UC Davis Strawberry Breeding, Genetics, & Genomics

04/19/2024

Abstract. Two decades have passed since the strawberry (Fragaria x ananassa) disease caused by Macrophomina phaseolina, a necrotrophic soilborne fungal pat

05/06/2023

https://www.ucdavis.edu/food/news/uc-davis-releases-5-strawberry-varieties-resistant-deadly-fungal-disease

08/01/2022

https://www.ucdavis.edu/food/news/researchers-identify-genes-making-strawberries-resistant-fusarium-wilt

UC Davis researchers discover genes that make strawberries resistant to the deadly disease Fusarium wilt.

01/23/2021

Our paper on the breeding history of strawberry came out in G3: Genes | Genomes | Genetics today. This work started in 2016 with Tom Poorten (now at Pairwise, a biotechnology company in Durham, North Carolina) and expanded in scale and scope over time. I want to thank Dominique Pincot, Mitchell Feldmann, and Mirko Ledda (co-first authors) for their excellent work and contributions to this study. We had great fun reconstructing the genealogy of strawberry as far back as humanly possible and then delving into what the genealogy taught us about the breeding history of strawberry, and what a cool history it is! Ironically, we are posting a story about a social network analysis (of a genealogy) on a social network!

Abstract. The widely recounted story of the origin of cultivated strawberry (Fragaria × ananassa) oversimplifies the complex interspecific hybrid ancestry of th

01/21/2021

Check out this study which partly focused on identifying sources of resistance to virulent races of Fusarium oxysporum in strawberry that are not yet found in the US. One of our goals was to identify sources of classic resistance genes that we could target to develop cultivars resistant to Fusarium wilt anywhere in the world. Congratulations to Peter Henry and Dominique Pincot on this excellent study.

The genes required for host‐specific pathogenicity in Fusarium oxysporum can be acquired through horizontal chromosome transfer (HCT). However, it is unknown if HCT commonly contributes to the div...

10/22/2020

A wonderful tribute to Chad Finn by John Clark.

This past year, the fruit industry lost Chad Finn unexpectedly. See why fellow berry breeding scientist John Clark calls him a lasting inspiration.

10/04/2020

The paper by Hardigan et al. (2020) from our laboratory describes several technical advances in strawberry genomics, including the application of whole-genome shotgun genotyping-by-sequencing, the development of 50K and 850K single nucleotide polymorphism (SNP) arrays anchored to the octoploid genome, the reconciliation of six discordant linkage group nomenclatures, and complete resolution of the four subgenomes through comparative genetic mapping of the genomes of five octoploid taxa. There is a ton of useful and interesting information packed into this paper. Everything is open source and available at Frontiers in Plant Sciences (https://doi.org/10.3389/fpls.2019.0178) and other public databases (see links below).

Short-read DNA sequences for this study were deposited in the NCBI Sequence Read Archive (https://www.ncbi.nlm.nih.gov/sra) under BioProject ID PRJNA578384.

Supplemental materials for this study were deposited in a DRYAD database (https://doi.org/10.25338/B8R31Q).

This research was supported by a United States Department of Agriculture NIFA Postdoctoral Fellowship ( #2018-67012-27980) awarded to Michael A. Hardigan and a USDA NIFA (http://dx.doi.org/10.13039/100000199) Specialty Crops Research Initiative ( #2017-51181-26833) grant awarded to Steven J. Knapp.

10/04/2020

Our paper (Pincot et al. 2020) on breeding for resistance to Verticillium wilt has been published at The Plant Genome. This research was part of the Ph.D. thesis of Dominique Pincot. The paper and supplemental materials (three files and five figures) are open access and can be found @ The Plant Genome. The supplemental materials include an EXCEL file with Verticillium wilt resistance phenotypes for 984 germplasm accessions.

https://acsess.onlinelibrary.wiley.com/doi/full/10.1002/tpg2.20054

This research was supported by grants to S.J.K. from the United Stated Department of Agriculture (https://doi.org/10.13039/100000199) National Institute of Food and Agriculture (NIFA) Specialty Crops Research Initiative ( #2017‐51181‐26833), California Strawberry Commission (https://doi.org/10.13039/100006760), and the University of California, Davis (https://doi.org/10.13039/100007707).

02/07/2020

https://www.frontiersin.org/articles/10.3389/fpls.2019.01789/full?&utm_source=Email_to_authors_&utm_medium=Email&utm_content=T1_11.5e1_author&utm_campaign=Email_publication&field=&journalName=Frontiers_in_Plant_Science&id=504896

Allo-octoploid cultivated strawberry (Fragaria × ananassa) originated through a combination of polyploid and homoploid hybridization, domestication of an interspecific hybrid lineage, and continued admixture of wild species over the last 300 years. While genes appear to flow freely between the octo...

03/01/2019

Our paper describing the origin and evolution of the octoploid strawberry genome is out in Nature Genetics. We made the cover of the March issue. Credit goes to Patrick Edger and the other bright young scientists that pulled this off. Check it out.

https://www.nature.com/articles/s41588-019-0356-4

URLs
Sequence Read Archive, https://www.ncbi.nlm.nih.gov/sra/; Dryad, https://doi.org/10.5061/dryad.b2c58pc; PhyDS, https://github.com/mrmckain/PhyDS/; GDR, https://www.rosaceae.org/; CoGe, https://genomevolution.org/r/tx72/; RefTrans, https://github.com/mrmckain/RefTrans/; annoBTD, https://github.com/mrmckain/annoBTD/; Mitofy, http://dogma.ccbb.utexas.edu/mitofy/; dotPlotly, https://github.com/tpoorten/dotPlotly/; NCBI Conserved Domain Database, www.ncbi.nlm.nih.gov/Structure/bwrpsb/bwrpsb.cgi/; Pfam database, www.ebi.ac.uk/Tools/pfa/pfamscan/; FastQC, https://www.bioinformatics.babraham.ac.uk/projects/fastqc/; R, https://www.r-project.org/; Repeat-Masker, http://www.repeatmasker.org/; RepeatModeler, http://www.repeatmasker.org/RepeatModeler/; Google Maps, https://www.google.com/maps/.

Chromosome-scale assembly for the cultivated octoploid strawberry (Fragaria × ananassa) uncovers the origin and evolutionary processes that shaped this complex allopolyploid, providing a useful resource for genome-wide analyses and molecular breeding.

02/26/2019

Beloved fruit has a tangled family tree — but owes much of its fragrance and sweetness to just one ancestor.

02/14/2019

Grown on family farms and picked at the peak of ripeness, Oregon strawberries are widely known for exceptional taste above all.