Abstract
Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 24) has climacteric and non-climacteric morphotypes and show wide variation for fruit firmness, an important trait for transportation and shelf life. We generated 13,789 SNP markers using genotyping-by-sequencing (GBS) and anchored them to chromosomes to understand genome-wide fixation indices (Fst) between various melon morphotypes and genomewide linkage disequilibrium (LD) decay. The FST between accessions of cantalupensis and inodorus was 0.23. The FST between cantalupensis and various agrestis accessions was in a range of 0.19–0.53 and between inodorus and agrestis accessions was in a range of 0.21–0.59 indicating sporadic to wide ranging introgression. The EM (Expectation Maximization) algorithm was used for estimation of 1436 haplotypes. Average genome-wide LD decay for the melon genome was noted to be 9.27 Kb. In the current research, we focused on the genome-wide divergence underlying diverse melon horticultural groups. A high-resolution genetic map with 7153 loci was constructed. Genome-wide segregation distortion and recombination rate across various chromosomes were characterized. Melon has climacteric and non-climacteric morphotypes and wide variation for fruit firmness, a very important trait for transportation and shelf life. Various levels of QTLs were identified with high to moderate stringency and linked to fruit firmness using both genome-wide association study (GWAS) and biparental mapping. Gene annotation revealed some of the SNPs are located in β-D-xylosidase, glyoxysomal malate synthase, chloroplastic anthranilate phosphoribosyltransferase, and histidine kinase, the genes that were previously characterized for fruit ripening and softening in other crops.
Highlights
Melon (Cucumis melo L.) is a phenotypically diverse eudicot diploid (2n = 2x = 12) which originated in Asia (Silberstein et al, 2003)
For generating GBS data, we considered only SNPs that mapped to the melon whole-genome sequence draft, as the chromosome location of SNPs helps prevent spurious linkage disequilibrium (LD), reducing errors in genome-wide association study (GWAS)
We found SNPs at average intervals of 30 kb across the melon genome
Summary
Momordica, conomon, dudaim, and chito in subspecies agrestis (Decker-Walters et al, 2002). Pitrat (2008) grouped melons into 15 widely accepted horticultural groups A genome-wide sequence of melon of size 375 Mb (83.3% of estimated size) has been made available. This genome has enabled an exhaustive phylogenetic comparison of the melon genome with cucumber (Garcia-Mas et al, 2012). SNP discovery in diverse melon botanical groups will allow marker-anchoring to the whole genome sequence (WGS), giving researchers a better understanding of the genetic control of domestication and diversification as shown in the study of Argyris et al (2015)
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