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The melon is an important fruit crop. Chloroplast genomes are widely used to analyze plant genetic diversity. The chloroplast genome was used to study melon population genetics. We identified 192 SNPs in the chloroplast genome of 348 melon tissue samples. These SNPs were mainly distributed in the large single copy and small single copy of the chloroplast genome. The two inverted repeat (IR) regions (IRa and IRb) contained almost no SNPs. The melon population structure, fruit-related traits, and genetic diversity within each group were analyzed based on these SNPs. The 192 SNPs effectively divided the melon populations into three groups: wild, thick-rind type cultivated melon, and thin-rind type cultivated melon groups, with genetic diversities of 1.12 × 10−3, 4.71 × 10−4, and 2.85 × 10−4, respectively. This study analyzed the single fruit weight, soluble solids content, flesh color value, and flesh thickness (FT) traits in the population to understand differences in important fruit-related traits, and there were remarkable differences in FT among the three groups. These results suggest the chloroplast genome can be used to study the population genetics of the melon, and they contribute to the classification and identification of core germplasm resources.

Citrullus amarus (citronmelon) is an important crop with resistance to many diseases. The chloroplast genome is important in studying the genetic evolution of plants. The C. amarus chloroplast genome was first reported in this study using a novel assembly method based on whole genome sequencing. We identified 82 SNP sites in chloroplast genome with 313 watermelon materials. The 82 SNPs could effectively divide the natural watermelon population into four groups: C. lanatus subsp. lanatus, C. lanatus subsp. mucosospermus, C. lanatus subsp. vulgaris (ecologically from the Americas) and C. lanatus subsp. vulgaris (ecologically from Asia), with decreasing genetic diversity (π) (6.6 × 10−5, 2.4 × 10−5, 9.8 × 10−6 and 5.41 × 10−6, respectively). The single fruit weight, soluble solids, fruit color and 1000-seed weight of C. lanatus subsp. lanatus were significantly different from those of the other three groups. These results indicate that the complete chloroplast genome can be used in studying population genetics of watermelon, which is helpful for classification among intra species subgroups and identification of core germplasm resources.

Citrullus mucosospermus (egusi watermelon) and Citrullus lanatus (dessert watermelon) are closely related subspecies. Variation in their seed coats underlies a key to understand the major differences in seeds between these two subspecies. Although the genetic model is understood, the candidate genes controlling the egusi seed trait in watermelon are unknown. In this study, a locus that controls the egusi seed trait, WEG6.1, which is located on chromosome 6 of the watermelon genome, was identified. A total of 195 polymorphic primers and 325 F2 plants were used to construct a primary mapping population and linkage maps. A large population of 758 F2 plants was used for fine mapping of the eg gene. The candidate gene was mapped to a 130.7 kb region on chromosome 6. Eleven genes were present within the corresponding region of the reference genome. All eleven candidate genes were sequenced, revealing that the CDS of the Cla007520 gene had a 3 bp deletion that resulted in the omission of one amino acid (serine) in C. mucosospermus. In addition, expression of the Cla007520 gene was highest at the early stage of seed formation, exhibiting a downward trend thereafter. The predicted protein of the Cla007520 gene belonged to the CPP protein family, and its amino acid constituents were similar to those of AtTSO1, which is associated with promoting integument cell proliferation in ovule development. This study revealed genes that facilitate the formation of egusi seed and might lead to a breakthrough in seed development and cultivated watermelon domestication.