SNPs. (Supports Figure 4.) Minor allele frequency is calculated … · 2019-01-15 · Supplemental Figure 1. Allele frequency spectrum of B. cinerea SNPs. (Supports Figure 4.) Minor

Supplemental Figure 1. Allele frequency spectrum of B. cinerea SNPs.

(Supports Figure 4.)

Minor allele frequency is calculated across 97 isolates including our GWA population, at 1,048,575

SNPs including the 272,672 used in our analysis.

0

4 x 105

3 x 105

2 x 105

1 x 105

0

Supplemental Data. Soltis et al. Plant Cell (2018) 10.1105/tpc.18.00857


Supplemental Figure 2. Genetic distance between selected tomato accessions.


Pairwise Euclidean distances between 426 wild and domesticated tomato accessions in the

SolCAP diversity panel calculated from Infinium SNP genotyping at 7,720 loci (Sim 2012).

Clustering is by R hclust's default UPGMA method. S. pimpinellifolium accessions in the current

study are marked with orange stars, S. lycopersicum accessions in the current study are marked

with blue stars. All of the wild S. pimpinellifolium included in this panel cluster with our 3

accessions. Mean ± SE of lesion size of B. cinerea across the full study is included for each

accession.


Supplemental Figure 3. Correlation between B. cinerea lesion size on tomato and on A.

thaliana.


Lesion size of 94 of our B. cinerea isolates on tomato was weakly correlated with lesion size on A.

thaliana from previous studies (Zhang 2017); both on domesticated tomato (r=0.247, p= 0.003) and

on wild tomato (r=0.301, p= 0.016).

(cm

2)

(cm

2)

(pixels)

(pixels)


Supplemental Figure 4. Rank order plot of B. cinerea lesion size on two tomato genotypes.

(Supports Figure 3 and Table 2.)

Each B. cinerea isolate is represented by a straight line tracing mean lesion size on LA1547 to

mean on LA0410, the two host genotypes with the most pronounced effect on the rank order of

isolates by lesion size (Wilcoxon signed-rank test with FDR-correction, p = 3.33 x 10-17, Table 2).


Supplemental Table 1. Results of ANOVA following removal of domestication-associated

isolates

Results of general linear modelling of lesion area for 12 tomato accessions by 93 B. cinerea

isolates is shown (R lme4 package version 1.1-18-1;(Bates, Maechler et al. 2015)). This analysis

includes the full 95 isolate sample, without the two domestication-associated isolates (Fd2, Rose).

The terms are as follows; Isolate is the 93 B. cinerea isolates, Domestication is wild tomato, S.

pimpinellifolium, versus domesticated tomato, S. lycopersicum, Plant is 12 tomato genotypes

nested within their respective domestication groupings, Experiment tests the random effect of 2

independent replicate experiments. The nested random effects of whole plant sampled, leaf

sampled, and leaflet pair are included. In addition, interactions of these factors are tested (:). The

degrees of freedom and p-value are shown. For fixed effects, the type II sum of squares and F-

value are shown, and for random effects the likelihood ratio test statistic (LRT) is shown.

Fixed Effect

% genetic

variance SS F value DF p

Mean lesion

area:

