QTL Mapping & Linkage Map Assembling For Melon Fruit Traits On The Basis Of Novel SNP-CAPS Markers

Melon?Cucumis melo L.?has prime worth among the fruits of Cucurbitaceae family,due to its splendid nutritional quality.It is diploid?2n=2x=24?and tremendously diverse fruit crop regarding its morpho-physiological traits.These fruit traits have vital impact on consumer's choice and the melon market significance.Various genes govern the bulk of fruit quality features and the manipulation of these genes occur by distinct factors.High-throughput sequencing progression has magnificently built up the opportunity to re-sequence the genomes of numerous crops in wide range and additionally fortified the facilitation of assembling unique molecular markers.Recently,CAPS markers development has been endorsed as a proficient approach along with detection of single nucleotide polymorphisms?SNPs?for QTL loci mapping.The existing experiment was undertaken to study the genetic inheritance of fruit traits in melon through assembling the innovative SNPs based CAPS markers,linkage map construction and QTL mapping.For the proposed study,two distinctive melon parental lines P₁?MR-1?and P₂?M4-7?were crossed for generating of F_2:3 segregated plant population.These two distinct parental lines were analyzed and re-sequenced by the retrieved data of high-through-put sequencing;SNP sites were detected and converted into unique CAPS markers.Utterly,91.54%and 90.00%assembled sequences were enclosed respectively within the reference genome of 2 parental lines.Constructed genomic data exploration exposed total2,761,801 SNPs&7,741 CAPS locus.Novel CAPS markers?total 410?were generated with their respective 4-RE?restriction endonuclease?on the basis of detected SNPs.Overall,160CAPS markers exposed the 39%polymorphism rate within 2-contrasted parental material and their F_1,with expectable polymorphic bands length with the polymerase chain reaction and enzyme digestion procedure.Assembling of genomic map was done by novel CAPS markers?n=160?genotyping in F_2:3 plant populace and the assembled genetic map was spread 2848.68cM lengthwise with average distance of 17.80 cM across 12 chromosomes.Among the whole constructed genetic linkage map,chromosome 3 showed the minimum?7?and chromosome 9showed maximum?20?numbers of CAPS markers.All the novel generated CAPS markers were consistently allocated on genetic linkage map according to their physical position of CAPS locus.The segregation of various traits such as;fruit weight,fruit shape,fruit length,fruit width,fruit firmness,flesh firmness,Brix,pH and TA?titratable acidity?was normal in F_2:3plant population,which indicated that all these traits were quantitatively controlled and these traits were significantly correlated to each other.Overall,49 QTLs?minors?were unveiled for 9 traits of melon fruit with different genetic loci on each chromosome and their LOD value was varied within the range of 2.53?minimum?to 52.77?maximum?,which justified the traits variations rate from 1.02%?minimum?to 12.98%?maximum?.Unfortunately,none of the QTL for fruit length was detected in whole genomic region.The total number of QTLs for fruit width?qFwid?and fruit shape?qFSh?were ten?6 for width and 4 for shape?,located on three different chromosomes?5,8 and 9?,and 15.23%individual effect was accounted for fruit width and 20.01%individual effect was accounted for fruit shape trait,respectively.Four fruit weight QTLs?qFWt?were mapped on three various chromosomes?2,5 and 10?with total effect of 26.57%.Total 5 QTLs responsive to fruit firmness?qFFir?were discovered on four different chromosomes?2,3,5 and 8?with 27.84%combined effect.Just two QTLs for flesh firmness?FlFir?were pinpointed on chromosome?3 and 6?with whole effect of 15.94%.One QTL of fruit firmness?qFFir-3-1?was overlapped with flesh firmness QTL?qFlFir-3-1?at the same genetic region of 22 cM and the genetic interval between these QTLs was 0 cM due to co-localization at same genetic point.Three QTLs for Brix?qBrix?were mapped on 3 different chromosomes?7,9 and 10?,and their total variance effect for traits was 5.32%.Twelve pH QTLs?qpH?were mapped on 9 distinct chromosomes?1,2,4,5,6,7,8,9 and 10?and total variation effect was 38.37%.Total 13 TA QTLs?qTA?were situated on 9 different chromosomes?2,5,6,7,8,9,10,11 and 12?with 11.76%total variation effect.On chromosome 6,a single pH QTL?qpH-6-1?was situated with titratable acidity QTL?qTA-6-1?by tightly overlapping on same genetic position with 0 cM distance between two flanking markers.In brief,the current study results validated that the whole genome re-sequencing considerably enhance the aptitude of development of advance molecular markers,linkage map assembling and QTL mapping efficiency.The melon linkage map exhibited herein was developed by the novel SNP-CAPS markers genotyping,based on sequencing information.Moreover,49 QTLs were effectively mapped for 9 quality traits of melon and possibly,the whole innovations will be valued for future MAS based breeding studies.