Watermelon is economically important member of Cucurbitaceae. Cultivated watermelons (C. lanatus subsp. lanatus) are divers in fruit size and shape, color of fruit flesh and fruit skin, and stripe pattern. In Chapter 1, whole genome of 19 watermelon inbred lines were resequenced, and genome wide seq...
Watermelon is economically important member of Cucurbitaceae. Cultivated watermelons (C. lanatus subsp. lanatus) are divers in fruit size and shape, color of fruit flesh and fruit skin, and stripe pattern. In Chapter 1, whole genome of 19 watermelon inbred lines were resequenced, and genome wide sequence variations for the development of markers for MABC(Marker assisted backcross) were analyzed. Based on SNP and InDel detected, distribution of genome wide diversity, genetic relationship, cultivar type-specific allele abundance, and divergence index at QTL were evaluated. For MABC, a total of 1,374 SNPs were selected at intervals of 0.5Mb based on the Polymorphism Information Content(PIC) value. PCA analysis of the 19 cultivars based on 1,374 SNPs classified them into three major groups, showing a clear grouping pattern between Crimson-type and the Jubilee-type watermelons. In addition, a set of SNPs(259) that discriminate the Crimson-type cultivars from Non-crimson-type was also selected. For the verification of SNPs, 26 CAPS were designed based on the SNPs and used for genotyping 11 cultivars, which resulted in high match rates above 0.8 for most of the CAPS makers.
In Chapter 2, NGS-based resequencing was performed for 3 high-lycopene NILs(Near Isogenic Lines) and their parents, and the distribution of the SNPs in the chromosomes were determined. Introgression regions in each NIL, presumed by extremely high proportions of SNPs specific to the donor parents were identified and a total of 76 HRM and CAPS markers were developed from the SNPs; only 25 markers were polymorphic between the recurrent parent and the NIL. In addition, among the 40 genes involved in lycopene biosynthesis, a CAPS from the HDR (Cla010297) gene located in the introgression region of a NIL DRD45NC was developed. Twenty-four watermelon accessions including the NILs and parental lines were analyzed for their lycopene contents and genotyped using these introgression region makers. The correlation between the lycopene content and marker genotype was assessed. High r2 values above 0.9 were found in 1 marker (C017463) located in the introgression region(Chr10-1) commonly detected from the NILs DRD45NC, DRDSBA1(BC3F6) and DRDSBA2(BC2F9), indicating the usability of these markers in MAS for high lycopene content.
Watermelon is economically important member of Cucurbitaceae. Cultivated watermelons (C. lanatus subsp. lanatus) are divers in fruit size and shape, color of fruit flesh and fruit skin, and stripe pattern. In Chapter 1, whole genome of 19 watermelon inbred lines were resequenced, and genome wide sequence variations for the development of markers for MABC(Marker assisted backcross) were analyzed. Based on SNP and InDel detected, distribution of genome wide diversity, genetic relationship, cultivar type-specific allele abundance, and divergence index at QTL were evaluated. For MABC, a total of 1,374 SNPs were selected at intervals of 0.5Mb based on the Polymorphism Information Content(PIC) value. PCA analysis of the 19 cultivars based on 1,374 SNPs classified them into three major groups, showing a clear grouping pattern between Crimson-type and the Jubilee-type watermelons. In addition, a set of SNPs(259) that discriminate the Crimson-type cultivars from Non-crimson-type was also selected. For the verification of SNPs, 26 CAPS were designed based on the SNPs and used for genotyping 11 cultivars, which resulted in high match rates above 0.8 for most of the CAPS makers.
In Chapter 2, NGS-based resequencing was performed for 3 high-lycopene NILs(Near Isogenic Lines) and their parents, and the distribution of the SNPs in the chromosomes were determined. Introgression regions in each NIL, presumed by extremely high proportions of SNPs specific to the donor parents were identified and a total of 76 HRM and CAPS markers were developed from the SNPs; only 25 markers were polymorphic between the recurrent parent and the NIL. In addition, among the 40 genes involved in lycopene biosynthesis, a CAPS from the HDR (Cla010297) gene located in the introgression region of a NIL DRD45NC was developed. Twenty-four watermelon accessions including the NILs and parental lines were analyzed for their lycopene contents and genotyped using these introgression region makers. The correlation between the lycopene content and marker genotype was assessed. High r2 values above 0.9 were found in 1 marker (C017463) located in the introgression region(Chr10-1) commonly detected from the NILs DRD45NC, DRDSBA1(BC3F6) and DRDSBA2(BC2F9), indicating the usability of these markers in MAS for high lycopene content.
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