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

Abstract

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 ~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 ~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.

Identification of Single Nucleotide Polymorphic Loci and Candidate Genes for Seed Germination Percentage in Okra under Salt and No-Salt Stresses by Genome-Wide Association Study

“…Only two SNPs were detected between these two LD blocks, SNP2619136 and SNP2619493. The key SNP locus that was detected in the three traits was not within an LD block, which may have been caused by missing data points or incorrect sequence assembly in a particular region during sequencing, which interrupted the haplotype block [ 17 ]. We inferred that there must be a key candidate gene near SNP2619493, so we screened for genes near this SNP.…”

“…SNPs within an LD block were usually considered key SNPs that were significantly associated with traits. If SNPs associated with traits were not within a particular LD block, the SNPs or genes within its closest up- and downstream LD blocks should also be considered [ 17 ]. Subsequently, we performed comparative analyses of GP in the accessions with different SNPs of the candidate gene associations and further excluded the candidate genes that were obtained from the inaccurate lead SNPs.…”

“…With the development of high-throughput sequencing technology and the widespread application of SNP markers, genome-wide association studies (GWASs) have become a more effective method for mining plant genes than traditional QTL mapping methods. At present, GWASs based on large-scale SNP markers have been widely used in gene mining for complex traits in plants, such as rice [ 12 ], wheat [ 13 ], cotton [ 14 ], soybean [ 15 ], watermelon [ 16 ], and cherry [ 17 ].…”

A New One-Tube Reaction Assay for the Universal Determination of Sweet Cherry (Prunus avium L.) Self-(In)Compatible MGST- and S-Alleles Using Capillary Fragment Analysis

“…Interestingly, the S54 allele shares 98.3% nucleotide sequence identity with the Prunus virginiana S2 allele, indicating the ‘Techlovicka’ cultivar might originate from an inter-species cross. However, the ‘Techlovicka’ cultivar looks like a common sweet cherry without any sign of Prunus virginiana traits (phenotypic and phenology traits may be found in [ 33 ]), thus the introgression of the Prunus virginiana S2 allele sequence presents a puzzle warranting further investigation. The predicted S54 S-RNase protein is similar to other Prunus spp.…”

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

“…(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; Holušová et al ., 2022). Holušová et al .…”