Development of DNA markers associated with harvest date using QTL-seq method in chandler x kaplan-86 F1 walnut population

Walnut (Juglans regia L.) is one of the most important hard-shelled nut species of our country early. Selection at early stage in breedng is very important, since the juvenile period of walnut is very long. In this study, it was aimed to develop DNA marker associated with harvest date in walnut by using QTL-seq mapping method. Within the scope of this study, a total of walnut 175 F1 genotypes for harvest date trait in for four observations years was used. In QTL-seq, one of the parents and two bulk DNA with extreme phenotyped samples, were sequenced at 20x sequencing coverage (approximately 10Gb) in Illumina HiSeq 2500 Next Generation Sequencing method with PE150 (paired-end) sequences. Responsible QTL regions and linked markers were identified using QTL-seq software. Totally, 229,307 SNPs and 45,223 InDels were identified as a result of mapping to walnut genome by QTL-seq analyses. As a result of QTL-seq analyses, genome annotation of the associated markers identified in the 'Chandler x Kaplan-86' population was performed with the Annovar programme, and as a result of the genome annotation, the highly associated locus on chromosome 2 and chromosome 11 were defined. In addition, GO and KEGG pathways were identified by functional annotation using the sequences to the right and left of the highly associated markers. HRM (High Resolution Melting) and SCAR primers were designed using sequences from the right and left of the highly associated loci. All primers were validated both in 'Chandler x Kaplan-86' F1 population and in cultivars and genotypes belonging to genetic resources. The results of the current thesis can be used in marker assisted selection in future walnut breeding programs.