Chilling stress (CS) is an important limiting factor for the growth and development of passion fruit (Passiflora edulis) in winter in South China. However, little is known about how the passion fruit responds and adapts to CS. In this study, we performed transcriptome sequencing of cold-susceptible cultivar Huangjinguo (HJG) and cold-tolerant cultivar Tainong 1 (TN1) under normal temperature (NT) and CS conditions, and a total of 47,353 unigenes were obtained by seven databases. Using differentially expressed unigenes (DEGs) analysis, 3,248 and 4,340 DEGs were identified at two stages, respectively. The Gene Ontology (GO) enrichment analysis showed that the DEGs were mainly related to phosphorylation, membrane protein, and catalytic activity. In Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway, the unigenes of plant-pathogen interaction, plant hormone signal transduction and fatty acid metabolism were enriched. Then, the 12,471 filtered unigenes were clustered into eight co-expression modules, and two modules were correlated with CS. In this two modules, 32 hub unigenes were obtained. Furthermore, the unigenes related to CS were validated using quantitative real-time PCR (RT-qPCR). This work showed that the expression levels of CS-related unigenes were very different in two passion fruit cultivars. The results provide information for the development of passion fruit with increased chilling tolerance.

Fragrance is a valuable trait in rice varieties, with its aroma significantly influencing consumer preference. In this study, we conducted comprehensive metabolome and transcriptome analyses to elucidate the genetic and biochemical basis of fragrance in the Shangsixiangnuo (SSXN) variety, a fragrant indica rice cultivated in Guangxi, China. Through sensory evaluation and genetic analysis, we confirmed SSXN as strongly fragrant, with an 806 bp deletion in the BADH2 gene associated with fragrance production. In the metabolome analysis, a total of 238, 233, 105 and 60 metabolic compounds exhibited significant changes at the seedling (S), reproductive (R), filling (F), and maturation (M) stages, respectively. We identified four compounds that exhibited significant changes in SSXN across all four development stages. Our analyses revealed a significant upregulation of 2-acetyl-1-pyrroline (2AP), the well-studied aromatic compound, in SSXN compared to the non-fragrant variety. Additionally, correlation analysis identified several metabolites strongly associated with 2AP, including ethanone, 1-(1H-pyrrol-2-yl)-, 1H-pyrrole, and pyrrole. Furthermore, Weighted Gene Co-expression Network Analysis (WGCNA) analysis highlighted the magenta and yellow modules as particularly enriched in aroma-related metabolites, providing insights into the complex aromatic compounds underlying the fragrance of rice. In the transcriptome analysis, a total of 5582, 5506, 4965, and 4599 differential expressed genes (DEGs) were identified across the four developmental stages, with a notable enrichment of the common pathway amino sugar and nucleotide sugar metabolism in all stages. In our correlation analysis between metabolome and transcriptome data, the top three connected metabolites, phenol-, 3-amino-, and 2AP, along with ethanone, 1-(1H-pyrrol-2-yl)-, exhibited strong associations with transcripts, highlighting their potential roles in fragrance biosynthesis. Additionally, the downregulated expression of the P4H4 gene, encoding a procollagen-proline dioxygenase that specifically targets proline, in SSXN suggests its involvement in proline metabolism and potentially in aroma formation pathways. Overall, our study provides comprehensive insights into the genetic and biochemical mechanisms underlying fragrance production in rice, laying the foundation for further research aimed at enhancing fragrance quality in rice breeding programs.

