Morphological diversity analysis in sweet watermelon revealed extensive variation in quantitative phenotypic traits, including plant architecture, flowering time and rates, fruit and seed yield, and fruit- and seed-related traits [41,77,78,79]. The section below outlines the genetic analysis of various quantitative traits.

High leaf biomass yield in watermelon is a desired trait for use as a leaf vegetable. High leaf biomass production is also vital to enhancing photosynthetic efficiency to promote high fruit production and yield. The number of leaves per plant, which is influenced by plant height and branching capacity, as well as the length, width and size of individual leaves, are important traits that influence the overall leaf biomass yield in watermelon. A genetic analysis of leaf traits has not been adequately studied in watermelon. There are no molecular markers or QTL mapping of leaf traits for efficient selection and marker-assisted breeding. Some accessions of white-fleshed citron watermelon (Citrullus lanatus var. citroides) exhibit a reduced leaf size compared to most commercially cultivated sweet watermelons. These germplasms may play a key role in understanding the genetic architecture of leaf yield and component traits in watermelon.

Plant height is an important trait that influences flower development and fruit yield potential in watermelon. The candidate gene Cla010726 is associated with reduced plant height in watermelon [80]. The expression levels of Cla010726 are significantly lower in short plants [80]. The genes designated as Cla015405 and Cla015406 are associated with a short phenotype in watermelon [81]. Recently, Cla015407, named Citrullus lanatus dwarfism (Cldf), has been thought to control short plant stature in watermelon [82]. A point mutation resulting in a 13 bp deletion in the coding sequence of Cldf led to a GA-deficient short phenotype [83]. The gene Cla010726 encodes for gibberellin 20-oxidase-like protein, whereas Cla015407 gene encodes gibberellic acid 3β-hydroxylase proteins, which are associated with the gibberellic acid metabolism, resulting in growth arrest and reduced plant height [82]. The gene designated as Cla010337, which encodes an ATP-binding cassette transporter (ABC transporter), reportedly conditioned dwarf plant height in watermelon [84]. The deletion of a single nucleotide of the gene Cla010337 causes the development of shorter watermelon plants [84]. Quantitative analysis revealed segregation ratios of 3:1 and 1:1 in the F₂ and backcross populations, suggesting that reduced plant height is controlled by a single recessive or dominant gene [82,85,86]. Cho et al. [86] identified the gene CICG09G018320, which encodes an ABC transporter, determining shorter watermelon plants in progenies derived between dwarf (Bush Sugar Baby) and normal (PCL-J1) watermelon cultivars. The ABC transporter gene results in shorter watermelon plants due to physiological changes in the levels of auxin, the phytohormone [86]. Internode length is a secondary trait that influences plant height in watermelon. Segregation ratios of 3:1 and 1:1 in the F₂ and backcross populations, respectively, were detected, suggesting that a single dominant gene controls the expression of short internode length in watermelon [29]. The gibberellin 3β-hydroxylase (GA 3β-hydroxylase) gene Cla015407 is associated with the short internode phenotype in watermelon [29]. GA 3β-hydroxylase is an important enzyme regulating GA biosynthesis by catalyzing the inactive precursors of GA₉, GA_20, and GA₅ into bioactive forms, namely, GA₄, GA_1, and GA₃, respectively [29].

Branching capacity is an important trait influencing leaf biomass production, flowering potential, vine and fruit yield in watermelon. In SSA, the dried branches of the crop are used as fodder for livestock. The branches are a good source of essential macro- and micro-nutrients [8]. Watermelon produces multiple lateral branches from the primary branches. A single recessive gene, Clbl (i.e., Citrullus lanatus branchless), causes branchlessness [87]. Bulked segregant sequencing (BSA-seq) analysis revealed a candidate gene, Cla018392, which encodes a TERMINAL FLOWER 1 protein associated with branchlessness in watermelon [87]. This gene reduces the formation and development of axillary and apical buds, thus limiting lateral branching in watermelon [87]. Genetic analysis of lateral branch development in watermelon is key for marker-assisted selection and QTL mapping. This enables the breeding of branchless watermelon cultivars for closed and protected production or open field environments. However, the branchless trait is not required in watermelon grown for high leaf biomass for food feed. Therefore, understanding the genetic regulation of profuse branching ability is essential for breeding of vegetable- and fodder-type watermelon varieties. We propose a comparative genetic analysis of watermelon genotypes with contrasting branching capacities to obtain insight into and elucidate the molecular mechanisms regulating this trait for breeding.

