Genetically Independent Tetranucleotide to Hexanucleotide Core Motif SSR Markers for Identifying Lentinula edodes Cultivars

Figures & data

Figure 1. Schematic illustration of the SSR marker development strategy used in this study.

Table 1. Details regarding the genome sequences used for developing SSR markers.

Strain name	Origin	Genome type	GenBank accession no.	Literature cited
akiyamaA567_pro_pm_17	Japan	Mitochondrial	AB697988	Unpublished
B17	South Korea	Whole	LSDU00000000	Shim et al. [19]
Le(Bin) 0899 ss11	Russia	Mitochondrial and Whole	–	https://genome.jgi.doe.gov/Lenedo1/ Lenedo1.home.html
NBRC 111202	Japan	Whole	BDGU00000000	Sakamoto et al. [29]
W1-26	China	Whole	LDAT00000000	Chen et al. [28]

Table 2. Characteristics of 13 SSR markers.

Primer name	Primer sequence (5′–3′)		Repeat motif	Scaffold no.^b	NA	HO	HE	PIC	F(Null)
	Forward^a	Reverse
LE_01	6-FAM-ATACTTGCACGGGGATGTTC	TACAGCGGGTGACAAATACC	(ATATCC)	1	3	0.800	0.609	0.511	−0.148
LE_06	VIC-GATAGGAATCTCGCAGGGGC	GCAGAGCCAGACTGGGATAC	(AAGG)	21	3	0.450	0.376	0.326	−0.120
LE_10	6-FAM-GCCGCCAGTCTAAATAGTCACC	CAGTCTTCCAGATGCTCTGCAG	(ACTCCC)	2	2	0.550	0.512	0.374	−0.049
LE_12	NED-GAACAGGCTCGGCACTACAC	CCCTCAACCTCGACTGTTGC	(AACTCG)	11	2	0.500	0.431	0.332	−0.087
LE_13	PET-CAAATGGTCAACAACGCGGA	GCTTCCTTCTCTGTGAAACTCG	(AGGATG)	17	3	0.550	0.545	0.468	−0.050
LE_15	VIC-GATCGCAGGGTTCGAGATCTT	GTCGTACTGAACTCCTGACCC	(ATCCT)	7	2	0.300	0.328	0.269	0.032
LE_17	PET-CAATGATGCTGAAGGGAGAGGA	TAAAATTTGCAGCGGATCCACT	(CCAGGT)	12	6	0.900	0.815	0.764	−0.066
LE_18	6-FAM-AGTGAGTTGGGAAAACTTCGT	TCTATCAGATGGTTTTCGGTGC	(AAAGT)	4	2	0.500	0.431	0.332	−0.087
LE_19	VIC-GGGTCCACAAATCCCCTCTAAG	ACCTGAGTACAAGTCTCTTAGGC	(TATAA)	Mitochondria	2	–	–	–	–
LE_20	6-FAM-AGTCCTTCGTGACACTCATGG	CACAGCACCACCTTTTACAGC	(GAGATTTCGA)	5	3	0.650	0.465	0.371	−0.188
LE_22	PET-AGCTCTACTTGACGGAACTAACA	GACGTTCACAACAGCAAAAACA	(TCTACC)	3	4	0.400	0.491	0.419	0.099
LE_23	NED-GGATGAATACGATTTCGACACGG	GTTATCGTTACCCTCCTCCCTC	(GGGAGT)	13	4	0.550	0.644	0.571	0.061
LE_24	PET-GGTCCTGTGGCCTGAGATTC	CGGTTGAGTGTCTCCGTTCT	(GAGAAAG)	6	2	0.650	0.501	0.369	−0.142

^aForward primers were fluorescently labeled at the 5′ end with 6-FAM, NED, PET, or VIC.

^bLocation of the markers in the draft genome of L. edodes monokaryon B17 (Shim et al. [19]).

N_A: Observed number of alleles; H_O: observed heterozygosity; H_E: expected heterozygosity; PIC: polymorphic information content; F(Null): estimated null allele frequency.

Table 3. P-values for the Chi-square test of independence between two markers.

