Identification of Candidate Genes for Rind Color and Bloom Formation in Watermelon Fruits Based on a Quantitative Trait Locus-Seq

Identification of Candidate Genes for Green Rind Color in Watermelon

The color of the rind is one of the most crucial agronomic characteristics of watermelon (Citrullus lanatus L.). Its genetic analysis was conducted to provide the identification of genes regulating rind color and improving the quality of watermelon appearance. In this study, a mapping population of 505 F2 plants, derived from a cross between green (CG058) and light-green (CG265) rinds, along with a high-density genetic linkage (average 0.9 cM distance between bin markers), was used to map and identify possible candidate genes. The green rind trait was determined to be regulated by a single Mendelian locus and was precisely located within a 110 kb genomic site on chromosome nine (Chr 9). In the respective region, two potential genes, Cla97C09G175170 and Cla97C09G175180, were substantially downregulated in the light-green rind in comparison to the green rind. Previous studies revealed that Cla97C09G175170, encoding a two-component response regulator-like protein (APRR2), is possibly involved in the green rind trait in watermelon. Virus-induced gene silencing (VIGS) assay confirmed that ClAPRR2 is a key gene responsible for green rind color. Moreover, qRT-PCR analysis revealed that the transcription levels of multiple key genes in the chlorophyll (Chl) biosynthesis pathway were downregulated in the light-green rind relative to the green rind. The current findings have the potential to clarify the regulatory mechanisms that underlie the color of the watermelon rind. These data would provide valuable insights for the targeted molecular design and development of watermelon rinds.

The dominant white color trait of the melon fruit rind is associated with epicuticular wax accumulation

MAIN CONCLUSION

Microscopic analyses and chemical profiling demonstrate that the white rind phenotype in melon fruit is associated with the accumulation of n-alkanes, fatty alcohols, aldehydes and wax esters. Serving as an indicator of quality, the rind (or external) color of fruit directly affects consumer choice. A fruit's color is influenced by factors such as the levels of pigments and deposited epicuticular waxes. The latter produces a white-grayish coating often referred to as "wax bloom". Previous reports have suggested that some melon (Cucumis melo L.) accessions may produce wax blooms, where a dominant white rind color trait was genetically mapped to a major locus on chromosome 7 and suggested to be inherited as a single gene named Wi. We here provide the first direct evidence of the contribution of epicuticular waxes to the dominant white rind trait in melon fruit. Our light and electron microscopy and gas chromatography-mass spectrometry (GC-MS) comparative analysis of melon accessions with white or green rinds reveals that the rind of melon fruit is rich in epicuticular waxes. These waxes are composed of various biochemical classes, including fatty acids, fatty alcohols, aldehydes, fatty amides, n-alkanes, tocopherols, triterpenoids, and wax esters. We show that the dominant white rind phenotype in melon fruit is associated with increased accumulation of n-alkanes, fatty alcohols, aldehydes and wax esters, which are linked with the deposition of crystal-like wax platelets on their surfaces. Together, this study broadens the understanding of natural variation in an important quality trait of melon fruit and promotes the future identification of the causative gene for the dominant white rind trait.

Fine mapping and transcriptome profiling reveal CpAPRR2 to modulate immature fruit rind color formation in zucchini (Cucurbita pepo)

