Virulence and genetic variability among Colletotrichum lindemuthianum (Sacc. & Magnus) Briosi & Cavara isolates from common bean (Phaseolus vulgaris L.)

Figures & data

Figure 1. Ethiopia map showing sample collection sites, DMS coordinate system.

Figure 2. Pure cultures of Colletotrichum lindemuthianum growing on PDA media.

Table 1. Standard differential cultivars used to characterize Colletotrichum lindemuthianum, their binary Codes, resistance genes and gene pool.

Differential cultivar	Seed type^a	Notation	Binary code	Resistance gene	Gene Pool^b
Michelite	S	0	1	Co-11	MA
Michigan Dark Red Kidney	L	1	2	Co-1	A
Perry Marrow	L	2	4	Co-1^3	A
Cornell 49-242	S	3	8	Co-2	MA
Widusa	L	4	16	Co-1^5	A
Kaboon	L	5	32	Co-1^2	A
Mexico 222	S	6	64	Co-3	MA
PI 207262	S	7	128	Co-4,^3 Co-9	MA
TO	S	8	256	Co-4	MA
TU	S	9	512	Co-5	MA
AB 136	S	10	1024	Co-6	MA
G2333	S	11	2048	Co-4^2,Co-5^2 Co-7	MA

^aS = Small seeded; L = Large seeded; S = small seeded. ^bMA = Mesoamerican; A = Andean.

Table 2. Race designation, number of isolates and susceptible (S) and resistant (R) reactions of common bean differential cultivars to 31 virulence races of Colletotrichum lindemuthianum identified from 40 isolates collected from Southern common bean growing area.

	Differential bean cultivars and their binary numbers												Races
Isolates**	Michalite	MDRK*	Perry Marow	Cornell 49242	Widusa	Kaboon	Mexico 222	Pi207262	TO	TU	AB136	G2333
	1	2	4	8	16	32	64	128	256	512	1024	2048
etg-061, etg-062, etg-063, etg-064, etg-065, etg-066, etg-067, etg-069, etg-070	R	R	R	R	R	R	R	R	R	R	R	R	0
eta-002	R	R	R	S	S	S	R	R	S	R	R	R	312
eta-003	R	S	R	S	S	S	R	R	S	R	R	R	314
etar-041	R	R	R	R	R	R	R	R	R	S	R	R	512
eta-006	R	R	R	R	S	S	R	S	S	S	R	R	944
eta-004	R	R	R	S	S	S	R	S	S	S	R	R	952
eta-010	S	S	R	R	R	R	S	S	S	S	R	R	963
etar-048	R	R	R	R	R	R	R	R	S	R	S	R	1280
eta-005	R	S	R	S	S	S	S	R	S	R	S	R	1402
eta-007	S	S	R	R	S	S	R	S	S	S	S	R	1971
eta-001	R	S	R	S	S	S	S	S	S	S	S	R	2042
eta-008	S	S	S	S	S	S	S	S	S	S	S	R	2047
etg-068	R	R	R	R	R	R	S	R	R	R	R	S	2112
etar-047	R	R	R	R	R	R	R	R	R	S	R	S	2560
etar-043, etar-049	R	S	R	R	R	R	R	R	R	S	S	S	3586
etar-045	R	R	R	S	R	R	R	R	R	S	S	S	3592
etar-044	R	S	R	R	R	S	R	R	R	S	S	S	3618
etar-050	S	R	R	S	R	S	R	R	R	S	S	S	3625
etar-042	R	R	S	S	S	R	R	R	S	S	S	S	3868
etar-046	R	R	S	S	S	R	R	S	S	S	S	S	3996
etar-086	S	S	S	S	S	S	S	R	S	S	R	R	3200
eta-009	S	S	S	S	S	S	R	S	S	S	S	S	4031
eta-083	S	S	R	S	S	S	S	S	S	S	S	R	2052
eta-088	S	S	S	S	R	S	S	S	S	S	S	R	2064
eta-087	S	S	S	S	S	S	S	S	R	S	S	R	2174
eta-081	S	S	S	S	S	S	S	R	S	S	S	R	2176
eta-084	S	R	S	S	R	S	S	R	S	S	S	R	2194
eta-085	S	S	S	S	S	S	S	R	S	S	R	R	3200
eta-082	S	S	R	S	S	S	S	R	S	S	R	R	3204
eta-089	S	S	S	R	S	S	S	S	R	R	R	R	3848
eta-080	R	S	R	S	S	S	S	R	R	S	R	R	3461