Isolate 13.5 36.5 1.7 92 0.009 Domesticated 0.725

Domestication 1.2 3.2 13.4 1 0.0008 Wild 0.62

Domest/Plant 15.2 41.1 17 10 4.3 x 10-11

Iso:Domest 5.7 15.3 0.7 92 0.99

Iso:Domest/Plant 64.4 173.8 0.8 920 1

Random Effect LRT DF p

1 | Experiment 134.3 1< 2.0 x 10-16

1 | Whole Plant 0.029 1 0.86

1 | WP/Leaf 24.4 1 7.7 x 10-7

1 | WP/Leaf/Leaflet

Pair 0 1 1

1 | Exp:Iso 308.6 1< 2.0 x 10-16


T4vanKan-

BROAD BcinB0510 Other name PFAM description

Linked

Phenotypes

BcT4_1873 Bcin09g04570 GMC_oxred_N GMC oxidoreductase 12

BcT4_2485 Bcin04g03540 HET Heterokaryon incompatibility protein (HET) 12

BcT4_3044 Bcin10g04750 12

BcT4_3048 Bcin10g04790 12

BcT4_475 Bcin03g04120 RRM_1 RNA recognition motif. (a.k.a. RRM) 12

BcT4_477 Bcin02g04880 12

BcT4_479 Bcin03g04080 CPSF73-100_C

Pre-mRNA 3'-end-processing endonuclease

polyadenylation factor C-term 12

BcT4_5778 Bcin15g04110 Pkinase Protein kinase domain 12

BcT4_6000 Bcin14g00870 MFS_1 Major Facilitator Superfamily 12

BcT4_7428 Bcin16g04640 2-Hacid_dh_C D-isomer specific 2-hydroxyacid dehydrogenase 12

BcT4_790 Bcin03g00550 12

BcT4_8803 Bcin01g10020 HET Heterokaryon incompatibility protein (HET) 12

BcT4_8813 Bcin01g10130 M20_dimer Peptidase dimerisation domain 12

BcT4_9744 Bcin15g04510 IBR IBR domain 12

BcT4_1316 Bcin06g01770 11

BcT4_1791 Aldedh Aldehyde dehydrogenase family 11

BcT4_1921 Bcin09g05080 Sugar_tr Sugar (and other) transporter 11

BcT4_2339 Bcin04g03640 CorA CorA-like Mg2+ transporter protein 11

BcT4_2664 Bcin10g00570 Pyr_redox_2 Pyridine nucleotide-disulphide oxidoreductase 11

BcT4_3043 Bcin10g04720 11

BcT4_3045 Bcin10g04760 11

BcT4_3046 Bcin10g04770 11

BcT4_3054 Bcin10g04840 11

BcT4_3124 Bcin10g05600 11

BcT4_3850 Bcin07g00190 11

BcT4_4121 Bcin11g05830 FPN1 Ferroportin1 (FPN1) 11

BcT4_4122 11

BcT4_4536 Bcin02g07420 11

BcT4_4537 Bcin02g07410 HEAT_2 HEAT repeats 11

BcT4_4564 Bcin02g07090 Oxidored_FMN

NADH:flavin oxidoreductase / NADH oxidase

family 11

BcT4_4566 Bcin02g07070 11

BcT4_476 Bcin03g04100 Het-C Heterokaryon incompatibility protein Het-C 11

BcT4_5054 Bcin01g05010 MFS_1 Major Facilitator Superfamily 11

BcT4_5586 Bcin15g01860 TPP_enzyme_N Thiamine pyrophosphate enzyme 11

BcT4_5624 11

BcT4_5627 Bcin15g02360 11

BcT4_5640 Bcin15g02520 Fungal_trans Fungal specific transcription factor domain 11

BcT4_5771 Bcin15g04030 Pyridox_oxidase Pyridoxamine 5'-phosphate oxidase 11

BcT4_5777 Bcin15g04090 11

BcT4_5825 Bcin14g02810 Sugar_tr Sugar (and other) transporter 11

BcT4_5838 Bcin14g02670 11

BcT4_5971 Bcin14g01160 11

BcT4_6001 Bcin14g00860 Pectinesterase Pectinesterase 11

BcT4_6002 Bcin14g00850 Glyco_hydro_28 Glycosyl hydrolases family 28 11

BcT4_6003 Bcin14g00840 DUF1279 Protein of unknown function (DUF1279) 11

BcT4_6020 Bcin14g00650 Glyco_hydro_31 Glycosyl hydrolases family 31 11

BcT4_6509 Bcin13g04750 Lactonase Lactonase 11

BcT4_663 Bcin03g02020

PKS17

GFO_IDH_MocA Oxidoreductase family 11

BcT4_6901 Bcin12g02910 Thi4 Thi4 family 11

BcT4_8116 Bcin05g06490 SnoaL SnoaL-like polyketide cyclase 11

BcT4_8414 Bcin11g01080 RVT_1

Reverse transcriptase (RNA-dependent DNA

polymerase) 11

Supplemental Table 2. Sixty-three genes highlighted for high-level overlap of significant

SNP hits across 11 to 12 tomato accessions.

