Temperature rising caused by global warming has imposed significant negative effects on crop qualities and yields. To get the well-known molecular mechanism upon the higher temperature, we carefully analyzed the RNA sequencing-based transcriptomic responses of two contrasting chieh-qua genotypes: A39 (heat-tolerant) and H5 (heat-sensitive). In this study, twelve cDNA libraries generated from A39 and H5 were performed with a transcriptome assay under normal and heat stress conditions, respectively. A total of 8705 differentially expressed genes (DEGs) were detected under normal conditions (3676 up-regulated and 5029 down-regulated) and 1505 genes under heat stress (914 up-regulated and 591 down-regulated), respectively. A significant positive correlation between RNA-Seq data and qRT-PCR results was identified. DEGs related to heat shock proteins (HSPs), ubiquitin-protein ligase, transcriptional factors, and pentatricopeptide repeat-containing proteins were significantly changed after heat stress. Several genes, which encoded HSPs (CL2311.Contig3 and CL6612.Contig2), cytochrome P450 (CL4517.Contig4 and CL683.Contig7), and bHLH TFs (CL914.Contig2 and CL8321.Contig1) were specifically induced after four days of heat stress. DEGs detected in our study between these two contrasting cultivars would provide a novel basis for isolating useful candidate genes of heat stress responses in chieh-qua.

Chieh-qua is an important cucurbit crop and very popular in South China and Southeast Asia. Despite its significance, its genetic basis and domestication history are unclear. In this study, we have successfully generated a chromosome-level reference genome assembly for the chieh-qua ‘A36’ using a hybrid assembly strategy that combines PacBio long reads and Illumina short reads. The assembled genome of chieh-qua is approximately 953.3 Mb in size and is organized into 12 chromosomes, with contig N50 of 6.9 Mb and scaffold N50 of 68.2 Mb. Notably, the chieh-qua genome is comparable in size to the wax gourd genome. Through gene prediction analysis, we have identified a total of 24 593 protein-coding genes in the A36 genome. Additionally, approximately 56.6% (539.3 Mb) of the chieh-qua genome consists of repetitive sequences. Comparative genome analysis revealed that chieh-qua and wax gourd are closely related, indicating a close evolutionary relationship between the two species. Population genomic analysis, employing 129 chieh-qua accessions and 146 wax gourd accessions, demonstrated that chieh-qua exhibits greater genetic diversity compared to wax gourd. We also employed the GWAS method to identify related QTLs associated with subgynoecy, an interested and important trait in chieh-qua. The MYB59 (BhiCQ0880026447) exhibited relatively high expression levels in the shoot apex of four subgynoecious varieties compared with monoecious varieties. Overall, this research provides insights into the domestication history of chieh-qua and offers valuable genomic resources for further molecular research.

(1) Background: Wax gourd is an economically important vegetable crop in many tropical and sub-tropical countries in Asia. Fruit color is an important fruit quality trait, but the genetic, biochemical basis and regulatory network of fruit color variation in wax gourd are rarely studied. (2) Methods: In this study, two wax gourd inbred lines with different pericarp colors were used as materials to conduct joint metabolomic and transcriptomic analyses on mature fruit pericarp: B214 with yellow and B227 with dark green color. (3) Results: It was found that the chlorophyll content in the pericarp of B214 was significantly lower than that of B227, consistent with the down-regulation of several genes involved in the chlorophyll biosynthesis pathway, including hemA, hemB, hemC, hemF, chlH, chlI, chlM, POR, and CAO. The 229 metabolites showed differential accumulation levels between B214 and B227, and 4 anthocyanins, 5 flavanones, 25 flavones, 25 flavone C-glycosides, 12 flavonols, and 3 isoflavones were identified. In particular, cyanidin 3-O-glucoside, an anthocyanin contributing to the coloration of dark color, showed higher accumulation in B227 than in B214, probably due to the higher expression of genes of F3′H and glucosyl transferases (GTs) in B227. Transcription factors such as MYBs and bHLHs showed differential expressions between the two lines including bHLH14, a homolog of Arabidopsis AtbHLH14 that had significantly higher expression in B227 than in B214. bHLH14 was located in a region where the pericarp color (pc) locus was mapped, suggesting it may be a candidate gene for the pc locus. (4) Conclusions: This work supports the association of chlorophyll and flavonoid synthesis in wax gourd fruit color variation and also provides a good foundation for understanding the regulatory network for wax gourd coloration.

Heat stress, as a negative factor, severely threatens the quality and production of bottle gourd, which prefers to grow in a warm environment. To understand which genes are involved in the resistance to heat stress in bottle gourd (Lagenaria siceraria (Mol.) Standl.), we analyzed the characteristics of two genetic bottle gourd varieties, “Mei feng”-MF (heat resistant) and “Lv long”-LL (heat sensitive). Under heat stress, MF plants exhibited a higher survival rate, lower relative electrolytic leakage, and decreased stomatal aperture compared with LL. In addition, RNA-Seq was carried out on the two varieties under normal conditions and heat stress. The results revealed a total of 1485 up-regulated and 946 down-regulated genes under normal conditions, while 602 genes were up-regulated and 1212 genes were down-regulated under heat stress. Among these genes, several differentially expressed genes (DEGs) involved in the MAPK (mitogen-activated protein kinase) signaling pathway and members of bHLH (basic helix-loop-helix) transcription factors showed significant up- or down-regulation after heat stress. Next, to validate these findings, we conducted quantitative real-time PCR (qRT-PCR) analysis, which confirmed the expression patterns of the genes detected through RNA-Seq. Collectively, the DEGs between the two contrasting cultivars identified in our study provide novel insight into excavating helpful candidate genes associated with heat tolerance in bottle gourd.