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

24 Nov 2023
1036

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

Agricooler: innovative new covers for heat management

Covers

13 Jun 2024

This innovative fabric, patented by the Spanish company Agralia, incorporates aluminium microparticles to improve cold storage. The microparticles in Agricooler block infrared radiation, which is responsible for heat transmission.

Michigan: sour cherry crisis continues

Production

09 Apr 2024

A reduction in sour cherry orchards and processing plants is expected. "The cost of planting and maintaining the current orchards is high," says Tim Brian, president of Smeltzer Orchard Co. "and there are not many to replace them."

In evidenza

Ciliegie di Ñuble: il nuovo bollettino tecnico INIA per qualità ed export

Tech management

22 Jul 2025

Un nuovo bollettino INIA aiuta i produttori di ciliegie della regione di Ñuble a migliorare qualità e conservazione lungo la filiera, fino all’export nei mercati asiatici. Un’opportunità concreta per affrontare la crescita e le sfide dell’export cileno 2024–2025.

Cherry tree training: comparing YLL-TS and SSS-TS systems for higher productivity

Tech management

22 Jul 2025

A Chinese study compares YLL-TS and SSS-TS cherry tree systems, focusing on photosynthetic efficiency, fruit quality, and yield. The innovative YLL-TS system shows remarkable performance, proving suitable for high-efficiency, intensive sweet cherry farming.

Tag Popolari