Chinese bayberry (Myrica rubra or Morella rubra; 2n = 16) produces fruit with a distinctive flavor, high nutritional, and economic value. However, previous versions of the bayberry genome lack sequence continuity. Moreover, to date, no large-scale germplasm resource association analysis has examined the allelic and genetic variations determining fruit quality traits. Therefore, in this study, we assembled a telomere-to-telomere (T2T) gap-free reference genome for the cultivar ‘Zaojia’ using PacBio HiFi long reads. The resulting 292.60 Mb T2T genome, revealed 8 centromeric regions, 15 telomeres, and 28 345 genes. This represents a substantial improvement in the genome continuity and integrity of Chinese bayberry. Subsequently, we re-sequenced 173 accessions, identifying 6 649 674 single nucleotide polymorphisms (SNPs). Further, the phenotypic analyses of 29 fruit quality-related traits enabled a genome-wide association study (GWAS), which identified 1937 SNPs and 1039 genes significantly associated with 28 traits. An SNP cluster pertinent to fruit color was identified on Chr6: 3407532 to 5 153 151 bp region, harboring two MYB genes (MrChr6G07650 and MrChr6G07660), exhibiting differential expression in extreme phenotype transcriptomes, linked to anthocyanin synthesis. An adjacent, closely linked gene, MrChr6G07670 (MLP-like protein), harbored an exonic missense variant and was shown to increase anthocyanin production in tobacco leaves tenfold. This SNP cluster, potentially a quantitative trait locus (QTL), collectively regulates bayberry fruit color. In conclusion, our study presented a complete reference genome, uncovered a suite of allelic variations related to fruit-quality traits, and identified functional genes that could be harnessed to enhance fruit quality and breeding efficiency of bayberries.

Chinese bayberry is a distinctive fruit tree native to southern China. However, it suffers from severe fruit abscission at mature stage, while the molecula

Chinese bayberry (Myrica rubra or Morella rubra) is a valuable fruit, yet the mechanism of its flesh segment development is not well understood. Using paraffin sectioning, we investigated the flower buds of the ‘Biqi’ and ‘Zaojia’ varieties, revealing that the flesh segment development in these Chinese bayberry varieties involved the formation of a primordium outside the ovary wall, the establishment of a simple columnar structure, and the formation of the primary flesh segment. Assessment of endogenous hormone levels indicated the significant reductions in jasmonic acid (JA) and indole-3-acetic acid (IAA) levels at the critical stages of flesh segment development. Correlation analysis highlighted the essential roles of IAA, JA, abscisic acid (ABA), and gibberellins in the flesh segment developmental process, underscoring the complex interactions driven primarily by the IAA, JA, and ABA networks. Gene modules positively correlated with flesh segment development were identified using transcriptome-based weighted gene co-expression network analysis (WGCNA). Differentially expressed genes (DEGs) were enriched in plant hormone signal transduction pathways, particularly for upregulated genes associated with auxin and JA signaling. Key genes predicted to be involved in flesh segment development included LAX2 and LAX3 (auxin transport), JAZ6 (JA signaling repression), and KAN1 and KAN4 (regulating multiple hormonal signaling pathways). Quantitative real-time polymerase chain reaction (qRT-PCR) validation confirmed that the expression trends for these genes were consistent across both varieties, particularly for CRC, SEP1, SEP3, IAA7, and JAZ6. Immunofluorescence localization studies revealed that auxin was primarily distributed in the central vascular bundle and outer cells of the flesh segment. This uneven auxin distribution might contribute to the unique morphology of flesh segments. Overall, this study provides insights into the hormonal regulation and genetic factors involved in the development of Chinese bayberry flesh segments.

Bayberry twig blight caused by the ascomycete fungus Pestalotiopsis versicolor is a devastating disease threatening worldwide bayberry production. However, the molecular basis underlying the pathogenesis of P. versicolor is largely unknown. Here, we identified and functionally characterized the MAP kinase PvMk1 in P. versicolor through genetic and cellular biochemical approaches. Our analysis reveals a central role of PvMk1 in regulating P. versicolor virulence on bayberry. We demonstrate that PvMk1 is involved in hyphal development, conidiation, melanin biosynthesis, and cell wall stress responses. Notably, PvMk1 regulates P. versicolor autophagy and is essential for hyphal growth under nitrogen-depleting conditions. These findings suggest the multifaceted role of PvMk1 in regulating P. versicolor development and virulence. More remarkably, this evidence of virulence-involved cellular processes regulated by PvMk1 has paved a fundamental way for further understanding the impact of P. versicolor pathogenesis on bayberry.

Chinese bayberry (Myrica rubra) is a subtropical fruit rich in anthocyanins, which are significantly regulated by light during ripening. This study employed integrated transcriptomic and metabolomic analyses to investigate the effects of light exposure on fruit quality and anthocyanin synthesis using various light-transmitting bag treatments. A greenhouse experiment demonstrated that no-transmitting bags (HQ) treatment during early fruit development significantly reduced coloration and quality indicators, including sucrose (55.3%), glucose (59.5%), fructose (37.5%), malic acid (36.6), oxalic acid (46.5), total flavonoids (60.1%), vitamin C (93.0%), and total anthocyanins (90.8%), while increasing acidity as compared to transmitting bags (WQ) treatment. Transcriptomic analysis revealed that expression levels of flavonoid synthesis genes were significantly reduced under light conditions. The expression of LDOX (Leucoanthocyanidin dioxygenase) gene was notably higher in WQ treatment, potentially contributing to bayberry fruit coloration. Metabolomic analysis identified 44 differential metabolites related to anthocyanin synthesis, with proanthocyanidins, delphinidin-3-O-galactoside, pelargonidin glucoside, and paeonidin glucoside levels significantly higher in WQ treatment compared to HQ. Furthermore, the integration of transcriptomic and metabolomic data identified the transcription factor HY5 as a key regulator in light-mediated anthocyanin accumulation. Overall, this study provides novel insights into the molecular mechanisms underlying light-regulated pigmentation in Chinese bayberry fruits. The findings contribute to understanding fruit quality development during ripening and offer a scientific basis for enhancing fruit quality and refining cultivation techniques in Chinese bayberry and similar fruit species.

The accurate assessment of Chinese bayberry (Myrica rubra) maturity is critical for intelligent harvesting. This study proposes a novel cascaded framework combining instance segmentation and multi-feature regression for accurate maturity detection. First, a lightweight SOLOv2-Light network is employed to segment each fruit individually, which significantly reduces computational costs with only a marginal drop in accuracy. Then, a multi-feature extraction network is developed to fuse deep semantic, color (LAB space), and multi-scale texture features, enhanced by a channel attention mechanism for adaptive weighting. The maturity ground truth is defined using the a*/b* ratio measured by a colorimeter, which correlates strongly with anthocyanin accumulation and visual ripeness. Experimental results demonstrated that the proposed method achieves a mask mAP of 0.788 on the instance segmentation task, outperforming Mask R-CNN and YOLACT. For maturity prediction, a mean absolute error of 3.946% is attained, which is a significant improvement over the baseline. When the data are discretized into three maturity categories, the overall accuracy reaches 95.51%, surpassing YOLOX-s and Faster R-CNN by a considerable margin while reducing processing time by approximately 46%. The modular design facilitates easy adaptation to new varieties. This research provides a robust and efficient solution for in-field bayberry maturity detection, offering substantial value for the development of automated harvesting systems.