth bass. The basal diet was enriched with ELE at 0 g/kg (control), 1.0 g/kg (ELE1.0), 2.0 g/kg (ELE2.0), and 3.0 g/kg (ELE3.0). Largemouth bass (initial body weight of 9.25 +/- 0.03 g) were assigned to one of the four diets and fed for five weeks. According to the result, ELE supplementation significantly increased weight gain (WG) and reduced feed conversion ratio (FCR) compared with controls (P < 0.05). In addition, ELE reduced hepatic inflammation and the mRNA level of nuclear factor kappa b p65 (nf kappa b). ELE improved intestinal structural integrity and notably upregulated the mRNA and protein expression of hypoxia-inducible factor 1-alpha (hif1 alpha), while nf-kappa b expression was significantly downregulated in the intestine of ELE2.0 and ELE3.0 groups. Moreover, the results of gut microbiota 16S rRNA sequencing analysis revealed that Bacillus showed a rising trend in the ELE2.0 group and principal coordinate analysis (PCoA) revealed a distinct shift in microbial community structure in the ELE 2.0 group. Furthermore, the ratio of (Firmicutes+ Bacteroidetes+ Fusobacteria) to Proteobacteria was significantly higher in the ELE 2.0 group compared to the control. The survival rate (SR) of largemouth bass in ELE supplementation groups were significantly improved following Aeromonas veronii NJ-1 and Aeromonas hydrophila Hm091 challenge. Taking together, dietary ELE enhanced growth, liver health, intestinal structure, bacterial disease resistance, and improved the gut microbiota structure in largemouth bass, with 2.0 g/kg identified as the optimal inclusion level.

Sex differentiation is a crucial developmental process accompanied by tightly regulated anther development or its selective abortion. In litchi (Litchi chinensis), anthers develop normally in male flowers but are defective in female flowers, with impaired pollen development. However, the underlying regulatory mechanism remains unclear. We report here that transcription factor SPOROCYTELESS/NOZZLE (SPL/NZZ) is critical for anther and pollen development in litchi. Notably, LcSPL/NZZ shows persistently high expression throughout anther development in female flowers. Ectopic overexpression of LcSPL/NZZ suppresses filament elongation, reduces anther size, impairs pollen development, and ultimately causes male sterility. We further show that the misexpression of LcSPL/NZZ in female flowers is likely mediated by a bHLH transcription factor (bHLH91). Mechanistically, LcbHLH91 binds the LcSPL/NZZ promoter to modulate its expression and physically interacts with LcSPL/NZZ in the nucleus, thereby enhancing its expression and protein activity. Phylogenetic and promoter analyses further indicate that the bHLH91-SPL/NZZ regulatory module is conserved within the Sapindaceae. Results obtained in this study imply a novel regulatory circuit controlling sex differentiation and anther development in litchi and related species.

The lychee industry is vital to agricultural economies, boosting the livelihood of farmers and regional growth. However, instability of flowering causes yield fluctuations, severely limiting industry sustainability. Stable pistil development in female flowers is essential for yield improvement, yet its molecular regulation remains poorly understood. Although APETALA2 (AP2) transcription factors regulate floral organ differentiation and pistil development, their functional role in woody perennials such as lychee is uncharacterized. In this study, two AP2 genes (LITCHI007109 and LITCHI010784) were found to exhibit high and specific expression in carpels. LITCHI007109, designated as LcANT1, is an ortholog of Arabidopsis AINTEGUMENTA (ANT). We next systematically identified the direct downstream target genes of LcANT1, the set of which were significantly enriched in biological processes related to floral organ development and carpel morphology. Notably, the carpel development-related gene LITCHI024703 (LcREV) exhibited a high level of co-expression with LcANT1. We found that the LcANT1 protein can directly bind to the promoter region of LcREV. Further evolutionary analysis indicates that the ANT-REV regulatory module is highly conserved in angiosperms, especially in Sapindaceae. Our findings establish a novel theoretical framework for understanding female flower development in lychee and offer critical gene resources and regulatory networks for molecular breeding strategies aimed at developing high-yield, stable cultivars.

