First microsatellite markers for Scaligeria lazica Boiss. (Apiaceae) by next-generation sequencing: population structure and genetic diversity analysis

Figures & data

Figure 1. Sampling sites of S. lazica accessions from four different locations in Turkey.

Table 1. S. lazica sampling locations in this study.

No.	Accession name	Acronym	Location	Latitude (N)	Longitude (W)
1	Camlıhemsin	RCH	Rize Camlıhemsin	41° 34′	41^o 10′
2	Cayeli	RCE	Rize Cayeli	40° 53′	40^o 44′
3	Altindere	TAD	Trabzon Altindere	40° 43′	39^o 38′
4	Sumela	TSM	Trabzon Sumela	40° 41′	39^o 39′

Figure 2. Electropherogram of SclgSSR1762 SSR locus in four S. lazica.

Figure 3. Number of different repeat motifs in S. lazica.

Table 2. Repeat motifs, product sizes, number of alleles (Na), number of effective alleles (Ne), observed homozygosity (Ho), expected heterozygosity (He) and polymorphism information content (PIC) values based on 40 SSR loci developed from S. lazica.

No.	SSR loci	Accession number	Motif	Na	Ne	Ho	He	PIC
1	SclgSSR164	KX234457	(AG)19	7	4.07	0.71	0.75	0.72
2	SclgSSR170	KX234458	(CT)14	5	3.43	0.50	0.71	0.66
3	SclgSSR179	KX234459	(AGA)9	2	1.74	0.10	0.43	0.34
4	SclgSSR285	KX234468	(AG)15	12	7.04	0.64	0.86	0.84
5	SclgSSR323	KX234470	(AG)14	3	1.35	0.25	0.26	0.24
6	SclgSSR709	KX234485	(CT)15	6	3.99	0.40	0.75	0.71
7	SclgSSR762	KX234491	(AG)21	12	6.26	0.76	0.84	0.82
8	SclgSSR774	KX234493	(GA)14	6	2.93	0.38	0.66	0.6
9	SclgSSR796	KX234495	(AG)14	3	2.47	0.43	0.60	0.53
10	SclgSSR810	KX234496	(TC)14	5	3.13	0.36	0.68	0.62
11	SclgSSR815	KX234497	(GT)15	6	2.56	0.46	0.61	0.57
12	SclgSSR858	KX234499	(AC)14	8	3.83	0.51	0.74	0.70
13	SclgSSR909	KX234502	(GAT)10	7	4.46	0.62	0.78	0.74
14	SclgSSR913	KX234503	(AGCAGA)5	3	2.17	0.53	0.54	0.43
15	SclgSSR915	KX234504	(TC)15	9	5.27	0.55	0.81	0.78
16	SclgSSR928	KX234505	(TTTTCC)5	4	1.92	0.40	0.48	0.39
17	SclgSSR929	KX234506	(GA)14	3	1.38	0.14	0.27	0.25
18	SclgSSR979	KX234507	(AG)17	8	2.86	0.45	0.65	0.59
19	SclgSSR1018	KX234511	(GT)21	5	2.92	0.25	0.66	0.6
20	SclgSSR1029	KX234512	(CT)14	5	2.77	0.11	0.64	0.58
21	SclgSSR1094	KX234517	(TG)14	6	3.06	0.31	0.67	0.63
22	SclgSSR1258	KX234527	(ATTA)6	8	4.38	0.24	0.77	0.74
23	SclgSSR1283	KX234528	(AG)15	6	3.06	0.49	0.67	0.63
24	SclgSSR1319	KX234532	(TC)14	7	3.75	0.22	0.73	0.69
25	SclgSSR1354	KX234535	(CT)22	8	5.15	0.43	0.81	0.78
26	SclgSSR1488	KX234545	(CAT)10	2	1.98	0.79	0.49	0.37
27	SclgSSR1544	KX234549	(GA)16	6	3.97	1.00	0.75	0.71
28	SclgSSR1547	KX234550	(AGA)10	4	2.74	0.50	0.64	0.58
29	SclgSSR1613	KX234553	(TC)14	4	1.87	0.15	0.46	0.42
30	SclgSSR1614	KX234554	(TC)15	11	3.08	0.51	0.68	0.65
31	SclgSSR1636	KX234555	(AG)59	13	4.93	0.31	0.80	0.78
32	SclgSSR1645	KX234556	(AG)19	9	4.71	1.00	0.79	0.76
33	SclgSSR1762	KX234560	(TC)15	8	3.63	0.36	0.72	0.69
34	SclgSSR2076	KX234569	(AG)24	10	5.49	0.67	0.82	0.79
35	SclgSSR2196	KX234572	(TG)16	8	2.59	0.88	0.61	0.54
36	SclgSSR2364	KX234577	(AGA)10	3	2.69	0.31	0.63	0.55
37	SclgSSR2475	KX234579	(GA)17	9	5.9	0.48	0.83	0.81
38	SclgSSR2548	KX234580	(TC)16	5	2.58	0.28	0.61	0.55
39	SclgSSR2725	KX234585	(GA)16	11	3.91	0.69	0.74	0.71
40	SclgSSR2798	KX234587	(TGG)11	7	2.27	0.44	0.56	0.53
	Total		–	264
	Mean			6.6	3.46	0.47	0.66	0.60

Table 3. Mean of population genetic parameters in this study.

Populations	Sample size	Na	Ne	Ho	He	PIC	Polymorphism (%)	Number of private alleles
RCH	10	3.10	2.12	0.43	0.42	0.37	92.4	65
RCE	10	4.10	2.76	0.57	0.57	0.52	97.3	44
TSM	10	2.53	1.74	0.42	0.35	0.30	91.3	4
TAD	10	2.93	2.11	0.44	0.46	0.40	94.7	16

Figure 4. An UPGMA dendrogram of 40 S. lazica accessions from four locations obtained by analyzing 40 SSR loci.

Figure 5. Population structure of 40 accessions estimated from 40 SSRs using STRUCTURE program. K = 2 to K = 5 represent the sub-population of the 40 accessions originating from different places of Turkey.

Figure 6. Values of ΔK, with its modal value detecting a most probable K of two subgroups (K = 2), including a small peak at four subgroups (K = 4).