Genetic relationships and diversity among wild Salvia accessions revealed by ISSR and SCoT markers

Figures & data

Table 1. Passport of Salvia accessions used in this study.

Code	Species	Section	Ploidy level	Basic chromosomes number	Sampling location
1	S. nemorosa	Plethiosphace	Diploid	7	Qazvin
2	S. nemorosa	Plethiosphace	Diploid	7	Ardabil
3	S. virgate	Plethiosphace	Tetraploid	8	Qazvin
4	S. virgate	Plethiosphace	Tetraploid	8	Mazandaran
5	S. virgata	Plethiosphace	Tetraploid	8	Esfahan
6	S. sclarea	Aethiopis	Diploid	11	Gilan
7	S. sclarea	Aethiopis	Diploid	11	Ardabil
8	S. sclarea	Aethiopis	Diploid	11	Qazvin
9	S. verticillata	Hemisphace	Tetraploid	8	Alborz
10	S. verticillata	Hemisphace	Tetraploid	8	Qazvin
11	S. macrosiphon	Aethiopis	Diploid	10	Yazd
12	S. macrosiphon	Aethiopis	Diploid	10	Fars
13	S. aethiopis	Aethiopis	Diploid	11	Ardabil
14	S. aethiopis	Aethiopis	Diploid	11	Gilan
15	S. aethiopis	Aethiopis	Diploid	11	Mazandaran
16	S. officinalis	Salvia	Diploid	7	Hamadan
17	S. officinalis	Salvia	Diploid	7	Esfahan
18	S. syriaca	Aethiopis	Diploid	10	Ilam
19	S. reuterana	Aethiopis	Diploid	10	Tehran
20	S. reuterana	Aethiopis	Diploid	10	Lorestan

Table 2. Details about the banding pattern revealed by ISSR and SCoT primers.

Primer	Sequence (5´ → 3´)	PB	TB	PIC	Rp	MI
ISSR-1	DBDACACACACACACACA	19	19	0.41	10.90	7.77
ISSR-2	GGATGGATGGATGGAT	14	14	0.29	4.90	4.04
ISSR-3	GACAGACAGACAGACA	14	14	0.45	9.50	6.28
ISSR-4	AGAGAGAGAGAGAGAGYT	20	20	0.41	11.70	8.28
ISSR-5	ACACACACACACACACC	13	13	0.38	6.60	4.92
ISSR-6	GAGAGAGAGAGAGAGARC	17	17	0.41	9.90	7.02
ISSR-7	CTCTCTCTCTCTCTCTG	13	13	0.28	5.70	3.63
ISSR-9	CACACACACACACACAG	19	19	0.42	11.30	7.94
ISSR-11	ACACACACACACACACYA	20	20	0.40	10.90	7.93
ISSR-12	GTGTGTGTGTGTGTGTYG	15	15	0.35	9.10	5.27
ISSR-13	GAGAGAGAGAGAGAGAYC	16	16	0.35	9.10	5.62
ISSR-14	AGAGAGAGAGAGAGAGT	21	21	0.39	11.30	8.26
ISSR-15	ACACACACACACACACYG	14	14	0.33	8.90	4.68
ISSR-17	GAAGAAGAAGAAGAAGAA	19	19	0.32	8.50	6.13
ISSR-18	ACCACCACCACCACCACC	17	17	0.43	12.90	7.24
ISSR-19	AGCAGCAGCAGCAGCAGC	17	17	0.47	13.30	7.92
ISSR-21	ATGATGATGATGATGATG	17	17	0.36	10.00	6.17
ISSR-23	CTCTCTCTCTCTCTCTRC	20	20	0.37	10.30	7.40
ISSR-24	GGCGGCGGCGGCGGCGGC	14	14	0.44	11.70	6.14
ISSR-25	CACACACACACACACARG	20	20	0.38	10.90	7.69
ISSR-26	CTCCTCCTCCTCCTCCTC	11	11	0.29	7.30	3.16
	Average	16.67	16.67	0.38	9.75	6.36
SCoT-1	CAACAATGGCTACCACCA	19	19	0.47	15.9	8.94
SCoT-2	CAACAATGGCTACCACCC	20	20	0.38	11.1	7.78
SCoT-3	CAACAATGGCTACCACCG	14	14	0.41	12	5.71
SCoT-6	CAACAATGGCTACCACGC	20	20	0.42	12.5	8.36
SCoT-7	CAACAATGGCTACCACGG	21	20	0.41	12.1	8.61
SCoT-10	CAACAATGGCTACCAGCC	20	20	0.35	9.6	7.05
SCoT-11	AAGCAATGGCTACCACCA	17	17	0.46	15.2	7.85
SCoT-12	ACGACATGGCGACCAACG	15	15	0.40	12	6.12
SCoT-13	ACGACATGGCGACCATCG	13	13	0.37	10.6	4.90
SCoT-14	ACGACATGGCGACCACGC	17	17	0.46	15.7	7.96
SCoT-15	ACGACATGGCGACCGCGA	17	17	0.47	16.1	8.04
SCoT-16	CCATGGCTACCACCGGCC	15	15	0.34	9.3	5.17
SCoT-17	CATGGCTACCACCGGCCC	11	11	0.45	14.1	4.91
SCoT-18	ACCATGGCTACCACCGCG	12	12	0.30	7.7	3.59
SCoT-19	GCAACAATGGCTACCACC	14	14	0.44	13.5	6.11
SCoT-20	AACCATGGCTACCACCGC	24	24	0.41	13.6	9.75
SCoT-21	CACCATGGCTACCACCAT	13	13	0.38	12.1	4.90
SCoT-23	ACCATGGCTACCACGGGC	17	17	0.32	9.7	5.48
SCoT-24	CCATGGCTACCACCGCCA	19	19	0.43	15.3	8.25
SCoT-26	ACAATGGCTACCACCATC	11	11	0.38	12.3	4.19
	Average	16.45	16.45	0.40	12.52	6.68

