High-density map is a valuable tool for genetic and genomic analysis. Although wax gourd is a widely distributed vegetable of Cucurbitaceae and has important medicinal and health value, no genetic map has been constructed because of the lack of efficient markers. Specific-locus amplified fragment sequencing (SLAF-seq) is a newly developed high-throughput strategy for large-scale single nucleotide polymorphism (SNP) discovery and genotyping. In our present study, we constructed a high-density genetic map by using SLAF-seq and identified a locus controlling pericarp color in wax gourd. An F2 population of 140 individuals and their two parents were subjected to SLAF-seq. A total of 143.38 M pair-end reads were generated. The average sequencing depth was 26.51 in the maternal line (B214), 27.01 in the parental line (B227), and 5.11 in each F2 individual. When filtering low-depth SLAF tags, a total of 142,653 high-quality SLAFs were detected, and 22,151 of them were polymorphic, with a polymorphism rate of 15.42 %. And finally, 4,607 of the polymorphic markers were selected for genetic map construction, and 12 linkage groups (LGs) were generated. The map spanned 2,172.86 cM with an average distance between adjacent markers for 0.49 cM. The inheritance of pericarp color was also studied, which showed that the pericarp color was controlled by one single gene. And based on the newly constructed high-density map, a single locus locating on chromosome 5 was identified for controlling the pericarp color of wax gourd. This is the first report of high-density genetic map construction and gene mapping in wax gourd, which will be served as an invaluable tool for gene mapping, marker assisted breeding, map-based gene cloning, comparative mapping and draft genome assembling of wax gourd.

Wax gourd is a widely used vegetable of Cucuribtaceae, and also has important medicinal and health values. However, the genomic resources of wax gourd were scarcity, and only a few nucleotide sequences could be obtained in public databases. In this study, we examined transcriptome in wax gourd. More than 44 million of high quality reads were generated from five different tissues of wax gourd using Illumina paired-end sequencing technology. Approximately 4 Gbp data were generated, and de novo assembled into 65,059 unigenes, with an N50 of 1,132 bp. Based on sequence similarity search with known protein database, 36,070 (55.4%) showed significant similarity to known proteins in Nr database, and 24,969 (38.4%) had BLAST hits in Swiss-Prot database. Among the annotated unigenes, 14,994 of wax gourd unigenes were assigned to GO term annotation, and 23,977 were found to have COG classifications. In addition, a total of 18,713 unigenes were assigned to 281 KEGG pathways. Furthermore, 6,242 microsatellites (simple sequence repeats) were detected as potential molecular markers in wax gourd. Two hundred primer pairs for SSRs were designed for validation of the amplification and polymorphism. The result showed that 170 of the 200 primer pairs were successfully amplified and 49 (28.8%) of them exhibited polymorphisms. Our study enriches the genomic resources of wax gourd and provides powerful information for future studies. The availability of this ample amount of information about the transcriptome and SSRs in wax gourd could serve as valuable basis for studies on the physiology, biochemistry, molecular genetics and molecular breeding of this important vegetable crop.

Caixin and Zicaitai (Brassica rapa) belong to Southern and Central China respectively. Zicaitai contains high amount of anthocyanin in leaf and stalk resulting to the purple color. Stalk is the major edible part and stalk color is an economically important trait for the two vegetables. The aim of this study is to construct a high density genetic map using the specific length amplified fragment sequencing (SLAF-seq) technique to explore genetic basis for anthocyanin pigmentation traits via quantitative trait loci (QTL) mapping. We constructed a high generation linkage map with a mapping panel of F2 populations derived from 150 individuals of parental lines “Xianghongtai 01” and “Yinong 50D” with purple and green stalk respectively. The map was constructed containing 4253 loci, representing 10,940 single nucleotide polymorphism (SNP) markers spanning 1030.04 centiMorgans (cM) over 10 linkage groups (LGs), with an average distance between markers of 0.27 cM. Quantitative trait loci (QTL) analysis revealed that a major locus on chromosome 7 and 4 minor QTLs explaining 2.69–61.21% of phenotypic variation (PVE) were strongly responsible for variation in stalk color trait. Bioinformatics analysis of the major locus identified 62 protein-coding genes. Among the major locus, there were no biosynthetic genes related to anthocyanin. However, there were several transcription factors like helix-loop-helix (bHLH) bHLH, MYB in the locus. Seven predicted candidate genes were selected for the transcription level analysis. Only bHLH49 transcription factor, was significantly higher expressed in both stalks and young leaves of Xianghongtai01 than Yinong50D. An insertion and deletion (InDel) marker developed from deletion/insertion in the promoter region of bHLH49 showed significant correlation with the stalk color trait in the F2 population. Using the constructed high-qualified linkage map, this study successfully identified QTLs for stalk color trait. The identified valuable markers and candidate genes for anthocyanin accumulation in stalk will provide useful information for molecular regulation of anthocyanin biosynthesis. Overall our findings will lay a foundation for functional gene cloning, marker-assisted selection (MAS) and molecular breeding of important economic traits in B. rapa.

Wax gourd, which belongs to Cucurbitaceae, is an excellent plant resource with the concomitant function of both medicine and foodstuff. Its unique taste and rich nutrition are deeply accepted by consumers. However, the main flavor and nutrients are still unclear, which restricts the quality breeding process of wax gourd. Here, we discovered that monosaccharides, malic acid and citrulline affect the flavor and nutrition of wax gourd and clarified the dynamic accumulation process of these metabolites. To gain insights into the underlying predominant genes regulating accumulation of these metabolites, we performed a time-course transcriptome analysis using RNA-sequencing analysis and compared the expression of screened genes among twenty-four germplasms with different metabolites levels. In addition, the expression abundance among the homologous genes were also analyzed. Finally, a total of 8 genes related to sugar [AGA2 (Bhi03G001926), SUS (Bhi12G001032)], malic acid [MDH (Bhi12G001426, Bhi01G000427), PEPC (Bhi12G000721, Bhi09G002867), ME (Bhi01G002616)] and citrulline [ASS (Bhi02G000401)], respectively were determined. In summary, understanding the core genes influencing taste or nutrition will provide a theoretical basis for fruit quality improvement in wax gourd.

(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.