Flowering time is another important trait influencing yield expression and potential in watermelon. Male and female flowers in watermelon are located separately on different nodes of the same plant. Male flowers appear first, followed by female flowers. The number of days before the appearance of the first male and female flowers extensively vary in watermelon. For example, McGregor and Waters [88] reported that the days to first male flower varied from 8 to 22 days after transplanting (DAT), and between 20 and 30 DAT to the first female flower among watermelon pollen parents. Stone et al. [89] reported days to first male flower varied between 44 and 60 days after planting (DAP), whereas days to first female flower varied between 52 and 70 DAP. Gimode et al. [32] reported that days to first female flower ranged from 16 to 37 DAP in watermelon. Flowering time in watermelon is subject to genotype, environment and genotype-by-environment interactions. The following genes: Cla009504 and Cla000855 [24] and Cla002795 (i.e., phosphatidylinositol-4-phosphate 5-kinase (PIP-kinase) [32] regulate flowering time in watermelon. The identified genes provide opportunities for breeding watermelon varieties with desired flowering times for different production environments, and in the development of molecular markers to ensure efficient selection for earliness.

Fruit yield is an economic trait in watermelon, and varies considerably among the diverse varieties. Fruit yield ranging from 40.5 to 84 tons/ha has been reported in watermelon [90]. Stone et al. [89] reported fruit yield varying from 2.8 to 5.7 tons per hectare. Fruit yield in watermelon is determined by fruit weight, length and width. Fruit weight vary considerably in watermelon. Stone et al. [89] reported a single fruit weight of watermelon varying from ~ 3 to 12 kg, whereas Singh et al. [72] reported fruit weight varying from 0.10 to 3.21 kg. A fruit weight ranging from 0.58 to 8.2 kg has been reported in a diverse panel of watermelon varieties [41]. Fruit length and width also vary considerably between 21 and 40 cm, and from 20 to 25 cm, respectively [89], and from 10.9 to 20.9 cm and 9.20 to 34.6 cm [41]. Other secondary traits including plant height, the number of primary, secondary and tertiary branches, the number of male and female flowers, and the number of fruits produced per plant from successfully fertilized female flowers indirectly contribute to fruit yield in watermelon. As a result, fruit yield is influenced by several yield components [23,30,58]. Multiple QTLs associated with yield component traits have been reported in watermelon [23,24,28,30,58]. The multiple QTLs conditioning yield component traits are useful for the strategic breeding of watermelon for high fruit yield potential.

Triploid seedless watermelons are preferred for fresh consumption. Triploid watermelons produce non-viable pollen and require a diploid (seeded) watermelon as a pollen parent [91,92,93]. The production and breeding of seeded watermelons has declined in recent years in favour of seedless watermelons. Elsewhere, seeded watermelons are preferred for seed consumption as snack and for developing value-added by-products. In such circumstances, breeding watermelon varieties with a high seed yield is an important objective. Seed yield potential is determined by the number of seeds per fruit, seed, length, width, weight and size, which are highly variable in watermelon [94,95]. Small seed sizes are preferred for fresh fruit consumption, whereas large seeds are preferred for planting and cooking. Seed size in watermelon is categorized as tomato, small, medium, and large [96]. Two candidate genes, namely, Cla97C05G104360 and Cla97C05G104380, and three other genes, namely, Cla97C05G104340, Cla97C05G104350 and Cla97C05G104390 [97], conditioned seed size through their involvement in abscisic acid metabolism. The genes Cla009290, Cla009291 and Cla009310 were reportedly involved in seed size development [27]. Seed size is determined by seed length and width, which are conditioned by several QTLs [25,27,30]. Various QTLs are reported to control seed component traits in watermelon [25,27,30]. The mapped QTLs for seed component traits offer strategic breeding of watermelon varieties, targeting high seed yield potential.