Identification of a major QTL region and candidate genes responsible for harvest date combining QTL mapping and QTL-seq approaches in walnut ( Juglans regia L.)

Walnut (Juglans regia L.) takes place within the Juglandaceae family and is one of the most popular nut species. In walnut breeding, several limiting factors need to be revealed regarding the genetic mechanism underlying important agronomical traits. In the current report, the monitoring of the 'Chandler x Kaplan-86' F1 walnut population was carried out four successive years (2015, 2016, 2017, 2018) and the distribution of the plants for harvest date from four years was ranged from August 27th to October 22nd. Then, we dissected the genomic regions associated with harvest date using classical Quantitative Trait Loci (QTLs) mapping and a rapid and costeffective QTL-seq approach in 'Chandler x Kaplan-86' F1 walnut population for the first time. In classical QTL mapping, a major QTL was recognized in LG4 corresponding to Chr1 in Chandler female map with 27.6 (%) phenotyping variance. In QTL-seq, we bulked the DNAs of the genotypes with extreme harvest date separately, the whole genome resequencing was performed for a parent Chandler and both bulks (early and late) to calculate Delta SNP indexes for each Single Nucleotide Polymorphisms (SNPs) and Insertion/Deletion (InDels). Approximately 48.04 million paired reads for Chandler, 149.72, and 150.14 million paired reads were obtained from early and late harvest bulks, respectively. A total of 229,307 SNPs and 45,223 InDels were mined from the merged sequences data covered whole chromosomes. The responsible genomic fragments were identified in Chr2 and Chr11 in QTL-seq. The highest linked InDel locus detected in QTL-seq in Chr11 around 17 million base pairs distinguished the plants according to harvest date. InDel Sequence Characterized Amplified Region (SCAR) marker is a candidate for marker-assisted selection for future walnut breeding studies.