*MDRK Michigan Dark Red Kidney; **eta, etg and etar are isolates collected from Hawassa, Gofa and Areka respectively. The designation of a race number was obtained by adding the binary number of all differential cultivars exhibiting susceptible (S) reactions to the isolate used for inoculation [11]. Disease severity was scored after 14 days after planting from a detached leaves using 1–9 scale. Where 1 no symptoms (resistant), 2–3 very small lesions (resistant) and 4–9 numerous enlarged lesions (susceptible).

Figure 3. Frequency of resistance reaction of 12 differential common bean cultivars using 40 Colletotrichum lindemuthianum isolates collected from southern Ethiopia.

Figure 4. Banding patterns of some Colletotrichum lindemuthianum isolates collected from common bean genotypes and generated by rep-PCR. Lane M is 100 bp DNA molecular size marker (Cleaver Scientific DNA Marker CSL-MDNA-100BP for Gel Electrophoresis 100–1500 bp, https://www.reagecon.com/en-gb/cleaver-scientific-dna-marker-csl-mdna-100bp-for-6256961); Lanes 1–20 represent of C. lindemuthianum isolates etar-041, eta-002, etar-043, etar-049, etar-045, eta-001, etar-042, etar-044, eta-083, eta-009, eta-007, eta-081, eta-003, eta-006, etg-068, etar-047, eta-010, etg-066, etar-046 and eta-080, respectively.

Table 3. Genetic diversity parameters indicating the presence of genetic diversity among three Colletotrichum lindemuthianum populations.

Population	N	No. PPL	%PPL	ND	SD	Na	Ne	He	I
Hawassa	20	8	100 %	0.433	0.273	2	1.548	0.324	0.490
Gofa	10	7	87.5 %	0.339	0.222	2	1.424	0.264	0.418
Areka	10	6	75 %	0.319	0.212	1.5	1.422	0.247	0.373
Average	13.3	7	87.5%	0.364	0.235	1.8	1.464	0.278	0.427

No. of PPL - number of polymorphic loci, %PPL - percentage of polymorphic loci, ND - Nucleotide diversity (average over Loci), SD - standard deviation, Na - observed number of alleles, Ne - effective number of alleles and I - Shannon’s information index of diversity.

Table 4. Analysis of variance (AMOVA) of 40 Colletotrichum lindemuthianum isolates collected from three sites of Southern Ethiopia, indicating genetic variation within and among the isolates.

Source of Var	df	SS	Est. var	% of var	Fst
Among populations	2	7.878	0.238	20	0. 198
Within populations	27	35.635	0.963	80
Total	29	43.513	1.201	100

df - degrees of freedom, SS - sum of squares, Est.var - estimated variance, % of var - percentage of variation FST - Fixation Index.

Figure 5. A two-dimensional plot of the Principal Coordinate Analysis (PCoA) of Colletotrichum lindemuthianum isolates from common bean based on rep-PCR data based on populations. Pop1, Pop2 and Pop3 indicate the isolates collected from Hawassa, Areka and Gofa, respectively.

Figure 6. Neighbor-Joining (NJ) tree showing genetic relationships among 40 Colletotrichum lindemuthianum isolates from common bean genotypes. The genogram was generated based on neighbor-joining algorithms [28] by MEGA 6 [29].

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Data availability statement

All data that support the findings reported in this study are available from the corresponding author [EW] upon reasonable request.