Supplemental Material for Pincot et al., 2018
datasetposted on 29.03.2018 by Dominique D.A. Pincot, Thomas J. Poorten, Michael A. Hardigan, Julia M. Harshman, Charlotte B. Acharya, Glenn S. Cole, Thomas R. Gordon, Michelle Stueven, Patrick P. Edger, Steven J. Knapp
Datasets usually provide raw data for analysis. This raw data often comes in spreadsheet form, but can be any collection of data, on which analysis can be performed.
Supplemental File 1. Statistics from a mixed model analysis of Fusarium wilt resistance among 565 strawberry germplasm accessions grown in randomized complete blocks experiment designs in 2016 and 2017 in Davis, California.
Supplemental File 2. Selected SNP genotypes and Fusarium wilt resistance phenotypes among 565 F. x ananassa germplasm accessions. The latter are identified by UCD accession numbers or USDA plant introduction numbers and aliases where appropriate. Genotypes are shown for 14 SNPs on the Affymetrix iStraw35 array in linkage disequilibrium with Fw1, a gene conferring resistance to isolate AMP132 of Fusarium oxysporum f. sp. fragariae. Least square means for Fusarium wilt resistance phenotypes are shown for plants phenotyped nine weeks post-inoculation in 2016 and 36 weeks post-inoculation in 2017 field experiments in Davis, California. Plants phenotyped in the summer of 2016 were spring-planted in 2016, whereas plants phenotyped in the summer of 2017 were fall-planted in 2016. Least square means were estimated from four clonal replicates/entry in each study. Chromosome positions are shown for SNPs mapped against a diploid F. vesca reference genome (Edger et al. 2018), in addition to p-values estimated from 2016 and 2017 genome-wide association studies and Affymetrix probes identifiers.
Supplemental File 3. QTL mapping statistics in two S1 populations for SNPs tightly linked to Fw1, a gene conferring resistance to isolate AMP132 of Fusarium oxysporum f. sp. fragariae in strawberry. The additive and dominance effects and of individual SNP loci were estimated using linear contrasts (p-values are shown for F-statistics associated with each linear contrast). Coefficients of determination (R2) and degrees of dominance (|d/a|) were estimated for each SNP locus.
Supplemental File 4. QTL mapping statistics for resistance to Fusarium wilt in two F. x ananassa S1 mapping populations genotyped with the Affymetrix iStraw35 SNP array. Collectively, 5,673 co-dominant SNP markers were genetically mapped in the Fronteras S1 population (n = 93) and assembled into 40 linkage groups, where n = number of S1 progeny. Similarly, 7,345 co-dominant SNP markers were genetically mapped in the Portola S1 population (n = 93) and assembled into 50 linkage groups. Linkage groups were numbered and aligned with 28 linkage groups previously described by van Dijk et al. (2014) and Mangandi et al. (2017) and are hypothesized to correspond to the 28 chromosomes in the haploid genome of F. x ananassa. Likelihood-odds (LOD) statistics and linkage group positions (cM) are shown for QTL interval mapping across linkage groups. Linkage groups that did not align to the reference or had fewer than 10 SNPs are excluded from the figure, but were included in the mapping and did not show significant LOD scores.
Supplemental File 5. Pedigree database for 1,663 F. x ananassa germplasm accessions. The parents and birth years are shown for each individual (germplasm accession). Throughout the database, unknown ancestors are identified with the pre-fix “Unknown” followed by a unique number. “NA” indicates not ‘available’.
Supplemental File 6. Genotypes and phenotypes for SNPs in linkage disequilibrium (LD) with a Fusarium wilt resistance gene (Fw1) on chromosome 2C in strawberry. The individual plots show Fusarium wilt phenotypes for 565 germplasm accessions among each of the three genotypic classes for 11 SNPs in LD with Fw1 on chromosome 2C. Plants were artificially inoculated with isolate AMP132 of Fusarium oxysporum f. sp. fragariae and phenotyped nine weeks post-inoculation in (A) 2016 and 36 weeks post-inoculation in (B) 2017 field experiments in Davis, California.
Supplemental File 7. Physical locations in the F. vesca genome, ontologies, and annotations for genes associated with SNPs in linkage disequilibrium with the Fusarium wilt resistance gene Fw1.
SUPPLEMENTAL DATA FILES
Supplemental Data File 1. Raw genotypic data for 565 strawberry germplasm accessions genotyped with the iStraw35 SNP array. Each row corresponds to a SNP marker.
Supplemental Data File 2. Raw genotypic data for 186 individuals of the mapping populations genotyped with the iStraw35 SNP array. Each row corresponds to a SNP marker.
Supplemental Data File 3. Affymetrix iStraw35 SNP probe set names, alleles, genomic locations per the diploid reference (Edger et al. 2018), and flanking sequences. Cross-reference information for SNPs shared with the iStraw90 SNP array is also provided (Bassil et al. 2015).
Supplemental Data File 4. Raw phenotypic data (six time points) for 565 germplasm accessions and the Fronteras and Portola S1 mapping populations (NA = missing data).