GWAS resolves molecular mechanisms underlying natural variation for carotenoids in Cucurbita maxima Duchesne

Abstract

Carotenoid levels and composition are essential nutraceutical traits in Cucurbita maxima influencing the fruit flesh and rind colors. In this study, Mr Fugly, Boston Marrow, Baby Green Hubbard, Chicago Warted Hubbard, Golden Hubbard, and Bush Buttercup of USA; Australian Butter (Australia); Marmellata and Marina di Chioggia of Italy contained the highest carotenoid content. EMMAX (Efficient Mixed-Model Association eXpedited) was employed for a Genome-wide association study (GWAS) to identify associated genomic regions underlying the regulation of carotenoids. Here, we profiled the contents of α-carotene, β-carotene, β-cryptoxanthin, lutein, and zeaxanthin from a diversity panel of C. maxima consisting of classical horticulture groups including buttercup, turban, banana, zapallito, hubbard, mammoth and australian. Lutein and β-carotene were the major carotenoids among C. maxima accessions. Furthermore, we used genotyping by sequencing to identify 12,996 single nucleotide polymorphisms (SNPs) that were used to resolve population structure with three primary clusters and their admixed genotypes. Our GWAS revealed several SNPs related to 289 genes involved in plastid biogenesis, protein ubiquitination, transcriptional regulation at the carotenoid biosynthesis level, fruit ripening, and regulation of carotenoid transport. Together, these results contribute to a better understanding of the molecular mechanisms of carotenoid biosynthesis in fruit flesh and would facilitate breeding for enhanced carotenoids in winter squashes.