Whole genome resequencing of watermelons to identify single nucleotide polymorphisms related to flesh color and lycopene content

Abstract

Cultivated watermelon (Citrullus lanatus) is one of the most important food crops in the Cucurbitaceae family. Diversification after domestication has led cultivated watermelons to exhibit diverse fruit flesh colors, including red, yellow, and orange. Recently, there has been increased interest in red-fleshed watermelons because they contain the antioxidant cis-isomeric lycopene. We performed whole genome resequencing (WGRS) of 24 watermelons with different flesh colors to identify single-nucleotide polymorphisms (SNPs) related to high lycopene content. The resequencing data revealed 203,894–279,412 SNPs from read mapping between inbred lines and the 97103 reference genome. In total, 295,065 filtered SNPs were identified, which had an average polymorphism information content of 0.297. Most of these SNPs were intergenic (90.1%) and possessed a transversion (Tv) rate of 31.64%. Overall, 2,369 SNPs were chosen at 0.5 Mb physical intervals to analyze genetic diversity across the 24 inbred lines. A neighbor-joining dendrogram and principal coordinate analysis (PCA) based on the 2,369 SNPs revealed that the 24 inbred lines could be grouped into high and low lycopene-type watermelons. In addition, we analyzed SNPs that could discriminate high lycopene content, red-fleshed watermelon from low lycopene, yellow or orange watermelon inbred lines. For validation, 19 SNPs (designated as WMHL1–19) were chosen randomly, and cleavage amplified polymorphic sequence (CAPS) markers were designed. Genotyping of the above 24 lines and 12 additional commercial cultivars using WMHL1–19 CAPS markers resulted in match rates of over 0.92 for most validated markers in correlation with the flesh color phenotypes. Our results provide valuable genomic information regarding the high lycopene content phenotype of red-fleshed cultivated watermelons, and the identified SNPs will be useful for the development of molecular markers in the marker-assisted breeding of watermelons with high lycopene content.

A Genome-Wide Analysis of the Pentatricopeptide Repeat (PPR) Gene Family and PPR-Derived Markers for Flesh Color in Watermelon (Citrullus lanatus)

“…For the utilization of ClaPPR genes in watermelon breeding, we investigated the relationship between the watermelon flesh color and sequence variations in ClaPPR genes. We identified the SNPs in the sequences of ClaPPR encoding genes from 24 different flesh colored watermelons (red, yellow, and orange) using our WGRS data (Bioproject: PRJNA516776) [ 29 ]. A total of 368 SNPs were observed from 139 ClaPPR genes in the WGRS data.…”

“…Single-nucleotide polymorphisms (SNPs) for ClaPPR genes in different flesh-colored (red, yellow, and orange) watermelons were identified from the whole genome resequencing (WGRS) data (Bioproject: PRJNA516776) of our recent study [ 29 ]. The SNP variant calling procedure was carried out according to our recent study [ 29 ] in which the reads of different flesh-colored watermelons from WGRS were mapped on to the watermelon 97103 reference genome.…”

“…Single-nucleotide polymorphisms (SNPs) for ClaPPR genes in different flesh-colored (red, yellow, and orange) watermelons were identified from the whole genome resequencing (WGRS) data (Bioproject: PRJNA516776) of our recent study [ 29 ]. The SNP variant calling procedure was carried out according to our recent study [ 29 ] in which the reads of different flesh-colored watermelons from WGRS were mapped on to the watermelon 97103 reference genome. From this SNP variant calling, we searched for the SNPs that were specific to either of the flesh types such as red, yellow, and orange in the SNP subset matrix by identifying protein-coding ClaPPR genes bearing SNPs that were 1) monomorphic among a chosen flesh color-type, 2) monomorphic among other unchosen flesh color-types, and 3) polymorphic between a chosen and an unchosen flesh color-types.…”

“…Then, the sequences of selected ClaPPR SNP variants were converted into CAPS markers using SNP2CAPS software [ 40 ] and simultaneously, primers were designed using Primer3Plus software ( ). To validate CAPS markers, genomic DNA extraction, PCR assays, restriction digestion of PCR amplicons, and match rate analyses were carried out according to a previous study [ 29 ].…”

“…Watermelon ( Citrullus lanatus ) is an important fruit crop with overall annual production of more than 103 million tons worldwide ( . Watermelon exhibits diverse variation in fruit-quality traits, including soluble sugars, firmness, fruit size, shape, skin, and flesh color, along with functional factors such as lycopene and β-carotene [ 28 , 29 ]. This extensive polymorphic variation motivates researchers to investigate the genetics of watermelon fruit-quality traits.…”