Background: The passion fruit (Passiflora edulis Sims) is a diploid plant (2n = 2x = 18) and is a perennial scrambling vine in Southern China. However, the occurrence and spread of stem rot in passion fruit severely impact its yield and quality. Methods: In this study, we re-sequenced a BC1F1 population consisting of 158 individuals using whole-genome resequencing. We constructed a high-density genetic linkage map and identified the quantitative trait locus (QTL), and analyzed candidate genes associated with stem rot resistance in passion fruit. Results: Based on the passion fruit reference genome (MER), a high-density genetic linkage map was constructed with 1,180,406 single nucleotide polymorphisms (SNPs). The map contains nine linkage groups, covering a total genetic distance of 1559.03 cM, with an average genetic distance of 311.81 cM. The average genetic distance between 4206 bins was 0.404 cM, and the average gap length was 10.565 cM. The collinearity correlation coefficient between the genetic map and the passion fruit genome was 0.9994. Fusarium solani was used to infect the BC1F1 population, and the resistance to stem rot showed a continuous distribution. A QTL, qPSR5, was mapped to the 113,377,860 bp–114,811,870 bp genomic region on chromosome 5. We performed RNA sequencing (RNA-seq) and real-time quantitative polymerase chain reaction (RT-qPCR) to analyze the expression levels of predicted genes in the candidate region and identified ZX.05G0020740 and ZX.05G0020810 as ideal candidate genes for stem rot resistance in passion fruit. Conclusions: The findings in this study not only lay the foundation for cloning the qPSR5 responsible for stem rot resistance but also provide genetic resources for the genetic improvement of passion fruit.

Chloroplasts are organelles responsible for photosynthesis in plants, providing energy for growth and development. However, the genetic regulatory mechanisms underlying early chloroplast development in rice remain incompletely understood. In this study, we identified a rice seedling thermosensitive chlorophyll-deficient mutant, osltsa8, and the genetic analysis of two F₂ populations suggested that this trait may be controlled by more than one pair of alleles. Through reciprocal F₂ populations and QTL-seq technology, OsLTSA8 was mapped to the interval of 24,280,402–25,920,942 bp on rice chromosome 8, representing a novel albino gene in rice. Within the candidate gene region of OsLTSA8, there were 258 predicted genes, among which LOC_Os08g39050, LOC_Os08g39130, and LOC_Os08g40870 encode pentatricopeptide repeat (PPR) proteins. RNA-seq identified 18 DEGs (differentially expressed genes) within the candidate interval, with LOC_Os08g39420 showing homology to the pigment biosynthesis-related genes Zm00001d017656 and Sb01g000470; LOC_Os08g39430 and LOC_Os08g39850 were implicated in chlorophyll precursor synthesis. RT-qPCR was employed to assess the expression levels of LOC_Os08g39050, LOC_Os08g39130, LOC_Os08g40870, LOC_Os08g39420, LOC_Os08g39430, and LOC_Os08g39850 in the wild-type and mutant plants. Among them, the differences in the expression levels of LOC_Os08g39050 and LOC_Os08g39430 were the most significant. This study will contribute to further elucidating the molecular mechanisms of rice chloroplast development.

The cultivated passion fruit (Passiflora edulis) is a diploid plant (2n=2x=18) and is an important fruit tree in southern China. However, the occurrence and spread of stem rot in passion fruit severely impact its yield and quality. This study aims to construct a high-density genetic linkage map and identify the quantitative trait locus (QTL) and candidate genes associated with stem rot resistance in passion fruit. In this study, we used an HG and ZG7 hybrid to develop a BC1F1 population consisting of 158 individuals. Take a previously published passion fruit genome as reference, a high-density genetic linkage map was constructed with 1,180,406 single nucleotide polymorphisms (SNPs). The map contains 9 linkage groups, covering a total genetic distance of 1559.03 cM, with an average genetic distance of 311.81 cM. The average genetic distance between 4206 bins was 0.404 cM, and the average gap length was 10.565 cM. The collinearity correlation coefficient between the genetic map and the passion fruit genome was 0.9994. Fusarium solani was used to infect the BC1F1 population, and the resistance to stem rot showed a continuous distribution. A QTL, qPSR5, was identified in the 145.878-152.951 cM region on the 5th linkage group. We performed RNA-seq and RT-qPCR to analyze the expression levels of predicted genes in the candidate region and identified ZX.05G0020740 and ZX.05G0020810 as ideal candidate genes for stem rot resistance in passion fruit. The findings in this study not only lay the foundation for cloning the qPSR5 responsible for stem rot resistance but also provide genetic resources for the genetic improvement of passion fruit.