Flower color is a key trait influencing insect pollination and ornamental value, yet the molecular mechanisms underlying heterozygous flower color remain unclear. In this study, we identified the creation of a yellow-white chimeric flower (cf) mutation in Brassica napus, characterized as the coexistence of yellow and white colors on petals of the same flower. Genetic analysis revealed that chimeric flower formation is controlled by a completely dominant gene. Map-based cloning, transgenic complementation, and CRISPR/Cas9 experiments consistently confirmed that BnaC05G0385300ZS on chromosome C05 is the causal gene of CF, which encodes a plastid DNA polymerase IB (BnaC05.POLIB). A G-to-A mutation in the seventh exon results in a D742N substitution, which disrupts Mg2+ binding and impairs polymerase activity. This leads to a reduced plastid genome copy number, decreased chromoplast formation, and aberrant carotenoid accumulation, ultimately resulting in the chimeric phenotype in a dosage-dependent manner. These findings reveal a novel role for BnaC05.POLIB in petal color patterning and provide a strategy for breeding ornamental plants with heterozygous flowers.

A high-quality reference genome requires not only accurate DNA sequences but also well-defined gene-structure annotations. However, many existing tools depend predominantly on automated pipelines that perform poorly when confronted with complex gene architectures, such as overlapping loci, alternative splicing patterns, and lowly expressed isoforms, resulting in incomplete or inaccurate annotations. To overcome these limitations, we developed GSAman, a standalone, ready-to-use tool that enables intuitive, what-you-see-is-what-you-get (WYSIWYG) editing of gene-structure annotations. In contrast to web-based platforms such as Apollo2, which generally require server deployment and do not provide full offline functionality, GSAman delivers a fully local, responsive interface for real-time annotation refinement, thereby improving accessibility across research settings. GSAman supports both fine-scale curations of individual genes and large-scale annotation of entire genomes. By enabling precise curation of gene models across varied genomic contexts, it directly facilitates downstream applications, including pan-genome construction, gene family evolutionary analyses, and precision crop enhancement. Using a telomere-to-telomere rice genome (MH63) annotation project as a case study, we demonstrate the practical utility of GSAman in producing a complete and accurate reference annotation, improving Benchmarking Universal Single-Copy Orthologs (BUSCO) completeness to 99.63% following manual curation. We believe GSAman will serve as a critical resource for advancing functional genomics across diverse species.

Seed size is a key agronomic trait that critically influences the commercial quality of fruit. In litchi (Litchi chinensis Sonn.), small-seeded cultivars are highly desirable due to their higher pulp-to-seed ratio. However, the molecular mechanisms controlling small-seed development remain poorly understood. Here, we identify LcTINY, an ERF/DREB transcription factor, that plays an essential role in seed development in litchi. LcTINY expression is both cultivar-specific and developmentally regulated, showing a strong correlation with seed morphological traits. Functional analyses show that silencing LcTINY reduces seed weight and size, whereas its overexpression promotes seed expansion, confirming its positive role in seed growth. Mechanistically, we demonstrate that LcTINY directly binds to the promoter of LcbZIP53, a bZIP transcription factor, and activates its expression, thereby coordinating seed growth though modulating hormone signaling and cell proliferation. We further show that the LcTINY-LcbZIP53 regulatory module is evolutionarily conserved across the Sapindaceae family. Our results reveal a novel transcriptional mechanism underlying litchi seed development and establish a theoretical foundation for breeding small-seeded litchi cultivars with enhanced fruit quality.

Fruit shape is a key horticultural trait affecting the market value and consumer preference of mango (Mangifera indica L.), but the genetic and molecular mechanisms underlying its variation remain unclear. In this study, a high-quality genome of 'Jinpingmang' (‘JPM’), a cultivar with spherical fruits, was obtained. The assembled genome size is 350.66 Mb, containing 34,035 protein-coding genes, with repetitive sequences accounting for 39.28% of the genome. Two cultivars with significantly different fruit shapes, 'Hongxiangya' (‘HXY’) and 'JPM', were selected for fruit development observation and transcriptome sequencing. It was found that DAP3, DAP5, and DAP10 are critical stages for fruit shape development, and a total of 467 fruit shape-related genes were identified. Seventy-five mango germplasms with different fruit shapes were resequenced to obtain 26,285,317 single-nucleotide polymorphisms (SNPs), based on which the 75 accessions were clustered into 4 groups with significant differences in fruit shape. Combined with 9 fruit-related traits from three-dimensional scanning, a genome-wide association study (GWAS) of 72 accessions on 6 key fruit shape traits identified 99 genetic loci (linked to 59 annotated genes) as well as fruit volume and fruit shape index. Integration of GWAS and transcriptome data identified 44 key candidate genes with significant differential expression during development, among which 8 genes including LOC123222869 (TCP4-like), LOC123213947 (bZIP61-like), LOC123210819 (ABC-G10), LOC123200572 (ARF3) and LOC123228419 (TTL1) were proposed as key candidates underlying fruit shape variation. This study provides high-quality resources for dissecting key genetic loci associated with mango fruit shape differences and can inform future genome-based breeding for improved fruit shape in mango.

