Primary mapping of quantitative trait loci regulating multivariate horticultural phenotypes of watermelon (Citrullus lanatus L.)

Abstract

Watermelon fruits exhibit a remarkable diversity of important horticultural phenotypes. In this study, we initiated a primary quantitative trait loci (QTL) mapping to identify the candidate regions controlling the ovary, fruit, and seed phenotypes. Whole genome sequencing (WGS) was carried out for two differentiated watermelon lines, and 350 Mb (96%) and 354 Mb (97%) of re-sequenced reads covered the reference de novo genome assembly, individually. A total of 45.53% non-synonymous single nucleotide polymorphism (nsSNPs) and 54.47% synonymous SNPs (sSNPs) were spotted, which produced 210 sets of novel SNP-based cleaved amplified polymorphism sequence (CAPS) markers by depicting 46.25% co-dominant polymorphism among parent lines and offspring. A biparental F2:3 mapping population comprised of 100 families was used for trait phenotyping and CAPS genotyping, respectively. The constructed genetic map spanned a total of 2,398.40 centimorgans (cM) in length and averaged 11.42 cM, with 95.99% genome collinearity. A total of 33 QTLs were identified at different genetic positions across the eight chromosomes of watermelon (Chr-01, Chr-02, Chr-04, Chr-05, Chr-06, Chr-07, Chr-10, and Chr-11); among them, eight QTLs of the ovary, sixteen QTLs of the fruit, and nine QTLs of the seed related phenotypes were classified with 5.32–25.99% phenotypic variance explained (PVE). However, twenty-four QTLs were identified as major-effect and nine QTLs were mapped as minor-effect QTLs across the flanking regions of CAPS markers. Some QTLs were exhibited as tightly localized across the nearby genetic regions and explained the pleiotropic effects of multigenic nature. The flanking QTL markers also depicted significant allele specific contributions and accountable genes were predicted for respective traits. Gene Ontology (GO) functional enrichment was categorized in molecular function (MF), cellular components (CC), and biological process (BP); however, Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways were classified into three main classes of metabolism, genetic information processing, and brite hierarchies. The principal component analysis (PCA) of multivariate phenotypes widely demonstrated the major variability, consistent with the identified QTL regions. In short, we assumed that our identified QTL regions provide valuable genetic insights regarding the watermelon phenotypes and fine genetic mapping could be used to confirm them.

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

“…Recently, a genome-wide association study (GWAS) uncovered valuable insights into the natural variation and phenotypic correlations in peel thickness and fruit weight of watermelon [9], indicating the shared genetic makeup of these traits [1,7,10,11]. Fruit and seed size are important factors for both consumers and breeding companies [12]. In earlier domestication, sweet watermelons were known with thin peels and small fruit and seed sizes, while the latter pursued higher profits and preferred products with big fruits, thick peels, and large seeds.…”

“…Fruit peel color also ranges from light to dark green [8,12]. The basic genetic model of green peel was proposed for the first time and stated that the dark green peel had more genetic effects than the light green peel, which is regulated by multiple major and minor genes and interferes with the synthesis of peel color in watermelon [13].…”

“…It was also found that the multi-allelic APRR2 gene significantly accumulated fruit pigmentation in melon and watermelon [17]. A recently developed hybrid generation with intermediate peel colors showed that peel color inheritance depends on whether a pair of alleles is homozygous or not [8,12,18]. All these experiments have differentiated the diverse genetic backgrounds of different botanical groups of watermelon, and the genes controlling peel color still need to be further explored.…”

“…Seed is a primary component of the plant life cycle that serves to propagate [12]. The size, weight, and thickness of watermelon seed exhibit a lot of variations due to natural and artificial adaptation to different localities [12,19,20].…”

“…Seed is a primary component of the plant life cycle that serves to propagate [12]. The size, weight, and thickness of watermelon seed exhibit a lot of variations due to natural and artificial adaptation to different localities [12,19,20]. It was reported that seed size is governed by non-allelic genes (l and s), and a good-fit Mendelian genetic segregation was seen.…”