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Research Project: Management of Temperate-Adapted Fruit, Nut, and Specialty Crop Genetic Resources and Associated Information

Location: National Clonal Germplasm Repository

Title: A synteny-based approach to identify candidate genes controlling blackberry fruit sweetness

item Zurn, Jason
item JUNG, SOOK - Washington State University
item MAIN, DORRIE - Washington State University
item YIN, MELINDA - University Of Arkansas
item Clark, Melissa
item CHENG, LAILIANG - Cornell University
item CLARK, JOHN - University Of Arkansas
item WORTHINGTON, MARGARET - University Of Arkansas
item Finn, Chad
item Bassil, Nahla

Submitted to: International Rubus Ribes Symposium
Publication Type: Abstract Only
Publication Acceptance Date: 11/26/2018
Publication Date: 6/25/2019
Citation: Zurn, J.D., Jung, S., Main, D., Yin, M.H., Clark, M.C., Cheng, L., Clark, J.R., Worthington, M., Finn, C.E., Bassil, N.V. 2019. A synteny-based approach to identify candidate genes controlling blackberry fruit sweetness. International Rubus Ribes Symposium. International Ruus Ribes Symposium.

Interpretive Summary: Sweet fruit is in high demand for blackberries. Similar genes are found in related species that control fruit sweetness because of shared evolution. We used genes that have previously been identified to control fruit sweetness in apple, peach, and strawberries to identify genes that may be responsible for controling fruit sugar in blackberry. A targeted DNA sequencing approach was used to sequence sugar genes in blackberry 20 varieties that have high sugar concentration and 20 varieties that have low sugar concentration. We are currently analyzing these genes to try and identify genetic differences that can be used to help breeders create varieties with sweeter fruit.

Technical Abstract: Sweeter fruit is often in high demand for blackberries (Rubus subgenus Rubus). In related fruit species, sugar production appears to be highly influenced by the environment and controlled by many genes each providing small contributions to the phenotype. A synteny-based approach was used to identify candidate genes responsible for sugar production in blackberry. Sugar quantitative trait loci (QTL) were identified from GDR QTL database for apple (Malus domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca). Synteny analysis was conducted to determine which QTLs were conserved across these Rosaceous species. Three conserved syntenic QTLs were found. The physical regions for these QTLs were identified in the F. vesca v1.1 assembly. Predicted genes within this region were annotated with Blast2GO and 26 genes with functions associated with sugar production were extracted. Additionally, 789 sugar-associated genes were extracted from the M. domestica v3.0.a1 assembly. The Fragaria and Malus genes were used to conduct a BLAST search in the GDR Rubus reference transcriptome. A total of 279 Rubus candidate transcripts were identified. Exons were predicted for each transcript using the Rubus occidentalis genome. The exons were separated into 2,122 individual sequences that were sent to Arbor Biosciences to design 9,355 Hyb-Seq baits. The baits had a 2X tiling density and covered 99.6% of the targeted regions. The Hyb-Seq baits were used in conjunction with PacBio sequencing approach to genotype 40 cultivars with high and low sugar content from the University of Arkansas and USDA blackberry breeding programs. A total of 430,167 high quality circular consensus sequences were generated. The sequence lengths ranged from 50 bp to 13,634 bp with a mean and median sequence length of 2661 bp and 2610 bp, respectively. Future work will consist of polymorphism identification, polymorphism-trait association analysis, and diagnostic test development and validation.