Genetic structure and genome-wide association study of a genomic panel of two-row, spring barley (Hordeum vulgare L.) with differential reaction to Fusarium head blight (Fusarium graminearum Schwabe) and deoxynivalenol production

Figures & data

Fig. 1. Pie chart of genetic panel composition by the breeding institutions (Agriculture and Agri-Food Canada, Brandon Research and Development Centre [AAFC-BRDC]; Crop Development Centre [CDC]; Field Crop Development Centre [FCDC]; D = Busch Agricultural Resources, Inc. [Bari]; WestBred LLC/ Highland Specialty Grains [WB/HSG]; North Dakota State University [NDSU]; Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre [AAFC-LeRDC]; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre [AAFC-ORDC]; Molson Coors Beverage Company [COORS]; Agricore United [AU]; Accessions are landrace or exotic cultivars).

Fig. 2. STRUCTURE Sub-population membership for 400 two-row barley grouped by breeding institution. A = Agriculture and Agri-Food Canada, Brandon Research and Development Centre (AAFC-BRDC); B = Crop Development Centre (CDC); C = Field Crop Development Centre (FCDC); D = Busch Agricultural Resources, Inc. (Bari); E = WestBred LLC/ Highland Specialty Grains (WB/HSG); F = North Dakota State University (NDSU); G = Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre (AAFC-LeRDC); H = Agriculture and Agri-Food Canada, Ottawa Research and Development Centre (AAFC-ORDC); I = Molson Coors Beverage Company (COORS); J = Agricore United (AU); K = Accession. Yellow = Cluster 1 and Orange = Cluster 2. The Y axis represents the proportion of cluster (K = 2) membership.

Fig. 3. Phylogenetic tree constructed by neighbor-joining (NJ) method based on single-nucleotide polymorphism (SNP) genetic markers (25 K) displaying selected cultivars and germplasm from the various institutions (Agriculture and Agri-Food Canada, Brandon Research and Development Centre [red]; Crop Development Centre [blue]; Field Crop Development Centre [green]; D = Busch Agricultural Resources, Inc. [purple]; WestBred LLC/ Highland Specialty Grains [Orange]; North Dakota State University [brown].

Fig. 4. Plots of the first two principal components of genotype information (single-nucleotide polymorphism genetic markers) of the genomic panel with colouration highlighting A) malting or feed barley types; B) breeding institution origin (Agriculture and Agri-Food Canada, Brandon Research and Development Centre [AAFC-BRDC]; Crop Development Centre [CDC]; Field Crop Development Centre [FCDC]; D = Busch Agricultural Resources, Inc. [Bari]; WestBred LLC/ Highland Specialty Grains [WB/HSG]; North Dakota State University [NDSU]; Agriculture and Agri-Food Canada, Lethbridge Research and Development Centre [AAFC-LeRDC]; Agriculture and Agri-Food Canada, Ottawa Research and Development Centre [AAFC-ORDC]; Molson Coors Beverage Company [COORS]; Agricore United [AU]; Accessions are landrace or exotic cultivars).

Table 1. Means and standard errors of height (HT, cm), fusarium head blight (FHB, 0–5) and days to fifty percent heading (HD50, days) and deoxynivalenol (DON, mg kg⁻¹) content over years and locations.

Location	Year	HD50^a	Min-Max	HT^b	Min-Max	FHB^c	Min-Max	DON^d	Min-Max
Brandon	2014	57.4 ± 0.1	49.0–62.5	83.5 ± 0.4	55.5–121.5	2.0 ± 0.1	0.0–5.0	7.1 ± 0.2	0.7–30.3
	2015	53.6 ± 0.1	39.0–64.0	82.2 ± 0.4	53.0–113.0	2.4 ± 0.1	0.0–5.0	19.7 ± 0.5	4.6–90.0
Carberry	2014	71.6 ± 0.1	57.0–76.0	75.9 ± 0.4	53.0–110.0	0.4 ± 0.0	0.0–5.0	27.2 ± 0.5	2.7–69.8
	2015	61.4 ± 0.2	43.0–67.5	67.6 ± 0.3	45.0–89.5	0.7 ± 0.0	0.0–4.5	6.0 ± 0.1	0.8–19.4
Carman	2014	-	-	89.3 ± 0.4	60.0–126.5	2.6 ± 0.1	0.0–5.0	12.2 ± 0.3	1.7–57.0
	2015	-	-	81.4 ± 0.4	55.5–103.0	2.4 ± 0.1	0.5–5.0	11.7 ± 0.4	2.3–32.6

^aHD50 = days to 50% of plot headed ^bHT = height from ground to top of spike excluding awns

^cFHB = fusarium head blight score

^dDON = deoxynivalenol content

Min = minimum

Max = maximum

Heading notes were not recorded at Carman.

