High-resolution genome-wide association study of a large Czech collection of sweet cherry (Prunus avium L.) on fruit maturity and quality traits

0570617 - ÚEB 2024 RIV GB eng J - Článek v odborném periodiku
Holušová, Kateřina - Čmejlová, J. - Suran, P. - Čmejla, R. - Sedlák, J. - Zelený, L. - Bartoš, Jan
High-resolution genome-wide association study of a large Czech collection of sweet cherry (Prunus avium L.) on fruit maturity and quality traits.
Horticulture Research. Roč. 10, č. 1 (2023), č. článku uhac233. ISSN 2662-6810. E-ISSN 2052-7276
Grant CEP: GA MZe(CZ) QK1910290
Institucionální podpora: RVO:61389030
Klíčová slova: POLYGALACTURONASE GENE * SKIN * BIOSYNTHESIS
Obor OECD: Genetics and heredity (medical genetics to be 3)
Impakt faktor: 8.7, rok: 2022
Způsob publikování: Open access
https://doi.org/10.1093/hr/uhac233

In sweet cherry (Prunus avium L.), quantitative trait loci have been identified for fruit maturity, colour, firmness, and size to develop markers for marker-assisted selection. However, resolution is usually too low in those analyses to directly target candidate genes, and some associations are missed. In contrast, genome-wide association studies are performed on broad collections of accessions, and assemblies of reference sequences from Tieton and Satonishiki cultivars enable identification of single nucleotide polymorphisms after whole-genome sequencing, providing high marker density. Two hundred and thirty-five sweet cherry accessions were sequenced and phenotyped for harvest time and fruit colour, firmness, and size. Genome-wide association studies were used to identify single nucleotide polymorphisms associated with each trait, which were verified in breeding material consisting of 64 additional accessions. A total of 1 767 106 single nucleotide polymorphisms were identified. At that density, significant single nucleotide polymorphisms could be linked to co-inherited haplotype blocks (median size similar to 10 kb). Thus, markers were tightly associated with respective phenotypes, and individual allelic combinations of particular single nucleotide polymorphisms provided links to distinct phenotypes. In addition, yellow-fruit accessions were sequenced, and a similar to 90-kb-deletion on chromosome 3 that included five MYB10 transcription factors was associated with the phenotype. Overall, the study confirmed numerous quantitative trait loci from bi-parental populations using high-diversity accession populations, identified novel associations, and genome-wide association studies reduced the size of trait-associated loci from megabases to kilobases and to a few candidate genes per locus. Thus, a framework is provided to develop molecular markers and evaluate and characterize genes underlying important agronomic traits.
Trvalý link: https://hdl.handle.net/11104/0341921