Abstract The multi-main-stem (MMS) trait presents considerable potential for improving plant architecture and increasing yield in rapeseed ( Brassica napus L.). However, the molecular mechanism underlying MMS formation remains poorly understood. In this study, we characterized a dominant MMS material, 1030R. Genetic analysis indicated that the MMS phenotype is controlled by a single dominant gene, designated BnaMMS . Utilizing BSA-seq combined with fine mapping, BnaMMS was localized to a 70 kb physical interval on chromosome A6, representing a novel genetic locus for MMS regulation. This region contains 17 annotated genes. Sequence analysis revealed multiple SNP and Indel variations between the parental lines. Transcriptome profiling further demonstrated that, among these candidates, two genes ( BnaA06G0092000ZS and BnaA06G0092200ZS ) were differentially expressed between near-isogenic lines (NILs) displaying MMS and single-main-stem (SMS) phenotypes. Mechanistic investigations suggested that, with no significant changes observed in the expression of core WUS-CLV pathway genes in our transcriptome data, BnaMMS likely regulates MMS formation by disrupting auxin biosynthesis and distribution. Our work identifies a novel genetic locus controlling MMS and provides valuable genetic resources and a theoretical framework for elucidating the molecular mechanisms of stem development and for breeding high-yielding rapeseed varieties with optimized plant architecture.

Fruits undergo a similar ripening process, yet they exhibit a range of differences in color, taste, and shape, both across different species and within the same species. How does this diversity arise? We uncovered a conserved fruit ripening process in lychee fruit in which a NAC transcription factor, LcNAC1, acts as a master regulator. LcNAC1 regulates the expression of two terpene synthase genes, LcTPSa1 and LcTPSa2, which belong to a gene cluster consisting of four TPS genes. LcTPSa1-LcTPSa3 are responsible for catalyzing the production of farnesol, which in turn dictates the aromatic diversity in fruit of different lychee varieties. Through comparative, transcriptomic, and genomic analyses across various lychee varieties, we found these four TPS genes exhibit distinct expression levels due to natural genetic variation. These include copy number variations, presence/absence variations, insertions and deletions, and single nucleotide polymorphisms, many of which affect the binding affinity of LcNAC1. A single nucleotide mutation in LcTPSa1 caused a premature translational termination, resulting in a truncated version of the TPS protein, which surprisingly remains functional. All these genomic changes in the LcNAC1-regulated TPS genes are likely to contribute to the great aromatic diversity observed in lychee fruit. This diversification of fruit aroma in lychee varieties offers a compelling example of how species- or variety-specific traits evolve - the phenotypic diversity is primarily derived from natural genetic variation accumulated in downstream structural genes within an evolutionarily conserved regulatory circuit.

Sexual systems in animals and plants are remarkably diverse, with dioecy having evolved independently in numerous lineages. In plants, dioecy often evolved more recently than in the best-studied animal systems, making plants especially important for understanding how separate sexes evolved independently from functionally hermaphrodite ancestors. Despite long-standing theories of developmental trade-offs in sex allocation, the underlying genetic mechanisms remain elusive. Here, we show that the XY sex determination system in the dioecious plant species Eurycorymbus cavaleriei in Sapindaceae involves two Y-linked mutations that act jointly within the developmental male-female trade-off: YUNΔ , a truncated allele that lowers the dosage of the D-class MADS-box gene YUN , and SUNMAO , a novel sRNA locus that silences the X-linked SUN allele. In females, SUN stabilizes the HD-ZIP transcription factor KUN, which is a known sex determinant in another dioecious plant, thereby promoting femaleness by increasing YUN expression; loss of SUN expression, together with the effect of YUNΔ , shifts development toward males. Two interlocking regulatory loops in this “SKY” module (SUN-KUN-YUN) fine-tunes YUN dosage. This dioecious system in E. cavaleriei likely evolved by sequential mutations in genes acting in the predicted male-female trade-off system, with their close linkage reflecting a translocation, and later recombination-suppressing inversions. ### Competing Interest Statement The authors have declared no competing interest.