Table 2. Selection of germplasm with low Fusarium head blight (FHB) score or deoxynivalenol (DON) content. Numbers represent grand average over site years, with standard errors in brackets.

Name	Type	Mean FHB (0–5)	Mean DON (mg kg^−1)
CN 5317 (396)	exotic	0.5 (0.2)	5.7 (0.9)
CIho 14 360	exotic	0.3 (0.1)	6.0 (1.2)
Kutahya	exotic cultivar	0.3 (0.1)	6.6 (1.4)
CIho 4196	exotic	0.4 (0.1)	8.0 (1.7)
CI 2208	exotic	0.4 (0.1)	9.3 (2.1)
Harbin	exotic cultivar	0.3 (0.1)	9.7 (1.2)
HDE84194-622-1	exotic	1.1 (0.3)	6.5 (1.3)
Bowman	NDSU cultivar	4.7 (0.2)	5.2 (1.3)
Conlon	NDSU cultivar	1.4 (0.3)	6.9 (1.4)
2ND27421	NDSU line	3.0 (0.5)	4.9 (0.9)
2ND24263	NDSU line	1.9 (0.5)	7.1 (1.5)
TR06676	FCDC line	2.1 (0.5)	7.0 (1.5)
TR10692	FCDC line	1.0 (0.3)	5.8 (1.4)
SB071676	CDC line	1.7 (0.3)	6.7 (1.5)
BM0332D-280	AAFC line	0.5 (0.2)	9.5 (1.9)
BM0124-347-1	AAFC line	0.5 (0.2)	10.3 (2.1)
BM9637-53	AAFC line	0.4 (0.1)	11.1 (2.5)
CDC Bold^a	CDC cultivar	3.9 (0.4)	26.3 (5.6)
BM9925-192^a	AAFC line	2.6 (0.4)	36.9 (5.5)

^asusceptible lines included for contrast.

AAFC = Agriculture and Agri-Food Canada; CDC = Crop Development Centre; FCDC = Field Crop Development Centre; NDSU = North Dakota State University.

Fig. 5. Manhattan plots ofall site years of 400 genotypes for days to fifty-percent heading (HD50), height (HT), FHB (Fusarium head blight score) and deoxynivalenol content (DON) over the chromosomal position. The horizontal red dashed line represents a genome-wide significance threshold (-Log₁₀ P-value ≥ 3.0). SNP markers are displayed cumulatively by chromosome (Chr) which are represented by colour.

Table 3. Significant molecular markers (-Log₁₀ [P value] ≥3) associated with Fusarium head blight (FHB) averaged over all site years (n = 6).

