Evaluation of genetic diversity on Prunus mira Koehne by using ISSR and RAPD markers

Figures & data

Table 1. Locations and sample size of three populations used in this study.

Code	Symbol	Species	Locality	Latitude (N)	Longitude (E)	Altitude (m)	Sample size
XZ	•	Prunus mira Koehne Kov et Kpst	The Tibetan Plateau, China	29°06′–30°04′	93°22′–95°57′	2693–3367	30
HN	♦	Prunus persica (L.) Batsch	Henan Province, China	34°65′–35°80′	113°76′–114°88′	Mean 200.00	11
HLJ	▴	Prunus persica (L.) Batsch	Heilongjiang Province, China	44°04′–46°40′	125°42′–130°10′	Mean 127.95	7

Table 2. Amplification of ISSR and RAPD markers in 48 samples.

Marker	Primer code	Sequences (5′–3′)	TNB	NPB	PPB (%)	Rp	PIC
ISSR	I-69	GAGAGAGAGAGAGAGAT	5	5	100	3.23	0.83
	I-70	ACACACACACACACACT	6	6	100	3.04	0.73
	I-71	CACACACACACACACAG	8	8	100	4.06	0.79
	I-72	AGAGAGAGAGAGAGAGC	8	8	100	3.74	0.71
	I-73	ACACACACACACACACYA	9	8	100	2.65	0.82
	I-74	CACACACACACACACART	8	8	100	3.75	0.83
	I-76	GGAGAGGAGAGGAGA	9	9	100	3.65	0.77
	I-80	AGAGAGAGAGAGAGAGG	5	5	100	3.94	0.87
	I-81	TCTCTCTCTCTCTCTCRT	8	8	100	3.91	0.88
	Mean		7.22	7.22	100	3.55	0.80
RAPD	S24	AATCGGGCTG	12	12	100	2.56	0.88
	S21	CAGGCCCTTC	10	10	100	3.08	0.86
	S38	AGGTGACCGT	10	10	100	2.67	0.88
	S32	TCGGCGATAG	6	6	100	3.74	0.76
	S36	AGCCAGCGAA	11	11	100	3.93	0.89
	S51	AGCGCCATTG	11	11	100	2.84	0.89
	S25	AGGGGTCTTG	10	10	100	2.05	0.81
	S34	TCTGTGCTGG	12	12	100	3.79	0.90
	S30	GTGATCGCAG	13	13	100	3.98	0.88
	S33	CAGCACCCAC	10	10	100	3.63	0.87
	Mean		10.56	10.56	100	3.29	0.86

Note: TNB, total number of bands; NPB, number of polymorphic bands; PPB (%), percentage of polymorphic bands; Rp, resolving power; PIC, polymorphic information content.

Table 3. Estimates of the genetic variability among three populations determined on the basis of ISSR and RAPD analysis.

Marker	Total gene diversity (Ht)	Population diversity (Hs)	Inter-population differentiation (Gst)	Estimate of gene flow (Nm)
ISSR	0.33 ± 0.07	0.26 ± 0.04	0.19	2.13
RAPD	0.28 ± 0.02	0.21 ± 0.02	0.28	1.29

Table 4. Summary of genetic variations among three populations as revealed through ISSR and RAPD analysis.

Markers	Population	Observed no. of alleles (Na) (mean ± SD)	Effective no. of alleles (Ne) (mean ± SD)	Nei's genetic diversity (H) (mean ± SD)	Shannon's information index (I) (mean ± SD)	No. of polymorphic loci	Percentage of polymorphic loci (PPB)
ISSR	XZ	1.921 ± 0.39	1.91 ± 0.43	0.26 ± 0.11	0.42 ± 0.15	59	82.23
	HN	1.871 ± 0.51	1.74 ± 0.45	0.22 ± 0.08	0.39 ± 0.08	55	79.05
	HLJ	1.683 ± 0.36	1.52 ± 0.26	0.18 ± 0.12	0.33 ± 0.15	46	72.13
	Mean	1.83 ± 0.45	1.72 ± 0.57	0.23 ±0.10	0.38 ±0.13	53.33	77.80
RAPD	XZ	1.93 ± 0.24	1.29 ± 0.27	0.20 ± 0.12	0.32 ± 0.20	62	93.94
	HN	1.86 ± 0.34	1.43 ± 0.33	0.27 ± 0.11	0.41 ± 0.13	57	86.36
	HLJ	1.37 ± 0.49	1.27 ± 0.40	0.15 ± 0.09	0.21 ± 0.13	25	37.88
	Mean	1.72 ± 0.67	1.33 ± 0.35	0.21 ± 0.19	0.31 ± 0.25	48.00	72.73

Table 5. Analysis of molecular variance (AMOVA) based on ISSR and RAPD for 48 samples.

Markers	Source of variance	df	Sum of squares	Mean squares	Variance components	Total variance (%)	Significance
ISSR	Among populations	2	488.39	244.20	9.73	73.66	P < 0.001
	Within populations	45	546.85	12.15	3.48	26.34	P < 0.001
	Total	47	1035.24	22.03	13.21	100.00
RAPD	Among populations	2	872.90	436.45	16.63	82.31	P < 0.001
	Within populations	45	792.83	17.62	3.19	17.69	P < 0.001
	Total	47	832.87	17.72	19.82	100.00

Note: df, degrees of freedom.

Figure 1. Dendrogram of 48 samples resulting from the UPGMA cluster analysis based on Jaccard's similarity coefficients obtained from ISSR (a) and RAPD (b).

Figure 2. Inferred genetic structure of 48 samples from different geographic groups based on ISSR (a) and RAPD (b).

Figure 3. Principle coordinates analysis of 48 samples based on ISSR (a) and RAPD (b).