B = non A; D = non C; Y = C or T; R = A or G

Table 3. Analysis of molecular variance (AMOVA) based on ISSR and SCoT markers for Salvia species.

		ISSR			SCoT			ISSR + SCoT
Grouping based on botanical classification	df	MS	Est. Var	Var	MS	Est. Var	Var	MS	Est. Var	Var
Among groups	1	106.08	6.01	9	124.05	8.88	13	230.13	14.89	11
Within groups	18	61.01	61.01	91	57.42	57.42	87	118.43	118.43	89
Grouping based on basic chromosome number		PhiPT = 0.09, P = 0.01			PhiPT = 0.13, P = 0.01			PhiPT = 0.11, P = 0.01
Among groups	3	101.71	9.16	14	110.08	11.75	19	211.79	20.91	16
Within groups	16	56.20	56.20	86	51.71	51.71	81	107.91	107.91	84
		PhiPT = 0.14, P = 0.01			PhiPT = 0.18, P = 0.01			PhiPT = 0.16, P = 0.01

SS, sum of squares; MS, mean squares; Est. Var, estimated variance components; Var, percentage of total variance

Table 4. Genetic variation features estimated using ISSR and SCoT markers in the studied Salvia species.

	Chromosomal group					Ploidy level
ISSR	x = 7	x = 8	x = 10	x = 11	Mean	Diploid	Tetraploid	Mean
Observed number of alleles (Na)	1.38	1.46	1.37	1.15	1.34	1.85	1.46	1.66
Effective number of alleles (Ne)	1.39	1.41	1.37	1.22	1.35	1.36	1.39	1.38
Nei's genetic diversity (H)	0.23	0.24	0.22	0.15	0.21	0.23	0.24	0.23
Shannon's information index (I)	0.34	0.37	0.34	0.24	0.32	0.36	0.39	0.37
Percentage of polymorphic loci (PPL)	66.00	71.71	66.29	57.43	65.36	92.57	72.29	82.43
SCoT
Observed number of alleles (Na)	1.31	1.44	1.37	1.36	1.37	1.85	1.37	1.61
Effective number of alleles (Ne)	1.35	1.39	1.36	1.29	1.35	1.47	1.38	1.42
Nei's genetic diversity (H)	0.20	0.23	0.21	0.19	0.21	0.28	0.22	0.25
Shannon's information index (I)	0.31	0.34	0.32	0.30	0.32	0.43	0.33	0.39
Percentage of polymorphic loci (PPL)	56.53	68.44	60.49	64.39	62.46	92.71	61.70	77.20

Figure 1. Dendrogram of Salvia accessions based on ISSR data using the neighbour-joining (NJ) method.

Figure 2. Dendrogram of Salvia accessions based on SCoT data using the neighbour-joining (NJ) method.

Figure 3. Dendrogram of Salvia accessions based on combined data (ISSR + SCoT) using the neighbour-joining (NJ) method.