Epigenetic mechanisms are integral to plant growth, development, and adaptation to environmental stimuli. Over the past two decades, our comprehension of these complex regulatory processes has expanded remarkably, producing a substantial body of knowledge on both locus-specific mechanisms and genome-wide regulatory patterns. Studies initially grounded in the model plant Arabidopsis have been broadened to encompass a diverse array of crop species, revealing the multifaceted roles of epigenetics in physiological and agronomic traits. With recent technological advancements, epigenetic regulations at the single-cell level and at the large-scale population level are emerging as new focuses. This review offers an in-depth synthesis of the diverse epigenetic regulations, detailing the catalytic machinery and regulatory functions. It delves into the intricate interplay among various epigenetic elements and their collective influence on the modulation of crop traits. Furthermore, it examines recent breakthroughs in technologies for epigenetic modifications and their integration into strategies for crop improvement. The review underscores the transformative potential of epigenetic strategies in bolstering crop performance, advocating for the development of efficient tools to fully exploit the agricultural benefits of epigenetic insights.

The HD-ZIP gene family, a group of plant-specific transcription factors, plays pivotal regulatory roles in various aspects of plant growth and development. Accumulating evidence has demonstrated the extensive involvement of HD-ZIP members in regulating reproductive developmental processes. This review systematically summarizes both the structural characteristics of the four HD-ZIP subfamilies (I–IV) and their distinct regulatory roles in plant reproductive development. Recent studies reveal that a conserved HD-ZIP I clade serves as a core regulator of key reproductive processes, ranging from spike development in monocots (e.g., barley Vrs1 and maize GT1) to sex determination in dicots (e.g., cucumber CmHB40 and persimmon MeGI). Meanwhile, members of other subfamilies (HD-ZIP II-IV) contribute significantly to diverse reproductive processes including pistil development, floral organ formation, and anther development, among others. This review provides a comprehensive synthesis of HD-ZIP subfamily functions in reproductive development, integrating current knowledge while highlighting critical research gaps. These insights aim to provide theoretical foundations for functional characterization and potential applications of HD-ZIP reproductive regulators, while advancing our understanding of transcriptional regulation mechanisms in plant reproductive development.

Quorum sensing (QS) is the communication system of bacteria that depends on QS signals. Quorum quenching (QQ) enzymes degrade QS signals and are promising alternatives of antibiotics to treat bacterial infections. Here, we found that dietary QQ N-acyl homoserine (AHL) lactonase led to microbiota dysbiosis in zebrafish, with reduction of Aeromonas and enrichment of Plesiomonas. Through gnotobiotic zebrafish colonized with a minimal microbiota, we found that QQ-mediated microbial alteration relies on host Myd88 signaling and neutrophil elastase. Mechanistically, quorum quenching increased the susceptibility of commensal Aeromonas to host neutrophil elastase by impairing bacterial lateral flagellar system, leading to reduced colonization of Aeromonas and subsequent enrichment of Plesiomonas due to ecological competition of the two species. Together, we found that dietary QQ lactonase led to microbiota alteration by impairing the adaptation of commensal Aeromonas to host innate immunity, which provided novel insight in the role of quorum sensing in host-microbiota interaction. ### Competing Interest Statement The authors have declared no competing interest.