Marker Test		2	3	4	5	6	7	8	9	10	11	12
population		LE_06	LE_10	LE_12	LE_13	LE_15	LE_17	LE_18	LE_20	LE_22	LE_23	LE_24
LE_01	ComCul_10	0.35	0.35	–	0.38	–	<0.0001	0.83	0.41	–	<0.0001	<0.0001
	ComCul_12	0.75	–	–	–	0.06	<0.0001	0.46	0.66	0.99	–	<0.0001
	ComCul_13	0.15	0.87	0.82	–	–	<0.0001	–	0.07	–	<0.0001	–
	LE_06	ComCul_10	0.55	–	1.00	–	0.76	1.00	0.93	–	0.80	1.00
		ComCul_12	–	–	–	0.14	0.69	0.69	0.68	0.91	–	0.55
		ComCul_13	0.98	0.67	–	–	0.68	–	0.21	–	0.68	–
		LE_10	MH009107	0.53	0.72	–	0.17	0.61	–	–	–	0.34
			ComCul_8	–	0.43	0.16	–	–	–	0.51	–	–
			ComCul_10	–	0.91	–	0.38	0.67	0.44	–	0.27	0.20
			ComCul_13	0.11	–	–	0.98	–	0.18	–	0.98	–
			LE_12	MH009107	0.14	–	0.80	0.68	–	–	–	0.79
				ComCul_13	–	–	0.42	–	0.45	–	0.42	–
				ComCul_14	–	0.66	0.88	–	0.45	0.18	0.78	–
				LE_13	ComCul_8	0.70	–	–	–	<0.0001	–	–
					ComCul_10	–	0.32	0.83	<0.0001	–	0.24	0.28
					LE_15	ComCul_8	–	–	–	0.52	–	–
						ComCul_12	0.40	0.11	0.58	0.30	–	0.34
						ComCul_14	0.88	–	0.45	0.86	0.32	–
						LE_17	MH009107	0.79	–	–	–	<0.0001
							ComCul_10	0.83	0.31	–	<0.0001	<0.0001
							ComCul_12	0.14	0.50	0.37	–	<0.0001
							ComCul_13	–	0.23	–	<0.0001	–
							ComCul_14	–	0.53	0.26	<0.0001	–
							LE_18	MH009107	–	–	–	0.45
								ComCul_10	0.83	–	0.67	0.53
								ComCul_12	0.10	0.25	–	0.56
								LE_20	ComCul_10	–	0.23	0.29
									ComCul_12	<0.0001	–	0.40
									ComCul_13	–	0.23	–
									ComCul_14	<0.0001	0.26	–
									LE_22	ComCul_12	–	0.20
										ComCul_14	0.26	–
										LE_23	ComCul_10	<0.0001

–: impossible to test or not determined.

Table 4. Genotypes of 20 L. edodes cultivars based on eight SSR markers.

Marker name	LE_06	LE_10	LE_12	LE_13	LE_15	LE_17	LE_18	LE_19
Cultivar name
MH009092	189/189	140/146	212/218	136/142	248/248	171/177	167/172	172
MH009093	185/189	140/146	212/218	136/142	248/248	171/177	172/172	172
MH009106	189/189	146/146	212/218	136/142	248/248	201/201	167/172	172
MH009107	189/189	140/146	212/218	136/142	248/248	171/201	167/172	172
MH009108	189/189	140/146	218/218	136/142	248/248	171/201	167/172	172
ComCul_1	189/189	140/140	212/218	136/136	248/248	171/195	172/172	167
ComCul_2	185/189	146/146	212/212	136/142	248/253	177/189	167/172	167
ComCul_3	185/189	140/146	212/212	136/136	253/253	171/177	167/167	167
ComCul_4	189/189	140/140	212/212	130/136	248/248	195/207	172/172	172
ComCul_5	189/189	140/140	212/218	136/136	248/248	189/195	172/172	167
ComCul_6	185/189	146/146	212/218	136/136	248/248	177/201	167/172	172
ComCul_7	185/189	140/146	212/212	136/136	248/248	177/177	167/172	172
ComCul_8	185/189	140/146	212/212	136/142	248/253	171/189	172/172	172
ComCul_9	189/189	140/146	212/212	136/142	248/248	189/201	167/172	172
ComCul_10	185/189	140/146	212/212	136/142	248/248	195/201	167/172	172
ComCul_11	189/189	140/146	212/218	136/142	248/248	171/177	172/172	172
ComCul_12	189/193	146/146	212/212	136/136	248/253	171/189	167/172	172
ComCul_13	189/193	140/146	212/218	136/136	248/253	171/201	172/172	172
ComCul_14	189/189	140/140	212/218	130/130	248/253	189/195	172/172	167
ComCul_15	189/189	140/140	212/218	136/136	248/253	171/201	172/172	167

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