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 & $SSL\mathit{4}$	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

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

^bSNPs: 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).

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

^eGenetic architecture. M, monogenic; P, polygenic; NA, not available.

^fName 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.