A rosaceae family-level approach to identify loci influencing soluble solids content in blackberry for DNA-informed breeding

Authors: Zurn, Jason; Driskill, Mandie; JUNG, SOOK - Washington State University; MAIN, DORRIE - Washington State University; YIN, MELINDA - University Of Arkansas; CLARK, MELISSA - Former ARS Employee; CHENG, LAILIANG - Cornell University; ASHRAFI, HAMID - North Carolina State University; ARYAL, RISHI - North Carolina State University; CLARK, JOHN - University Of Arkansas; WORTHINGTON, MARGARET - University Of Arkansas; Finn, Chad; PEACE, CAMERON - Washington State University; IEZZONI, AMY - Michigan State University; Bassil, Nahla

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 8/4/2020
Publication Date: 10/1/2020
Citation: Zurn, J.D., Driskill, M.J., Jung, S., Main, D., Yin, M.H., Clark, M., Cheng, L., Ashrafi, H., Aryal, R., Clark, J., Worthington, M., Finn, C.E., Peace, C., Iezzoni, A., Bassil, N.V. 2020. A rosaceae family-level approach to identify loci influencing soluble solids content in blackberry for DNA-informed breeding. G3, Genes/Genomes/Genetics. 10(10):3729-3740. https://doi.org/10.1534/g3.120.401449.
DOI: https://doi.org/10.1534/g3.120.401449

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. Many variations were identified in the DNA between these samples and 111 DNA markers were developed to determine if any of the DNA variations were associated with fruit sweetness. A total of 48 markers were found to have significant association with fruit sweetness in 192 samples representing the USDA and University of Arkansas breeding programs. One of these locations, known as qSSC-Ruh-ch1.1, was stable across three environments. This discovery represents the first environmentally stable sweetness locus identified in blackberry. Additionally, the approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.

Technical Abstract: A Rosaceae family-level candidate gene approach was used to identify genes associated with sugar content in blackberry (Rubus subgenus Rubus). Three conserved regions containing sweetness-related quantitative trait loci (QTLs) were identified from the Genome Database for Rosaceae that were conserved among apple (Malus × domestica), peach (Prunus persica), and alpine strawberry (Fragaria vesca). Sugar related genes in these conserved regions and 789 sugar-associated apple genes were used identify 279 Rubus candidate transcripts. A Hyb-Seq approach was used in conjunction with PacBio sequencing to generate haplotype level sequence information of sugar-related genes for 40 cultivars with high and low soluble solids content from the University of Arkansas and USDA blackberry breeding programs. Polymorphisms were identified relative to the ‘Hillquist’ blackberry (R. argutus) and ORUS 4115-3 black raspberry (R. occidentalis) genomes and tested for their association with soluble solids content. 173 alleles were identified that were significantly (a = 0.05) associated with sugar content. KASP genotyping was conducted for 92 of these alleles on a validation set of blackberries from each breeding program and 48 markers were identified that were significantly associated with SSC. One QTL, qSSC-Ruh-ch1.1, identified in both breeding programs accounted for an increase of 1.5 °Brix and the polymorphisms were detected in the intron space of a sucrose synthase gene. This discovery represents the first environmentally stable sweetness QTL identified in blackberry. The approach demonstrated in this study can be used to develop breeding tools for other crops that have not yet benefited directly from the genomics revolution.