Phenological variation associates with the stability of fruit quality traits in cultivated tetraploid blueberry

Authors: Babiker, Ebrahiem; NAGASAKA, KYOKA - Kyoto University; NISHIYAMA, SOICHIRO - Kyoto University; YAMANE, HISAYO - Kyoto University; TAO, RYUTARO - Kyoto University

Submitted to: G3: Genes, Genomes, Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/9/2025
Publication Date: 5/15/2025
Citation: Babiker, E.M., Nagasaka, K., Nishiyama, S., Yamane, H., Tao, R. 2025. Phenological variation associates with the stability of fruit quality traits in cultivated tetraploid blueberry. G3: Genes, genomics, genetics. 1-39. https://doi.org/10.1093/g3journal/jkaf108 c.
DOI: https://doi.org/10.1093/g3journal/jkaf108 c

Interpretive Summary: Fruit quality directly impacts fruit marketability and consumer acceptance. However, breeding blueberry with improved fruit quality is challenging due to complex genetic control and genotype by environment interaction. Despite previous efforts to detect genomic regions associated with fruit quality traits, most of the identified regions explain only a fraction of the total variability or lack stability across multiple years or locations. In this study, we investigated multiple fruit quality traits and phenology-related traits of 187 diverse southern high-bush (SHB) blueberry germplasm over two to four years. The analysis of phenotypes within the SHB germplasm collection revealed substantial variation in fruit-related traits across different observation years. Genome-wide association study (GWAS) conducted on normalized phenotypic values identified stable genomic regions across multiple years. This result suggested that fruit-related traits in blueberry are under complex genetic control. Spearman’s correlation coefficient between observed phenotypic values and the stability measure indicated that phenology-related traits are associated with stability of fruit-related traits. Specifically, notable positive correlation was observed between observed ripening date and berry size stability, while negative correlations were observed between observed flowering/ripening date and berry firmness stability. Understanding the biological processes underlying these correlations would enhance our comprehension of the complex genetic control of fruit quality from previously unconsidered perspectives. GWAS conducted on the stability measure provided insights into the genomic regions associated with phenological variability across observation years, which contributed to identification of novel marker-trait associations.

Technical Abstract: In blueberry cultivation, fruit quality is a critical determinant of commercial success. However, breeding for fruit quality is challenging due to its complex inheritance and genotype × environment interaction. Despite previous efforts to detect quantitative trait loci (QTLs) associated with fruit quality traits, most of the identified QTLs explain only a fraction of the total variability or lack stability across multiple environments. In this study, we investigated multiple fruit quality traits and phenology-related traits of 187 diverse southern highbush blueberry germplasm over two to four years. Significant phenotypic variation across observation years was detected for most traits. Genome-wide association study (GWAS) failed to identify stable peaks supported by multiple observation years, indicating complex control of fruit-related traits. To elucidate factors contributing to phenotypic variation, the relationship between observed phenotypic values and the stability measure of these values was examined. Significant correlations were found between the variation of phenology-related traits and the stability of fruit-related traits; it was found that early blooming and ripening plants tended to exhibit variable firmness over the years. Additionally, size variability was influenced by the fruit size itself: plants producing smaller fruits tended to show more variation in size over the years. Furthermore, GWAS conducted on the stability indices identified novel marker-trait associations that were not detected using normalized phenotypic values only. Collectively, these findings deepen our understanding of variability in fruit-related traits and provide insights into their genetic control, thereby advancing blueberry breeding for superior cultivars with stable phenotypic performance.