Genome-wide association mapping in a sweet cherry germplasm collection (Prunus avium L.) reveals candidate genes for fruit quality traits

Abstract

In sweet cherry (Prunus avium L.), a large variability exists for various traits related to fruit quality. There is a need to discover the genetic architecture of these traits in order to enhance the efficiency of breeding strategies for consumer and producer demands. With this objective, a germplasm collection consisting of 116 sweet cherry accessions was evaluated for 23 agronomically fruit quality traits over two to six years, and characterized using a genotyping-by-sequencing (GBS) approach. The SNP coverage collected was used to conduct a genome-wide association study (GWAS) using two multi-locus models and three reference genomes. We identified numerous SNP-trait associations for the global fruit size (weight, width and thickness), fruit cracking, fruit firmness and stone size, and we pinpointed several candidate genes involved in phytohormones, calcium and cell wall metabolisms. Finally, we led a precise literature review focusing on the genetic architecture of fruit quality traits in sweet cherry to compare our results with potential colocalizations of marker-trait associations. This study brings new knowledge of the genetic control of important agronomic traits related to the fruit quality, and to the development of marker-assisted selection (MAS) strategies targeted towards the facilitation of breeding efforts.

A 5.2‐kb insertion in the coding sequence of PavSCPL, a serine carboxypeptidase‐like enhances fruit firmness in Prunus avium

“…However, our findings demonstrate that a single gene, PavSCPL, with a 5.2-kb insertion, has led to firmer fruit in the F 1 population derived from the cross 'Rainier' 9 'Summit'. The AFLP markers of PavSCPL associated with fruit firmness developed in this study, as well as several SNPs markers associated with fruit firmness-related traits identified by Holu sov a et al (2022) and Donkpegan et al (2023) will be used for MAS in breeding improvement of the fruit firmness trait.…”

“…For example, using the 'Ambrun es' 9 'Sweetheart' F 1 population, qP-FF1.1, qP-FF1.2 and qP-FF6.1 were identified, while only qP-FF4.1 was identified in the 'Fercer' 9 'X' (an unknown parent) F 1 population (Cai et al, 2019;Campoy et al, 2015). Meanwhile, several significant SNPs associated with the fruit firmness trait have been identified and localized with QTLs qP-FF1.1, qP-FF1.2, qP-FF4.1 and qP-FF6.1 in GWASs with 116 or 235 sweet cherry accessions (Donkpegan et al, 2023;Holu sov a et al, 2022), especially qP-FF4.1 (approximately 1.8 Mbp, 12 928 603-14 860 789 bp). Despite the identification of numerous SNP markers for the sweet cherry fruit firmness trait, few have been successfully applied to breeding for fruit firmness .…”

“…Another SNP marker (chr1_31855038) associated with fruit firmness was collocated with qP-FF1.2 and qP-FF1.1 identified by . Donkpegan et al (2023) identified seven SNPs associated with fruit firmness in GWASs using 116 sweet cherry accessions, located on chromosomes 3, 4, 5, 6 and 8 (Donkpegan et al, 2023). And one SNP marker Chr4-15 932 813 bp using 'Satonishiki' was identified on chromosome 4 at 15.9 Mbp explaining 20.6% of the variance (Donkpegan et al, 2023), which was also identified on chromosome 4 at 16.0 Mbp using 'Tieton' by Holu sov a et al (2022).…”

“…Donkpegan et al (2023) identified seven SNPs associated with fruit firmness in GWASs using 116 sweet cherry accessions, located on chromosomes 3, 4, 5, 6 and 8 (Donkpegan et al, 2023). And one SNP marker Chr4-15 932 813 bp using 'Satonishiki' was identified on chromosome 4 at 15.9 Mbp explaining 20.6% of the variance (Donkpegan et al, 2023), which was also identified on chromosome 4 at 16.0 Mbp using 'Tieton' by Holu sov a et al (2022). The identification of different QTLs and SNPs suggests that sweet cherry fruit firmness is a quantitative trait; therefore, precise identification of the corresponding genes associated with fruit firmness phenotypes remains a daunting task.…”

“…In a genome-wide association study (GWAS), Crump et al (2022) detected fruit firmness QTLs on LGs 1 (qFirm-LG1.2), 3 (qFirm-LG3.2) and 6 (qFirm-LG6.2), which explained 8.8%-21.8%, 1.7%-10.1% and 4.2% of the phenotypic variance, respectively (Crump et al, 2022). In addition, several SNP-trait associations with fruit firmness were identified in other GWASs (Donkpegan et al, 2023;Holu sov a et al, 2022). Holu sov a et al (2022) identified 18 SNP markers associated with the fruit firmnessrelated traits, located on chromosomes 1, 2, 3, 4, 6, 7 and 8 in GWASs with 235 sweet cherry accessions (Holu sov a et al, 2022).…”