Analysis of Genetic Diversity and Population Structure of Wild Strains and Cultivars Using Genomic SSR Markers in Lentinula edodes

Figures & data

Figure 1. Distribution of 77 wild strains of Lentinula edodes in Korea (thin line, river; thick line, mountains).

Table 1. Information of SSR markers and diversity statistics for 100 Lentinula edodes strains.

Marker	Forward primer	Reverse primer	Motifs	NA	HE	HO	PIC	HWE
								χ^2	p-value
RL-LE-001^a	GTGTGACAGATTACACGGGTC	ACTCAAGTAGGTCCAAGTCGC	(TA)n	25	0.84	0.40	0.82	489.05	0.000***
RL-LE-002^a	GTAGAGGGATACGCGAAGTAAG	ACAATGGTCGTTCACAGTCG	(AT)n	36	0.88	0.44	0.87	725.68	0.000***
RL-LE-003^a	CGTTTGCTTGCCCTTTTC	GGAGATACCAACACCACTACTAC	(AC)n	11	0.81	0.02	0.79	477.07	0.000***
RL-LE-004^a	TGAGCTATGGTGCTACTCCTTC	GCGCCTATATCCGATGGT	(CCA)n	27	0.87	0.21	0.85	697.28	0.000***
RL-LE-006^a	CTCTGGATAAGAACGCAAGC	CAGTGTTCTCCAGTCCGAGT	(TC)n	25	0.83	0.58	0.81	572.07	0.000***
RL-LE-010^a	GTAAGCTCATGGTAACAGTGCC	AACTTGGAAGCCTTCTCCC	(AT)n	26	0.75	0.35	0.72	394.67	0.000***
RL-LE-017^b	GTGCACTGTGCGATTGTTC	CAGCAAGGATGACTCTTGGA	(CA)n	40	0.94	0.18	0.94	1823.55	0.000***
RL-LE-018^b	CCCACAGGTTTACAGAGTTCCT	GTGGACATCCACCTTTTGTC	(TA)n	17	0.84	0.20	0.82	400.53	0.000***
RL-LE-021^b	GCTTGAAGAGCGAGTTTGAG	CAAGACACGCTTCGTAGTCA	(AG)n	19	0.71	0.32	0.66	145.61	0.000***
RL-LE-025^b	TTGGGAGATGCGAGTAGTTC	ATTCAGTCGCTCAGTAGGAGAC	(AT)n	15	0.70	0.29	0.66	252.98	0.000***
RL-LE-026^b	GATTTGACGCTCACATCCC	CCCCTAAGTATGAGCTTCCGTA	(AG)n	16	0.74	0.51	0.70	126.33	0.000***
RL-LE-028^b	GAGACGACACGAGGAATTTG	GTCGTTCTCATTGGAGACTCTG	(CA)n	9	0.63	0.12	0.57	218.63	0.000***
RL-LE-033^b	GACAGAAGAAGGACTTACCAGC	CCAGAGCCCAAGGATAACTT	(CT)n	21	0.75	0.37	0.71	435.69	0.000***
RL-LE-038^b	CGTTTGAGTGTCAACGGTCT	CATGTCAGACTAGTCAGGGGTC	(AT)n	15	0.77	0.29	0.73	355.74	0.000***
RL-LE-045^b	ACATCTGAGAGGTCGTACGCT	GTACCGAAGCGAGCAAGTT	(CA)n	13	0.75	0.44	0.71	210.89	0.000***
RL-LE-046^b	GCACGCAGTGATGAATAGAGAG	ACACTTACGGATTTGGCAGG	(AG)n	10	0.72	0.06	0.68	452.79	0.000***
RL-LE-048^b	GTGGTGAAGTTACCGACAGG	AGGTGCCCAACTTCTGGT	(GC)n	11	0.63	0.16	0.59	382.95	0.000***
RL-LE-051^b	ACTCTGCTGCCACTCTTGAC	GACCGTCTCTAGCTTCTTGATG	(CT)n	13	0.62	0.24	0.57	274.91	0.000***
RL-LE-053^b	CTCAACGTCTCATTCCCTTC	CTCGAGTTGAGGGTGAGGTTAT	(GTT)n	24	0.80	0.51	0.77	203.92	0.000***
RL-LE-059^b	CGGAGATGTACCAATTCCTG	GCATTCGCCGTCTATACGAT	(TG)n	16	0.74	0.23	0.70	513.50	0.000***

N_A: number of alleles; H_E: expected heterozygosity; H_O: observed heterozygosity; PIC: polymorphic information content; HWE: Hardy–Weinberg equilibrium, ***p < 0.001.

^aMoon et al. (2017).

^bLee et al. (2017).

Figure 2. Clustering of distance- and model-based for 100 Lentinula edodes strains including 77 wild strains and 23 cultivars using 20 genomic SSR markers. (A) UPGMA dendrogram based on Nei’s genetic distance; (B) population structure analysis (green, Pop1; red, Pop2; the strains that did not share more than 70% of ancestry were assigned to admixture).

Figure 3. (A) Log probability of the data (LnP(D)) for each K range from 1 to 10; (B) ΔK values calculated as method by Evanno et al. [28].

Table 2. Diversity statistics as determined by collection regions and types.

	NA	HE	HO	PIC
Collection regions
Seorak	7	0.71	0.23	0.67
Odae	12	0.72	0.27	0.68
Jiri	6	0.66	0.22	0.62
Type
Wild strains	15	0.73	0.25	0.69
Cultivars	9	0.76	0.44	0.73

N_A: number of alleles; H_E: expected heterozygosity; H_O: observed heterozygosity; PIC: polymorphic information content.

Table 3. Analysis of molecular variance (AMOVA) by collection regions and types.

	df	SS	MS	Est. Var.	%
Collection regions
Among regions	2	31.30	15.65	0.08	1
Among strains	74	899.29	12.15	4.86	66
Within strains	77	187.50	2.44	2.44	33
Total	153	1118.08		7.38	100
FST	0.01
Nm	22.48
Types
Among types	1	56.4	56.43	0.63	8
Among strains	98	1183.72	12.08	4.61	57
Within strains	100	286.00	2.86	2.86	35
Total	199	1526.14		8.10	100
FST	0.08
Nm	2.98

df: degrees of freedom; SS: sum of squares; MS: mean of squares; Est. Var.: estimate of variance; %: percentage of total variation; F_ST: genetic differentiation; Nm: gene flow; among regions: variation between collection regions; among strains: variation between strains; within strains: variation by difference of molecular markers such as alleles in individual strain.

Evanno G, Regnaut S, Goudet J. Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol. 2005;14(8):2611–2620.

 PubMed Web of Science ®Google Scholar