SNPs identification and association study of fruit quality genes from selected whole-genome sequenced peach cultivars grown in Greece

Abstract

In Greece, peach is one of the largest cultivations both in terms of hectares and in economic profit, with table peaches representing a 40% and industrial peaches the 60%. Next generation sequence technologies can prove valuable in evaluating present peach cultivars and getting the necessary knowledge to develop new cultivars with appreciable quality traits. Whole genome sequencing was performed on selected peach cultivars (‘Romea’, ‘Virgil’, ‘Catherina’, ‘Fergold’, ‘Crimson Lady’, ‘Rubirich’, ‘Rebus 028’, ‘Early Top’) and a local cultivar called ‘Lemonato’. These cultivars were selected according to their differences in specific fruit quality traits, such as slow melting flesh, stone adhesion and hardness, fruit color (skin and flesh), fruit size, along with maturity date and fruit productivity. Sequencing was performed using Illumina Nextseq 550 platform, with Nextera DNA Flex indexes, resulting in over 150 million reads with an average GC of 38.5%. The aim of this study is the identification of SNPs associated with genes that control important fruit quality characteristics and the development of molecular markers linked to these traits. The number of SNPs associated with each of these genes and the number of useful SNPs for marker-assisted selection varied accordingly. A total of 1,535 SNPs with high impact effect on known and putative genes were identified across all cultivars. SNPs identified in genes that are involved in biological processes (cellular and metabolic process) were the most abundant. © 2022 International Society for Horticultural Science. All rights reserved.