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. 2017 May 23;8:763. doi: 10.3389/fpls.2017.00763

Table 1.

Genome-wide association studies in plant pathosystems.

Plant species name Number of linesa Polymrophismsb Pathogen species name Phenotypic traitc Growth conditionsd Gen. Arch.e Functional validationf References
Bacteria Arabidopsis thaliana 84 NA >17 k SNPs Pseudomonas syringae—Pst DC3000::avrRpm1 B Hypersensitive response G M RPM1 Aranzana et al., 2005
87 NA >17 k SNPs Pseudomonas syringae—Pst DC3000::avrB B Hypersensitive response G M RPM1 Aranzana et al., 2005
90 NA >17 k SNPs Pseudomonas syringae—Pst DC3000::avrPphB B Hypersensitive response G M RPS5 Aranzana et al., 2005
89 NA >17 k SNPs Pseudomonas syringae—Pst DC3000::avrRpt2 B Hypersensitive response G M RPS2 Aranzana et al., 2005
84 NA >216 k SNPs Pseudomonas syringae—Pst DC3000::avrRpm1 B Hypersensitive response G M RPM1 Atwell et al., 2010
87 NA >216 k SNPs Pseudomonas syringae—Pst DC3000::avrB B Hypersensitive response G M RPM1 Atwell et al., 2010
90 NA >216 k SNPs Pseudomonas syringae—Pst DC3000::avrPphB B Hypersensitive response G M RPS5 Atwell et al., 2010
89 NA >216 k SNPs Pseudomonas syringae—Pst DC3000::avrRpt2 B Hypersensitive response G M RPS2 Atwell et al., 2010
95 NA >216 k SNPs Pseudomonas syringae—Pst DC3000 Q Bacterial growth G P No Atwell et al., 2010
96 NA >205 k SNPs Pseudomonas syringae—Pst DC3000 Q Bacterial growth G P AtABCG36 Ji et al., 2014
64 NA 4,004,754 SNPs Pseudomonas syringae—Pst DC3000D28E (virulence factor HopAM1) Q DI (time point that cell death was first observed) G P No Iakovidis et al., 2016
B Chlorotic rosette phenotype G P No Iakovidis et al., 2016
75 NA >216 k SNPs Pseudomonas syringae—natural strain PNA29.1a B Hypersensitive response G M RPS5 Karasov et al., 2014
175 NA >216 k SNPs Pseudomonas viridiflava—natural strain LP23.1a Q DI (chlorosis) and bacterial growth G P No Atwell et al., 2010
175 NA >216 k SNPs Pseudomonas viridiflava—natural strain RMX23.1a Q DI (chlorosis) and bacterial growth G P No Atwell et al., 2010
175 NA >216 k SNPs Pseudomonas viridiflava—natural strain RMX3.1b Q DI (chlorosis)and bacterial growth G P No Atwell et al., 2010
175 NA >216 k SNPs Pseudomonas viridiflava—natural strain PNA3.3a Q DI (chlorosis) and bacterial growth G P No Atwell et al., 2010
175 NA >216 k SNPs Pseudomonas viridiflava—natural strain ME3.1b Q DI (chlorosis)and bacterial growth G P No Atwell et al., 2010
163 NA >214 k SNPs Ralstonia solanacearum—crop strain GMI1000 Q DI (wilting) G P RRS1/RPS4 & SSL4 Aoun et al., in review
384 NA >214 k SNPs Xanthmonas campestris pv. campestris—crop strain Xcc568 Q DI (chlorosis)and bacterial growth G P RKS1 Huard-chauveau et al., 2013
Arabidopsis thaliana 384 NA >214 k SNPs Xanthmonas campestris pv. campestris—crop strain Xcc12824 Q DI (chlorosis) G P AT5G22540 Debieu et al., 2016
176 NA >214 k SNPs Xanthmonas campestris pv. campestris—crop strain XccCFBP6943 Q DI (chlorosis) G P RRS1/RPS4 Debieu et al., 2016
Glycine max 3,173 Accessions 37,659 SNPs Xanthomonas axonopodis pv. glycines Q Di (percentage of lesions) F (NE) P No Chang et al., 2016
Fungi Arabidopsis thaliana 96 NA 115,301 SNPs Botrytis cinerea—strain Apple 517 Q Lesion area + camalexin production G P Yes Corwin et al., 2016
96 NA 115,301 SNPs Botrytis cinerea—strain B05.10 Q Lesion area + camalexin production G P Yes Corwin et al., 2016
96 NA 115,301 SNPs Botrytis cinerea—strain Supersteak Q Lesion area + camalexin production G P Yes Corwin et al., 2016
96 NA 115,301 SNPs Botrytis cinerea—strain UKRazz Q Lesion area + camalexin production G P Yes Corwin et al., 2016
350 NA >214 k SNPs Botrytis cinerea Q Percentage of leaves with spreading lesions G P No Thoen et al., 2016
350 NA >214 k SNPs Botrytis cinerea—strain B05.10 Q rosette fresh weight G P No Davila Olivas et al., 2016
