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Updated: Jan 29, 2026

Large-Scale Multi-Omics Genome-Wide Association Studies Mo-GWAS: Guidelines for Sample Preparation and Normalization
Published on: July 27, 2021
Multi-Season Genome-Wide Association Study Reveals Loci and Candidate Genes for Fruit Quality and Maturity Traits in
María Osorio1, Arnau Fiol1, Paulina Ballesta1,2
1Laboratorio de Biología Vegetal e Innovación en Sistemas Agroalimentarios-Grupo Nutribreeding, Instituto de Nutrición y Tecnología de Alimentos Dr. Fernando Monckeberg Barros (INTA), Universidad de Chile, El Líbano #5524, Macul 7830490, Chile.
Abstract:
Peaches are a fruit crop with global importance due to their economic value. Fruit quality (e.g., weight, soluble solids content (SSC)) and phenology traits (e.g., maturity date) are essential for generating novel varieties. Nevertheless, modern germplasm's narrow genetic diversity hampers breeding efforts to enhance these traits. To identify genetic markers helpful for marker-assisted breeding, this work leveraged a diverse panel of 140 peach commercial cultivars and advanced breeding lines phenotyped across three harvest seasons for the maturity date (MD), chlorophyll absorbance (IAD), SSC, and fruit weight (FW). Genotypic data were generated via ddRADseq, identifying 5861 SNPs. A rapid linkage disequilibrium decay (critical r2 = 0.308 at 950 kb) was determined, and a population structure analysis revealed two admixed genetic clusters, with phenotypic distributions influenced by seasonal environmental factors. A total of 599 marker-trait associations were detected by using single and multi-year analysis, and for each trait the surrounding genomic regions explored to identify potential candidate genes annotated with functions related to the trait under study, and expressed in peach fruits. This study highlights multiple loci potentially responsible for phenotypic variations in plant phenology and fruit quality, and provides molecular markers to assist peach breeding for fruit quality.
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