Location: Horticultural Crops Production and Genetic Improvement Research Unit
Project Number: 2072-21000-060-024-A
Project Type: Cooperative Agreement
Start Date: Sep 1, 2026
End Date: Dec 31, 2028
Objective:
The objectives of the research will involve evaluating fruit firmness and skin toughness in a population of Oregon blackberries, performing genomic sequencing of the population, using these data to perform genetic mapping of blackberry fruit quality traits, and developing predictive genetic markers for breeders to utilize. Specific objectives are:
1) Evaluate fruit firmness and skin toughness in Oregon trailing blackberry breeding population including diverse progeny, advanced selections, and cultivars (200 total).
2) Sequence the blackberries used for fruit evaluation, identify genomic variants based on sequence alignment to newly developed ‘Columbia Star’ genome assembly.
3) Perform genetic mapping of firmness and skin toughness to identify predictive genomic variants and associated genes. Convert predictive variants to low-cost PCR marker assays for deployment in breeding program.
Approach:
Fruit sampling and quality measurement will occur in summer of 2026. We will harvest mature berry samples (n=50) from a population of 200 blackberries including 150 progeny from bi-parental crosses and 50 cultivars and breeding lines representing the broader genetic diversity of Oregon blackberry. Fruit samples will be harvested over 2-3d in peak trailing blackberry season, targeting the first week of July. Samples will be harvested early morning to avoid heat stress, stored overnight at 4C, and the following day allowed to reach uniform room temperature for texture analysis. We will measure whole-berry firmness using a FruitFirm 1000 device and skin toughness using an Imada DST-1A digital force gauge with 2mm penetrating probe, each using 25 berries. Immature leaf samples will be collected from the 200 blackberry genotypes. Genomic DNA will be extracted for whole-genome sequencing (WGS). We will perform WGS library preparation using commercial kits and sequence libraries to 10x genome coverage on the DNBSEQ T7 platform. Sequences will be aligned to the ‘Columbia Star’ draft genome assembly using BWA-MEM2. Genomic variant calling for identification of single nucleotide polymorphism (SNP) sites will be performed using FreeBayes. Estimation of population structure and admixture will be performed using STRUCTURE. Estimation of the kinship matrix will be performed using TASSEL. A genome wide association study (GWAS) analysis will be performed in TASSEL using structure and kinship as covariates. Marker significance thresholds will be determined based on strict Bonferroni correction. ‘Columbia Star’ gene models in proximity to significant predictive variant sites will be assessed for functions related to fruit texture in the small fruit literature. A subset of 10-20 of the most predictive SNP sites will be selected for conversion to low-cost Kompetitive Allele Specific PCR (KASP) or high-resolution melting (HRM) marker assays. Marker validation will be performed using firmness and skin toughness data from selections in trial at OSU-NWREC.