Brassica napus 179 Diverse accessions 18,804 SNPs Leptosphaeria maculans—12 single spore isolates (04MGPS021, 06MGPP041, D8, D9, IBCN13, IBCN15, IBCN16, IBCN17, IBCN18, IBCN75, IBCN76 and PHW1223) Q DI (lesion size) G P No Raman et al., 2016
179 Diverse accessions 18,804 SNPs Leptosphaeria maculans—mix of pathotypes from four canola stubble sources Q Percentage of internal canker infection G P No Raman et al., 2016
116 Varieties 4,239 SNS Leptosphaeria maculans Q DI (area of necrosis) F (NE) P No Fopa Fomeju et al., 2014
Glycine max 392 Diverse cultivars + 300 advanced breeding lines 52,041 SNPs + 5,361 SNPs Fusarium virguliforme Q DI (disease incidence * disease severity/9) F (NE) P No Wen et al., 2014
214 Germplasm accessions 31,914 SNPs Fusarium virguliforme—isolate Mont-1 Q DI (percentage of foliage affected) + disease progressive curve G P No Zhang et al., 2015
4,771 Accessions 37,991 SNPs Fusarium virguliforme—isolate Mont-1 Q DI (percentage of foliage affected) G P No Chang et al., 2016
130 Lines 7,864 SNPs Sclerotina sclerotorium—strain NB5 Q Lesion length G P No Bastien et al., 2014
Fungi Glycine max 2773 Accessions 33,240 SNPs Cadophora gregata B Combination of foliar and stem observations F (NE) P No Rincker et al., 2016
540 Accessions 33,486 SNPs Cadophora gregata Q Percentage of plants exhibiting symptoms + proportion of nodes exhibiting brown pith F (NE) NA No Rincker et al., 2016
825 Accessions 32,150 SNPs Cadophora gregata—strain Oh2 Q Proportion of plants exhibiting foliar symptoms G P No Rincker et al., 2016
606 Accessions 29,815 SNPs Cadophora gregata—strain Oh2 Q Proportion of nodes exhibiting brown pith G P No Rincker et al., 2016
608 Accessions 34,424 SNPs Cadophora gregata Q Four classes of phenotypes based on foliar and stem symptoms G + F (NE) P No Chang et al., 2016
1,426 Accessions 33,549 SNPs Diaporthe phaseolorum var. caulivora Q DI (length of the visible lesions + proportion of dead plants) G P No Chang et al., 2016
112 accessions 34,210 SNPs Diaporthe phaseolorum var. meridionalis Q DI (percentage of infected/dead plants) G P No Chang et al., 2016
2,385 Accessions 38,608 SNPs Phakopsora pachyrhizi—mixture of four isolates Q DI (symptom and lesion development) + type of lesion G P No Chang et al., 2016
Hordeum vulgare 92 Commercial cultivars 6,970 SNPs Puccina graminis—mixture of isolates representative of the most prevailing races of the pathogen in Central Asia Q DI (uredinia size, chlorosis and necrosis) F (AI) P No Turuspekov et al., 2016
Medicago sativa 179 Elite breeding lines 19,801 SNPs Verticillium alfalfae—mix of six strains (Berg, Sevcik, Freitag, Kunderts, VP6 and VP11) Q DI (severity of disease symptoms) G P No Yu et al., 2016
Oryza sativa 413 Cultivars 44,100 SNPs Pyricularia oryzae—mix of US races IB-49, IC-17 and IE-1K Q DI (lesions) F (AI) P No Zhao et al., 2011
362 cultivars 700 k SNPs Magnaporthe oryzae—isolate R01-1 Q DI (lesion area) G P Pi5 locus Kang et al., 2016
331 Cultivars 700 k SNPs Magnaporthe oryzae—isolate RB22 Q DI (lesion area) G P Pi5 locus Kang et al., 2016
312 Cultivars 700 k SNPs Magnaporthe oryzae—isolate 75-1-127 Q DI (lesion area) G P Pi5 locus Kang et al., 2016
335 Cultivars 700 k SNPs Magnaporthe oryzae—isolate 0-249 Q DI (lesion area) G P Pi5 locus Kang et al., 2016
333 Cultivars 700 k SNPs Magnaporthe oryzae—isolate P06-6 Q DI (lesion area) G P Pi5 locus Kang et al., 2016
Setaria italica 916 Varieties (traditional landraces + modern cultivars) 845,787 SNPs Magnaporthe grisea Q not available F (NE) P No Jia et al., 2013
Rhizoctonia solani Q not available F (NE) P No Jia et al., 2013
Uromyces setariae-italicae Q not available F (NE) P No Jia et al., 2013
Sorghum bicolor 300 Genotypes (251 tropical sorghums + 49 breeding lines) 79,132 SNPs Macrophomina phaesolina Q Length of the visible lesions F (AI) P No Adeyanju et al., 2015
Fusarium thapsinum Q Length of the visible lesions F (AI) P No Adeyanju et al., 2015
Zea mays 4,699 RILs (NAM population) 1.6 M SNPs Cochliobus heterostrophus Q DI (number and area of lesions) F (NE + AI) P No Kump et al., 2011
