Leveraging synteny across Rosaceae to identify loci controlling fruit sweetness in blackberry

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

Submitted to: American Society of Horticulture Science Meeting
Publication Type: Abstract Only
Publication Acceptance Date: 3/1/2019
Publication Date: 7/21/2019
Citation: Zurn, J.D., Driskill, M., Jung, S., Main, D., Yin, M.H., Clark, M.C., Cheng, L., Clark, J.R., Worthington, M., Finn, C.E., Bassil, N.V. 2019. Leveraging synteny across Rosaceae to identify loci controlling fruit sweetness in blackberry. American Society of Horticulture Science Meeting. American Society of Horticulture Science Meeting.

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: There is a high consumer demand for sweet blackberries (Rubus subgenus Rubus). Fruit sugar production in related species is highly influenced by the environment and controlled by many genes, each providing small contributions to the phenotype. Many of the molecular pathways mediating sugar production are conserved across species. Therefore, a synteny-based approach was used to identify candidate genes responsible for sugar production in blackberry. Sugar quantitative trait loci (QTL) were identified from the Genome Database for the Rosaceae (GDR) QTL database for apple (Malus domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca) and synteny analysis was conducted to find conserved QTLs. Three syntenic QTLs that were conserved in at least two species were recovered. The physical regions for these QTLs were identified in the F. vesca v1.1 assembly and predicted genes within this region were annotated with Blast2GO. A total of 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. A BLAST search of the GDR Rubus reference transcriptome using the Fragaria and Malus genes was conducted. A total of 279 Rubus candidate transcripts were identified. Exons were predicted for each transcript using the Rubus occidentalis v 2 genome. The exons were separated into 2,122 individual sequences that were sent to Arbor Biosciences to design 9,355 Hyb-Seq baits with a 2X tiling density that covered 99.6% of the targeted regions. The Hyb-Seq baits were used in conjunction with a 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 reads were mapped to the R occidentalis v 3 genome using MiniMap2 and polymorphisms were identified using FreeBayes. Polymorphism-trait associations are being identified for the high and low sugar groups for each breeding program. Future work will focus on developing diagnostic tests to predict sugar phenotypes.