QTL mapping for melon ( Cucumis melo L.) fruit traits by assembling and utilization of novel SNPs based CAPS markers

Abstract

Abstract Fruit traits influence consumer’s choice and the market worth of melons. Multiple genes controlled the majority of fruit quality traits and these genes are influenced via differential factors. Cleaved amplified polymorphism sequence (CAPS) molecular markers have been validated as efficient tool for detection of numerous SNPs (single nucleotide polymorphisms). In the current study, genetic linkage map was assembled and QTL discovery was conducted for melon quality traits in F2:3 population, generated from crossing of MR-1 and M4-7. SNPs were detected and converted into CAPS markers from retrieved data of high-throughput resequencing. Two parental lines (MR-1 and M4-7) of melon were analyzed and resequenced for assembling the novel CAPS markers. Totally, 91.54% and 90.00% of assembled sequences covered the reference genome of these two distinct parental lines, respectively. Analysis of assembled genomic data revealed total 2,761,801 SNPs and 7741 CAPS locus. Overall, 410 novels CAPS molecular markers were assembled along with 4-restriction endonuclease and 160 CAPS pairs displayed polymorphic bands of predictable length after screening by the use of PCR and process of enzyme digestion, with 39% rate of polymorphism. Genetic linkage map construction was done by genotyping of these novel CAPS markers within F2:3 population and this map totally spanned 2848.68 cM length with 12 chromosomes and 160 CAPS markers. Total 24 minor QTLs were discovered for fruit weight, firmness, flesh firmness, Brix, fruit length, width and shape with different genetic loci on various chromosomal locations. These newly assembled CAPS markers will be valuable and potent for future breeding and genetic schemes in melon.