4,413 RILs (NAM population) 28.5 M genomic variants (SNPs + read-depth variants) Cochliobus heterostrophus Q DI (number and area of lesions) F (NE + AI) P No Bian et al., 2014
4,630 RILs (NAM population) 1.6 M SNPs Setosphaeria turcica—race 1 Q Percentage of diseased leaf area F (AI) P No Poland et al., 2011
3,678 RILs (NAM population) 1.6 M SNPs Cercospora zeae-maydis + Cercospora zeina Q DI (dimension of each lesion + number of lesions) F (NE) P No Benson et al., 2015
1487 European inbred lines 8,244 SNPs Setosphaeria turcica Q DI (Percentage of diseased leaf area) F (NE + AI) P No Van Inghelandt et al., 2012
144 Inbred lines 45,868 SNPs Sphacelotheca reiliana—spores collected from the field in the previous growing season Q Percentage of infected plants F (AI) P No Wang et al., 2012
267 Inbred lines 47,445 SNPs Fusarium verticilliodes—local isolates Q Percentage of the ear presenting disease symptoms + DI (percentage of kernels exhibiting visual symptoms of infection) F (AI) P No Zila et al., 2013
274 Inbred lines 246,497 SNPs Puccina sorghi—mix of races of spores collected during the previous season Q DI (scale of rust infection on the plant) F (AI) P No Olukolu et al., 2016
Oomycete Arabidopsis thaliana 86 NA >216 k SNPs Hyaloperonospora arabidopsidis—natural strain Emco5 B Presence/absence of sporangiophores G P RPP13,RPP5 Atwell et al., 2010; Nemri et al., 2010
85 NA >216 k SNPs Hyaloperonospora arabidopsidis—natural strain Emwa1 B Presence/absence of sporangiophores G P No Atwell et al., 2010; Nemri et al., 2010
76 NA > 216k SNPs Hyaloperonospora arabidopsidis—natural strain Emoy2 B Presence/absence of sporangiophores G P RPP13 Atwell et al., 2010; Nemri et al., 2010
Arabidopsis thaliana 84 NA >216 k SNPs Hyaloperonospora arabidopsidis—natural strain Hiks1 B Presence/absence of sporangiophores G P RPP7 Atwell et al., 2010; Nemri et al., 2010
87 NA >216 k SNPs Hyaloperonospora arabidopsidis—natural strain Noco2 B Presence/absence of sporangiophores G P RPP5, RPP7 Atwell et al., 2010; Nemri et al., 2010
Glycine max ~879 Accessions (range from 44 to 7,431) ~33,709 SNPs (range from 24,490 to 41,911) Phytophthora sojae—19 individual races Q DI (proportion of alive plants or plants with non-killing lesions; three classes) G P No Chang et al., 2016
Medicago truncatula 179 NA ~5.1 M SNPs Aphanomyces euteiches—strain ATCC 201684 Q Porportion of brown symptomatic tissues on roots and stem + amounts of cotyledon yellowing + proportion of dead plants + DI (discoloration of the roots) G P No Bonhomme et al., 2014
Pisum sativum 175 Lines (cultivars + breeding lines + germplasm lines) 13,204 SNPs Aphanomyces euteiches—French strain RB84 Q DI (Percentage of browning symptoms on roots and epicotyls) G P No Desgroux et al., 2016
13,204 SNPs Aphanomyces euteiches—American strain Ae109 Q DI (Percentage of browning symptoms on roots and epicotyls) G P No Desgroux et al., 2016
13,204 SNPs Aphanomyces euteiches Q DI (Percentage of browning symptoms on roots and epicotyls + yellowing symptoms on a plot) F (NE) P No Desgroux et al., 2016
Setaria italica 916 Varieties (traditional landraces + modern cultivars) 845,787 SNPs Sclerospora graminicola Q Not described F (NE) P No Jia et al., 2013
a

Number of genetic lines that have been phenotyped for pathogen response. NA: natural accessions.

b

SNPs: Single Nucleotide Polymorphisms.

c

“B” and “Q” stand for binary and quantitative traits, respectively. DI: disease index (generally based on a scale from 0 to 9).

d

G, greenhouse conditions; F, field conditions; NE, natural exposition to the pathogen; AI, artificial inoculation.

e

Genetic architecture. M, monogenic; P, polygenic; NA, not available.

f

Name of the genes underlying QTLs that have been functionally validated. Genes in red indicate genes that have been functionally validated after QTL detection by GWA mapping.