SNP marker ID ^a	Chr ^b	Allele ^c	Position ^d	Estimate	F value	-Log10 (P value)	R^2 (%)
JHI-Hv50k-2016-10 994	1H	A/G	11796532	0.3	16.9	4.3	4.1
JHI-Hv50k-2016-55 687	1H	A/G	510489416	−0.1	11.0	3.0	2.7
JHI-Hv50k-2016-90 430	2H	A/C	357421942	0.3	11.3	3.1	2.8
JHI-Hv50k-2016-92 837	2H	A/G	355524119	0.3	10.9	3.0	2.7
JHI-Hv50k-2016-93 148	2H	A/G	382064575	0.3	12.7	3.4	3.1
JHI-Hv50k-2016-94 189	2H	A/G	416370735	0.3	12.7	3.4	3.1
JHI-Hv50k-2016-94 503	2H	A/C	425608540	0.3	12.7	3.4	3.1
JHI-Hv50k-2016-101 173	2H	G/A	538658014	0.3	15.5	4.0	3.8
JHI-Hv50k-2016-163 997	3H	G/A	35959325	−0.3	11.1	3.0	2.7
JHI-Hv50k-2016-200 089	3H	A/G	542418217	−0.2	12.7	3.4	3.1
JHI-Hv50k-2016-201 074	3H	G/A	547887089	0.2	13.5	3.6	3.3
JHI-Hv50k-2016-201 914	3H	A/G	552148262	0.2	10.8	3.0	2.7
JHI-Hv50k-2016-226 348	4H	G/A	200043	0.3	11.2	3.0	2.7
JHI-Hv50k-2016-226 367	4H	A/G	210117	0.3	11.2	3.0	2.7
JHI-Hv50k-2016-225 695	4H	A/G	2006309	0.3	11.0	3.0	2.7
JHI-Hv50k-2016-227 048	4H	A/G	2600202	0.2	12.8	3.4	3.1
JHI-Hv50k-2016-227 104	4H	G/A	2772321	0.3	20.9	5.2	5.0
JHI-Hv50k-2016-227 095	4H	G/C	2772483	0.3	19.5	4.9	4.7
JHI-Hv50k-2016-227 292	4H	C/G	3371574	−0.3	11.9	3.2	2.9
JHI-Hv50k-2016-228 556	4H	G/A	7766003	0.3	13.1	3.5	3.2
JHI-Hv50k-2016-271 609	4H	C/G	600783796	−0.2	11.4	3.1	2.8
JHI-Hv50k-2016-278 585	5 H	T/A	4185576	0.3	11.4	3.1	2.8
JHI-Hv50k-2016-278 627	5H	C/G	4290748	0.3	11.4	3.1	2.8
JHI-Hv50k-2016-282 091	5H	G/C	10988013	0.3	12.5	3.3	3.1
JHI-Hv50k-2016-282 179	5H	G/A	10993387	0.3	12.5	3.3	3.1
JHI-Hv50k-2016-283 470	5H	C/G	15019718	0.2	10.9	3.0	2.7
JHI-Hv50k-2016-284 034	5H	C/A	17366809	0.2	12.1	3.3	3.0
JHI-Hv50k-2016-284 439	5H	A/T	18246675	0.3	11.9	3.2	2.9
JHI-Hv50k-2016-286 464	5H	G/A	25035335	0.2	15.0	3.9	3.6
SCRI_RS_7368	5H	A/G	25203928	0.3	21.0	5.2	5.0
SCRI_RS_196566	5H	G/A	474102141	0.3	12.2	3.3	3.0
JHI-Hv50k-2016-312 973	5H	G/A	474233116	0.3	12.2	3.3	3.0
BOPA1_6833-658	5H	C/A	474574103	0.3	11.0	3.0	2.7
JHI-Hv50k-2016-313 362	5H	C/A	474867454	0.3	12.2	3.3	3.0
JHI-Hv50k-2016-321 425	5H	A/G	499317939	0.4	16.7	4.3	4.0
JHI-Hv50k-2016-321 503	5H	A/G	499524364	0.3	12.4	3.3	3.0
JHI-Hv50k-2016-324 079	5H	G/C	507354940	0.3	11.3	3.1	2.8
JHI-Hv50k-2016-332 519	5H	A/G	522216590	0.2	12.4	3.3	3.0
JHI-Hv50k-2016-372 853	6 H	G/A	9839643	−0.2	10.9	3.0	2.7
JHI-Hv50k-2016-386 716	6 H	A/G	50211492	0.3	10.8	3.0	2.6
JHI-Hv50k-2016-386 764	6H	G/A	50905912	0.3	12.2	3.3	3.0
SCRI_RS_219709	7 H	G/A	28232544	0.1	11.7	3.2	2.9
JHI-Hv50k-2016-468 635	7 H	G/A	71317253	0.3	11.3	3.1	2.8
JHI-Hv50k-2016-488 566	7 H	G/C	483488573	0.2	11.0	3.0	2.7
JHI-Hv50k-2016-488 570	7 H	A/G	484010690	0.2	12.3	3.3	3.0
JHI-Hv50k-2016-488 582	7 H	T/A	484148180	0.2	12.3	3.3	3.0
BOPA1_3232-201	7 H	G/C	488294965*	0.2	10.8	3.0	2.6
JHI-Hv50k-2016-488 814	7 H	G/A	489070312	0.2	11.6	3.1	2.8
JHI-Hv50k-2016-488 919	7 H	G/A	490959746	0.2	11.6	3.1	2.8
JHI-Hv50k-2016-498 095	7 H	G/A	584016335	0.3	11.1	3.0	2.7
JHI-Hv50k-2016-498 181	7 H	A/G	584342965	0.3	12.2	3.3	3.0

^aMolecular marker of 50 K SNP array (Bayer et al. 2017)

^bChr = Chromosome

^cAllele (Major/Minor)

^dGenomic position in base pairs (bp), reference genome ‘Morex v3’ gene models (Mascher et al. 2021).