KEY MESSAGE

A large fragment deletion of CpAPRR2, encoding a two-component response regulator-like protein, which influences immature white rind color formation in zucchini (Cucurbita pepo). Fruit rind color is an important agronomic trait that affects commodity quality and consumer choice in zucchini (Cucurbita pepo). However, the molecular mechanism controlling rind color is unclear. We characterized two zucchini inbred lines: '19' (dark green rind) and '113' (white rind). Genetic analysis revealed white immature fruit rind color to be controlled by a dominant locus (CpW). Combining bulked segregant analysis sequencing (BSA-seq) and Kompetitive Allele-Specific PCR (KASP) markers, we mapped the CpW locus to a 100.4 kb region on chromosome 5 and then narrow down the candidate region to 37.5 kb using linkage analysis of 532 BC1 and 1613 F2 individuals, including 6 coding genes. Among them, Cp4.1LG05g02070 (CpAPRR2), encoding a two-component response regulator-like protein, was regarded to be a promising candidate gene. The expression level of CpAPRR2 in dark green rind was significantly higher than that in white rind and was induced by light. A deletion of 2227 bp at the 5' end of CpAPRR2 in '113' might explain the white phenotype. Further analysis of allelic diversity in zucchini germplasm resources revealed rind color to be associated with the deletion of CpAPRR2. Subcellular localization analysis indicated that CpAPRR2 was a nuclear protein. Transcriptome analysis using near-isogenic lines with dark green (DG) and white (W) rind indicated that genes involved in photosynthesis and porphyrin metabolism pathways were enriched in DG compared with W. Additionally, chlorophyll synthesis-related genes were upregulated in DG. These results identify mechanisms of zucchini rind color and provide genetic resources for breeding.

Development of a Gene-Based Marker Set for Orange-Colored Watermelon Flesh with a High β-Carotene Content

The fruit flesh of watermelons differs depending on the distinct carotenoid composition. Orange-colored flesh relates to the accumulation of β-carotene, which is beneficial to human health. Canary-yellow-fleshed OTO-DAH and orange-β-fleshed (orange-fleshed with high β-carotene) NB-DAH near-isogenic lines (NILs) were used to determine the genetic mechanism attributed to orange watermelon flesh. For genetic mapping, an F2 population was developed by crossing the two NILs. The segregation ratio of flesh color in the F2 population indicated that the orange-β flesh of the NB-DAH NIL was controlled by a single incompletely dominant gene. Through a comparative analysis of the whole-genome sequences of the parent lines and NILs, a major introgression region unique to the NB-DAH NIL was detected on Chr. 1; this was considered a candidate region for harboring genes that distinguish orange from canary-yellow and red flesh. Among the 13 genes involved in the carotenoid metabolic pathway in watermelons, only ClPSY1 (ClCG01G008470), which encodes phytoene synthase 1, was located within the introgression region. The genotyping of F2 plants using a cleaved amplified polymorphic sequence marker developed from a non-synonymous SNP in ClPSY1 revealed its relationship with orange-β flesh. The insights gained in this study can be applied to marker-assisted breeding for this desirable trait.

Molecular Mapping of Putative Genomic Regions Controlling Fruit and Seed Morphology of Watermelon

The genetic regulatory basis of qualitative and quantitative phenotypes of watermelon is being investigated in different types of molecular and genetic breeding studies around the world. In this study, biparental F2 mapping populations were developed over two experimental years, and the collected datasets of fruit and seed traits exhibited highly significant correlations. Whole-genome resequencing of comparative parental lines was performed and detected single nucleotide polymorphism (SNP) loci were converted into cleaved amplified polymorphic sequence (CAPS) markers. The screened polymorphic markers were genotyped in segregating populations and two genetic linkage maps were constructed, which covered a total of 2834.28 and 2721.45 centimorgan (cM) genetic lengths, respectively. A total of 22 quantitative trait loci (QTLs) for seven phenotypic traits were mapped; among them, five stable and major-effect QTLs (PC-8-1, SL-9-1, SWi-9-1, SSi-9-1, and SW-6-1) and four minor-effect QTLs (PC-2-1 and PC-2-2; PT-2-1 and PT-2-2; SL-6-1 and SSi-6-2; and SWi-6-1 and SWi-6-2) were observed with 3.77-38.98% PVE. The adjacent QTL markers showed a good fit marker-trait association, and a significant allele-specific contribution was also noticed for genetic inheritance of traits. Further, a total of four candidate genes (Cla97C09G179150, Cla97C09G179350, Cla97C09G180040, and Cla97C09G180100) were spotted in the stable colocalized QTLs of seed size linked traits (SL-9-1 and SWi-9-1) that showed non-synonymous type mutations. The gene expression trends indicated that the seed morphology had been formed in the early developmental stage and showed the genetic regulation of seed shape formation. Hence, we think that our identified QTLs and genes would provide powerful genetic insights for marker-assisted breeding aimed at improving the quality traits of watermelon.