Genetic variation within and among three Egyptian Mesembryanthemum species using different genetic markers

Peer review under responsibility of Mansoura University.

Figures & data

Table 1 Location and habitat type of the sampled twelve populations representing the three studied species of Mesembryanthemum L.

Pop. no.	Species	Location	Governorate	GPS Record		Habitat
				Latitude (N)	Longitude (E)
1	Mesembryanthemum crystallinum L.	El-Deeba	Port said	31° 12′ 19.32″	32° 18′ 2.24″	Road side
2		New Demiatta	Demiatta	31° 22′ 32.78″	31° 48′ 44.6″	Coastal sand flats
3		Zaian (Kalabshou)	El-Dakahlia	31° 30′ 28.4″	31° 21′ 35.88″	Road side
4		Baltim	Kafer El-Sheikh	31° 35′ 9.88″	31° 05′ 39.84″	Coastal sand dunes
5		Rosetta	El-Beheira	31° 22′ 57.81″	30° 25′ 54.63″	Road side
6	Mesembryanthemum forsskaolii Hochst. ex Bioss.	El-Gamil	Port said	31° 15′ 54.37″	32° 18′ 6.63″	Calcareous sand flats
7		Port said city	Port said	31° 15′ 57.6″	32° 18′ 6.72″	Calcareous sand flats
8	Mesembryanthemum nodiflorum L.	El-Gamil	Port said	31° 15′ 54.37″	32° 18′ 6.63″	Calcareous sand flats
9		New Demiatta	Demiatta	31° 22′ 32.78″	31° 48′ 44.6″	Coastal sand flats
10		Zaian (Kalabshou)	El-Dakahlia	31° 30′ 28.4″	31° 21′ 35.88″	Road side
11		Baltim	Kafer El-Sheikh	31° 35′ 9.88″	31° 05′ 39.84″	coastal sand dunes
12		Rosetta	El-Beheira	31° 22′ 57.81″	30° 25′ 54.63″	Road side

Fig. 1 Geographic map of sampling localities (*) of Mesembryanthemum populations along the International Coastal Road, Egypt.

Table 2 Data matrix of SDS-PAGE of protein pattern of twelve different populations of Mesembryanthemum L. in Egypt.

Plate 1 Electrophenogram illustrating protein banding profile of twelve different populations of Mesembryanthemum L. in Egypt M = marker 1,2,3,4 and 5 = M. crystallinum 6,7 = M. forsskaolii and 8,9,10,11 and 12 = M. nodiflorum.

Table 3 List of primers and their nucleotide sequences, range of band products, number of common and polymorphic bands and the percentage of polymorphism produced by different RAPD and ISSR primers.

Molecular type	Primer code	Nucleotide sequence 5′to 3′	Size range (bp)	Total bands	Mono-morphic bands	Poly- morphic bands	% Polymorphism
RAPD	OPO9	TCC CAC GCA A	1465–350	8	2	6	75
	OPO10	TCA GAG CGC C	910–130	7	2	5	71.42
	OPO11	GAC AGG AGG T	1112–115	8	2	6	75
	OPO12	CAG TGC TGT G	950–305	8	6	2	25
	OPO13	GTC AGA GTC C	1120–95	8	3	5	62.5
			Average	7.8	3	4.8	61.78%
ISSR	HB11	(GT)6 CC	1500–450	8	4	4	50
	HB12	(CAC)3 GC	1800–400	9	4	5	55.55
	HB13	(GAG)3 GC	1900–300	10	6	4	40
	HB14	(CTC)3 GC	1200–500	4	3	1	25
	HB15	(GTG)3 GC	1300–700	6	4	2	33.33
			Average	7.4	4.2	3.2	40.77%

Table 4 RAPD and ISSR profiles of different genotypes in Mesembryanthemum L. using five primers for each marker, for population number see Table 1.

Table 5 Comparative analysis of bands characteristics generated by RAPD and ISSR markers in Mesembryanthemum species.

No.	Parameters	RAPD	ISSR
1	Species screened	3	3
2	No. of primer used	5	5
3	Range of markers	95–1465 bp	700–1500 bp
4	Total No. of bands	39	37
5	No. of monomorphic bands	15	21
6	No. of polymorphic bands	24	16
7	% Polymorphism	61.78%	40.77%

Plate 2 DNA polymorphasim based on RAPD-PCR and ISSR-PCR analysis of Mesembryanthemum L. populations in Egypt, for population number see Table 1.

Table 6 Genetic diversity parameters revealed by different genetic markers (RAPD, ISSR and SDS-PAGE).

Genetic marker	Species	N	NB	NBF ≥5%	PS	Na	Ne	SI	He	uHe	%P	AMOVA (%)
												Within	Among
RAPD	M. crystallinum	5	37	37	3	1.282 (0.090)	1.207 (0.055)	0.179 (0.043)	0.120 (0.030)	0.133 (0.033)	33.33%
	M. forsskaolii	2	28	28	1	0.795 (0.091)	1.054 (0.031)	0.047 (0.026)	0.032 (0.018)	0.042 (0.024)	7.69%
	M. nodiflorum	5	35	35	1	1.359 (0.107)	1.259 (0.057)	0.233 (0.044)	0.154 (0.031)	0.171 (0.034)	46.15%
	Total/mean	4	39	39	0	1.145 (0.060)	1.174 (0.029)	0.153 (0.023)	0.102 (0.016)	0.115 (0.018)	29.06% (11.31)	77	23
ISSR	M. crystallinum	5	34	34	3	1.162 (0.091)	1.154 (0.053)	0.131 (0.040)	0.088 (0.028)	0.097 (0.031)	24.32%
	M. forsskaolii	2	29	29	0	0.838 (0.082)	1.038 (0.027)	0.033 (0.023)	0.022 (0.016)	0.030 (0.021)	5.41%
	M. nodiflorum	5	34	34	3	1.243 (0.098)	1.172 (0.052)	0.158 (0.041)	0.103 (0.028)	0.114 (0.031)	32.43%
	Total/mean	4	37	37	0	1.081 (0.055)	1.121 (0.027)	0.107 (0.021)	0.071 (0.014)	0.081 (0.016)	20.72% (8.01)	53	47
SDS-PAGE	M. crystallinum	5	15	15	4	1.500 (0.185)	1.359 (0.085)	0.332 (0.064)	0.217 (0.045)	0.241 (0.050)	66.67%
	M. forsskaolii	2	11	11	1	0.944 (0.206)	1.236 (0.081)	0.202 (0.069)	0.138 (0.047)	0.184 (0.063)	33.33%
	M. nodiflorum	5	13	13	0	1.167 (0.202)	1.191 (0.068)	0.196 (0.058)	0.124 (0.039)	0.137 (0.043)	44.44%
	Total/mean	4	18	18	0	1.204 (0.116)	1.262 (0.045)	0.243 (0.037)	0.160 (0.025)	0.188 (0.030)	48.15% (9.80)	73	27

N = number of samples; NB = no. of different bands; NBF ≥ 5% = no. of different bands with a frequency ≥5%; PS = no. of bands unique to a single species; Na = no. of different alleles (bands); Ne = no. of effective alleles = 1/(pˆ2 + qˆ2); He = expected heterozygosity = 2*p*q; uHe = unbiased expected heterozygosity = (2N/(2N − 1))* He; SI = Shannon's information index = −1* (p*Ln(p) + q*Ln(q)); %P = percentage of polymorphic loci; Mean + standard errors in (parentheses).