QTL analysis and candidate gene SNP for harvest day in sweet cherry (Prunus avium L.)

Abstract

Sweet cherries are harvested from early June to mid-July in Yamagata, Japan. Because early ripening cultivars of sweet cherry can be sold at higher prices, harvest day is an important trait in sweet cherry breeding programs, and since sweet cherry plants require more than 4 years to reach maturity, marker-assisted selection, which enables the selection of superior seedlings, is a valuable tool for conducting such breeding programs more efficiently. The goal of the present study was to develop DNA markers for harvest day using QTL analysis of a segregating population (C-303, ‘Beniyutaka’ × ‘Benikirari’, n=93) and to perform polymorphism analysis of harvest day-related candidate genes, i.e., NAC transcription factors (TFs), using the genome sequences of seven sweet cherry cultivars that varied in harvest day. The QTL analysis identified four and one QTLs in ‘Beniyutaka’ and ‘Benikirari’, respectively, and all the QTLs were located on linkage group 4. Two NAC TF-like genes were located in the QTL with the highest phenotypic variance (48.4%). Further comparative analysis of the two genes across the seven cultivars revealed 21 single nucleotide polymorphisms (SNPs), one of which was a nonsynonymous SNP located in the coding sequence. This SNP could be used to predict harvest day with high probability when applied to either the segregating population (C-303) or a group of 82 sweet cherry cultivars and therefore, may be a useful DNA marker for selecting early harvest sweet cherries.