T4vanKan-BROAD = Staats and van Kan 2012 gene identification number. BcinB0510 = van Kan

et al., 2017 gene identification number. Other name = abbreviated common name for gene. PFAM

description = protein family annotation. Linked Phenotypes = number of plant accessions in which

one or more significant SNPs at the 99.9% threshold are within 1kb of the gene of interest.

T4vanKan-

BROAD BcinB0510 Other name PFAM description

Linked

Phenotypes

BcT4_8440 Bcin11g01360 STAS STAS domain 11

BcT4_8731 Bcin01g09090 AAA

ATPase family associated with various cellular

activities (AAA) 11

BcT4_8749 Bcin01g09300 Ecm29 Proteasome stabiliser 11

BcT4_8805 Bcin01g10040 DUF3506 Domain of unknown function (DUF3506) 11

BcT4_9107 Bcin02g08460 Mito_carr Mitochondrial carrier protein 11

BcT4_9395 Bcin04g00920 NACHT NACHT domain 11

BcT4_9402 Bcin04g00840 11

BcT4_9404 Bcin04g00810 Ank_2 Ankyrin repeats (3 copies) 11

BcT4_9429 11

BcT4_9754 Bcin15g04410 Peptidase_M3 Peptidase family M3 11

Supplemental Data Set 1. Mean of B. cinerea lesion size of all isolates across all tomato

accessions.


Supplemental Data Set 2. Results of single-isolate ANOVA on mixed effect model

Results of general linear modelling of lesion area within each of the 95 B. cinerea isolates are

shown. The terms are as follows; Domestication is wild tomato, S. pimpinellifolium, versus

domesticated tomato, S. lycopersicum, Plant is 12 tomato genotypes nested within their respective

domestication groupings, Experiment tests the random effect of 2 independent replicate

experiments. The Chi squared value, degrees of freedom, p-value, and FDR-corrected p-value are

shown for each fixed effect term in each isolate model.


Supplemental Data Set 3. Gene and Functional Annotation based on T4 GWA Results

a) Genes with significant SNPs from bigRR on T4 for Botrytis virulence in 11 or 12 of the tomato

accessions.

b) Functional categories significantly overrepresented in genes linked to Botrytis virulence response

to tomato domestication by bigRR on T4.


Supplemental References

Bates, D., M. Maechler, B. Bolker and S. Walker (2015). "Fitting Linear Mixed-Effects

Models Using lme4." Journal of Statistical Software 67(1): 1-48.

R Development Core Team (2008). "R: A language and environment for statistical

computing." R Foundation for Statistical Computing,Vienna, Austria. ISBN 3-900051-07-

0.

Sim, S.-C., G. Durstewitz, J. Plieske, R. Wieseke, M. W. Ganal, A. Van Deynze, J. P.

Hamilton, C. R. Buell, M. Causse and S. Wijeratne (2012). "Development of a large SNP

genotyping array and generation of high-density genetic maps in tomato." PloS one 7(7):

e40563.

Staats, M. and J. A. van Kan (2012). "Genome update of Botrytis cinerea strains B05. 10

and T4." Eukaryotic cell 11(11): 1413-1414.

Van Kan, J. A., Stassen, J. H., Mosbach, A., Van Der Lee, T. A., Faino, L., Farmer, A. D.,

Papasotiriou, D. G., Zhou, S., Seidl, M. F., Cottam, E. and D. Edel (2017). “A gapless

genome sequence of the fungus Botrytis cinerea.” Molecular plant pathology, 18(1): 75-

89.

Zhang, W., J. A. Corwin, D. Copeland, J. Feusier, R. Eshbaugh, F. Chen, S. Atwell and

D. J. Kliebenstein (2017). "Plastic transcriptomes stabilize immunity to pathogen

diversity: the jasmonic acid and salicylic acid networks within the Arabidopsis/Botrytis

pathosystem." The Plant Cell: tpc. 00348.02017.


Documents

SNPs. (Supports Figure 4.) Minor allele frequency is calculated … · 2019-01-15 · Supplemental Figure 1. Allele frequency spectrum of B. cinerea SNPs. (Supports Figure 4.) Minor