A stop-gained mutation in a Peroxiredoxin gene may underlie the low-chill phenotype of the apricot spontaneous mutant ‘Búlida Precoz’

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ABSTRACT

Somatic mutations in clonally propagated fruit trees, known as “bud sports,” are a primary source of new and agronomically valuable traits. This study addresses the study of ‘Búlida Precoz’, a spontaneous somatic variant of the ‘Búlida’ apricot characterized by an early flowering (low-chill) phenotype. The main objective of this work was to design and implement a comprehensive bioinformatic workflow to identify the specific somatic mutation(s) responsible for this significant developmental change, using whole-genome sequencing (WGS) data.

A comparative genomics approach was employed, analyzing the genomes of four biological replicates from the ‘Búlida Precoz’ mutant and four from the original ‘Búlida’ wild-type. The analysis was centered on a specialized somatic variant-calling workflow using <monospace>GATK Mutect2</monospace>, chosen for its high sensitivity in detecting low-frequency mutations. The results were cross-validated against an independent analysis using the germline caller <monospace>GATK HaplotypeCaller.</monospace>

The final candidates were functionally annotated to predict their biological impact on gene function. This work establishes a solid foundation for future experimental validation and provides valuable molecular targets that could be used in marker-assisted breeding programs aimed at developing new apricot cultivars better adapted to climates with mild winters.