Decade-long study identifies more than one million polymorphisms on cherry genome

24 Nov 2023
1011

The progress in sweet cherry (Prunus avium L.) breeding has been marked by the identification of molecular markers for crucial traits, utilizing genome sequencing for marker-assisted selection (MAS). Despite these achievements, quantitative trait locus (QTL) analyses have often lacked resolution, leading to missed gene associations.

Traditional breeding methods face challenges related to low efficiency and high costs. Recent developments in whole-genome sequencing have uncovered nearly 2 million single nucleotide polymorphisms (SNPs), promising higher marker density for genome-wide association studies (GWAS). However, uneven SNP distribution remains an obstacle, hindering the identification of candidate genes. The current hurdle is to leverage GWAS potential for high-resolution mapping to expedite the breeding of improved sweet cherry varieties.

Researchers employed paired-end sequencing on the Illumina NovaSeq 6000 platform, generating a 4.15-Tb sequence with samples contributing 7.6–36.8 Gb each. The extensive genome coverage allowed the identification of 1,767,106 high-quality SNPs distributed across the accessions. Principal component analysis (PCA) and Bayesian information criterion (BIC) indicated a homogeneous population without distinct genetic subgroups.

Phenotypic diversity assessed from 2012 to 2020 revealed significant variability across traits, with Collection of Genetic Resources (CGR) accessions displaying more pronounced diversity than breeding materials (BM). Notable differences in color traits and fruit size were observed, aligning with the goals of selective breeding.

Collection of Genetic Resources population structure analysis. A) Principal component (PC) analysis plot of the first two PCs identified from 235 accessions based on 1,767,106 single nucleotide polymorphisms. B) Heat map of a kinship matrix estimated using the VanRaden algorithm. Both plots were generated with GAPIT.


Source: EurekAlert!

Image: High-resolution genome-wide association study of a large Czech collection of sweet cherry (Prunus avium L.) on fruit maturity and quality traits - Scientific Figure on ResearchGate. https://www.researchgate.net/figure/Collection-of-Genetic-Resources-population-structure-analysis-A-Principal-component_fig1_364394570.


Cherry Times - All rights reserved

What to read next

Late-ripening cherries: the advantages of Calatayud varieties

Markets

05 Dec 2024

Cherries grown in the regions of Calatayud and Aranda, in the province of Zaragoza, have become a national reference. With over 3,000 hectares cultivated in 20 municipalities, this region is the leader in the Spanish market with an annual harvest exceeding 20.000 tonnes.

2025 Cherries: Yakima Valley Crop Grows 9% Over Previous Year

Production

19 Jun 2025

The 2025 cherry season in the U.S. Northwest looks promising: 21.4 million boxes forecasted, a 9% increase over 2024. Optimism rises for exports and domestic sales, thanks to an evenly set crop, better timing, and less overlap with California’s cherry harvest.

In evidenza

Native cherry trees better support local moths in Massachusetts landscapes

Crop protection

01 Jul 2025

A scientific study confirms native moths thrive best on cherry trees native to Massachusetts. Non-native species slow growth and raise mortality in larvae. Native trees are crucial for preserving biodiversity and supporting birds and insects in gardens and cities.

How genetics shapes cherry flavor: from sweet sorbitol to tart malic acid

Breeding

01 Jul 2025

Researchers from Clemson University and Spain’s CITA discovered the genetic basis of sweetness and acidity in sweet cherries. With QTL mapping and haplotype analysis, breeders can now develop better-tasting, more stable varieties tailored to consumer preferences in Europe.

Tag Popolari