* = 100% BLASTn alignment.

Table 4. Significant molecular markers (-Log₁₀ [P value] ≥3) associated with deoxynivalenol (DON) content averaged over all site years (n = 6).

SNP marker ID ^a	Chr ^b	Allele ^c	Position ^d	Estimate	F value	-Log10 (P value)	R^2 (%)
JHI-Hv50k-2016-65 236	2H	G/A	11377865	1.3	13.7	3.6	3.3
JHI-Hv50k-2016-69 936	2H	A/G	18121966	1.3	10.8	3.0	2.6
JHI-Hv50k-2016-70 485	2H	C/A	19058700	1.4	11.6	3.1	2.8
JHI-Hv50k-2016-180 623	3H	G/C	403198090	−1.8	12.9	3.4	3.2
JHI-Hv50k-2016-185 349	3H	A/G	457715004	1.5	11.8	3.2	2.9
JHI-Hv50k-2016-185 889	3H	A/G	461002904	1.5	11.3	3.1	2.8
JHI-Hv50k-2016-186 010	3H	A/G	461910907	1.6	12.5	3.3	3.0
JHI-Hv50k-2016-216 594	3H	G/A	595248892	1.5	11.2	3.0	2.7
JHI-Hv50k-2016-228 552	4H	C/G	7701844	1.7	14.9	3.9	3.6
JHI-Hv50k-2016-261 905	4H	A/G	571137453	1.4	14.5	3.8	3.5
JHI-Hv50k-2016-262 043	4H	A/C	571707652	1.3	10.9	3.0	2.7
JHI-Hv50k-2016-270 157	4H	C/G	597834082	−1.4	12.4	3.3	3.0
SCRI_RS_179365	5H	G/A	4178434	1.5	11.8	3.2	2.9
JHI-Hv50k-2016-278 585	5H	T/A	4185576	1.8	14.7	3.8	3.6
JHI-Hv50k-2016-278 627	5H	C/G	4290748	1.8	14.7	3.8	3.6
SCRI_RS_114102	5H	C/A	4849576	1.7	15.0	3.9	3.6
SCRI_RS_155555	5H	G/A	4880406	1.7	13.1	3.5	3.2
JHI-Hv50k-2016-279 292	5H	C/A	5494556	1.8	13.4	3.5	3.3
JHI-Hv50k-2016-288 841	5H	G/A	34036714	2.3	13.4	3.5	3.3
JHI-Hv50k-2016-288 993	5H	G/A	35094836	2.3	13.4	3.5	3.3
JHI-Hv50k-2016-290 535	5H	G/C	48340379	1.6	12.4	3.3	3.0
JHI-Hv50k-2016-290 781	5H	A/G	55083578	2.0	11.9	3.2	2.9
JHI-Hv50k-2016-290 990	5H	C/A	56917275	2.0	11.9	3.2	2.9
JHI-Hv50k-2016-291 313	5H	A/G	60783173	2.1	12.3	3.3	3.0
JHI-Hv50k-2016-337 389	5H	A/T	530890859	1.7	20.6	5.1	4.9
JHI-Hv50k-2016-337 660	5H	G/A	531560545	1.6	12.3	3.3	3.0
JHI-Hv50k-2016-437 412	7H	G/A	2991267	−1.5	12.0	3.2	2.9
JHI-Hv50k-2016-512 584	7H	G/A	615711190	0.9	12.3	3.3	3.0
BOPA1_8758-564	7H	A/G	615732324*	0.9	12.3	3.3	3.0

^aMolecular marker of 50 K SNP array (Bayer et al. 2017)

^bChr = Chromosome

^cAllele (Major/Minor)

^dGenomic position in base pairs (bp), reference genome ‘Morex v3’ gene models (Mascher et al. 2021).

* = 100% BLASTn alignment.

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Data availability statement

The data discussed in this publication have been deposited in NCBI’s Gene Expression Omnibus (Edgar 2002) and are accessible through GEO Series accession number GSE188791 (https://www.ncbi.nlm.nih.gov/geo/query/acc.cgi?acc=GSE188791). LSMeans of phenotypic data are also available (Supplementary Table S1).