The function and safety of probiotics are specific at the strain level. Accurate identification and evaluation of probiotics is very important for the development of the industry. In this work, five strains of Bacillus velezensis isolated from large yellow croaker (Larimichthys crocea) were classified into two genotypes by random amplification polymorphic DNA (RAPD) strain typing.The representative strain T1 had a strong ability to inhibit pathogenic bacteria, and T23 has a strong ability to secrete digestive enzymes in vitro. The growth-promoting and disease-resistance abilities of T1 and T23 in zebrafish were then compared. The results illustrated that T23 significantly promoted the weight gain of zebrafish. T23 significantly enhanced the activity of lipase, and reduced the feeding metabolic energy to reduce the total metabolic energy. Although the T1 group had higher protease activity, but there were no obvious changes in total metabolic energy, and its growth-promoting effect was not obvious. In terms of intestinal morphology, both strains significantly increased the length of intestinal villi, but T23 had a stronger ability to maintain the thickness of the muscle layer, also significantly reduced serum lipopolysaccharide (LPS) level. qPCR detection of genes related to innate immunity showed that T1 significantly down-regulated the expression of TNF-α and IL-1β, and significantly up-regulated the expression of hepcidin. T23 significantly reduced the expression of TNF-α, and significantly improved the expression of hepcidin. In the A. versonii challenge test both T1 and T23 improved the survival rate of zebrafish, and T23 showed better capacity. 16S rRNA sequencing of intestinal microbiota showed that T1 and T23 could change the structure of the microbiota. The intestinal microbiota induced by the two supplement groups both affected the expression levels of growth-related genes and innate immunity-related genes in germ-free zebrafish (GF-zebrafish). When GF-zebrafish were directly immersed with T1 and T23, the results illustrated no significant changes in the expression of growth-related genes, but T1 significantly increased the expression of TNF-α, while T23 significantly affected the expression of IL-1β and IL-10. Comparative genomic analysis of T1 and T23 implicated that T23 strain may be more comprehensive and complex in function. Together, our results showed strain specific property of probiotic effects, and revealed potential microbiota-associated mechanism of the effect of B. velezensis strains on growth and immunity of fish.

Fleshy fruits are popular among consumers due to their significant nutritional value, which includes essential bioactive compounds such as pigments, vitamins, and minerals. Notably, plant-derived pigments are generally considered safe and reliable, helping to protect humans against various inflammatory diseases. Although the phytochemical diversity and their biological activities have been extensively reviewed and summarized, the status of bioactive nutrients in fleshy fruits, particularly with a focusing on different colors, has received less attention. Therefore, this review introduces five common types of fleshy fruits based on coloration and summarizes their major bioactive compounds. It also provides the latest advancements on the function, biosynthesis, and metabolic engineering of plant-derived pigments. In this review, we emphasize that promoting the consumption of a diverse array of colorful fruits can contribute to a balanced diet; however, optimal intake levels still require further clinical validation. This review may serve as a useful guide for decisions that enhance the understanding of natural pigments and accelerate their application in agriculture and medicine.

BACKGROUND:Tiller number is a critical component of rice yield, as it directly influences overall productivity. While upland rice varieties are well adapted to lowland environments and prove resilient to fluctuating water availability, their typically low tillering capacity limits their performance in lowland ecosystems where conditions are more conducive to achieving higher yields. RESULTS:To facilitate the marker-assisted selection (MAS) breeding of upland rice cultivars suitable for lowland conditions, we performed QTL-seq analysis using populations derived from a cross between a high-tillering lowland indica parent (PTT1) and a low-tillering upland tropical japonica line (NDCMP49). Two major QTLs associated with tiller number were identified on chromosomes 4 and 5 and designated as qTN4 and qTN5, respectively. Candidate gene analysis revealed NAL1 and OsOFP19 as putative genes underlying these loci. Functional validation of NAL1 using CRISPR-Cas9 knockout mutants confirmed its role as a negative regulator of tillering, as two independent alleles of nal1 mutant plants exhibited significantly increased tiller numbers compared with the wild type. Marker-trait association analysis further supported the additive effect of qTN4 (NAL1) and qTN5 (OsOFP19), indicating their potential for pyramiding in breeding programs. Functional KASP markers of NAL1 and OsOFP19 were developed and successfully validated in segregating populations, demonstrating their applicability for marker-assisted selection. CONCLUSIONS:Collectively, these findings advance our understanding of the genetic regulation of tillering in rice and provide molecular tools for improving plant architecture and yield in upland rice varieties cultivated under lowland conditions.