SNP analysis of sweet pumpkin to corroborate carotenoid accumulation using different inbred lines

The differential fruit color of the sweet pumpkin (Cucurbita maxima) is due to the presence of variant levels of carotenoids. Apart from appealing culinary fruit characteristics, carotenoid composition is responsible for high nutritional values of sweet pumpkin. Single nucleotide polymorphism-based DNA markers is widely used in agronomic crops to understand the genetic architecture, physiology of the trait, and selection of cultivars. In this study, we analyzed various distinguishable SNP markers in CmaCh06G005910, CmaCh14G015700, CmaCh15G000800, CmaCh08G002870, CmaCh04G017950, and CmaCh17G014010 genes using HRM techniques in small, medium, and large sized pumpkin lines cultivated in South Korea. These genes are closely related to carotenoid biosynthesis pathway in sweet pumpkin. Mesocarp of the selected pumpkin were also subjected to HPLC quantification for α-carotene, β-carotene, β-cryptoxanthin, and zeaxanthin content. The genetic profiling and HPLC analysis revealed a pleotropic effect of carotenoid related genes. As an additional analysis, SNP markers in the CmaCh08G000410 gene previously reported to be associated with fruit length were evaluated because the study population included cultivars with diverse fruit sizes. The fruit length-linked marker produced distinguishable HRM peaks among lines exhibiting different fruit lengths. This genotype data will be aided as an exploratory data on understanding the carotenoid genes in the Korean cultivars. Furthermore, it helps the breeder to select the genetically informed nutrient enhanced cultivars.