Genome-wide Differentiation of Various Melon Botanical Groups for Use in GWAS for Fruit Firmness and Construction of a High-resolution Genetic Map

Melon has climacteric and non-climacteric morphotypes that exhibit wide variation for fruit firmness, a very important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing and anchored them to various chromosomes to understand genome-wide fixation index between various melon morphotypes and linkage disequilibrium (LD) decay for inodorus and cantalupensis, the two leading economically important morphotypes. In the current research, we focused on the genome-wide footprints of divergence underlying formation of inodorus and cantalupensis in comparison with the highly diverse subspecies agrestis. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. Our study further resolved a strong selective sweep and high LD on chromosomes 11 and 5 indicating importance of these chromosomes in genetic differentiation. The high-resolution genetic map with 7153 loci constructed in the current study could be used to understand colinearity with the genome sequence. Genome-wide segregation distortion and recombination rate across various chromosomes is characterized. Various levels of QTLs were identified with high to moderate stringency and linked to fruit pressure using genome-wide association study (GWAS), with the majority of them found to be in agreement with the QTL mapping based on a biparental cross. Gene annotation revealed some of the SNPs are located in b-D-xylosidase and histidine kinase, the genes that were previously characterized for fruit ripening and softening on other crops.