Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

Ziya Motalebipour, Elmira; Kafkas, Salih; Khodaeiaminjan, Mortaza; Çoban, Nergiz; Gözel, Hatice

doi:10.1186/s12864-016-3359-x

Table 2 Novel SSR loci with genetic diversity measures in 44 Pistacia genotypes: allele ranges, number of alleles (Na), number of effective alleles (Ne), observed heterozygosity (Ho), expected heterozygosity (He), and PIC values of 206 loci

From: Genome survey of pistachio (Pistacia vera L.) by next generation sequencing: Development of novel SSR markers and genetic diversity in Pistacia species

No	Loci	Allele ranges (bp)	Na	Ne	Ho	He	PIC
1	CUPVSiirt15^a	96–123	10	5.12	0.45	0.80	0.79
2	CUPVSiirt17	103–109	2	1.26	0.00	0.20	0.18
3	CUPVSiirt18	181–185	2	1.09	0.09	0.08	0.08
4	CUPVSiirt22a	134–182	13	8.64	0.46	0.88	0.87
5	CUPVSiirt26^ab	164–190	9	4.39	0.39	0.77	0.74
6	CUPVSiirt37^ab	140–167	14	7.43	0.60	0.87	0.85
7	CUPVSiirt45^a	123–133	2	1.89	0.12	0.47	0.36
8	CUPVSiirt50	155–190	10	4.94	0.33	0.80	0.77
9	CUPVSiirt71^a	128–168	11	5.75	0.37	0.83	0.81
10	CUPVSiirt76^a	153–188	8	5.72	0.29	0.83	0.80
11	CUPVSiirt86^a	111–159	19	8.96	0.82	0.89	0.88
12	CUPVSiirt95^a	191–235	13	5.74	0.40	0.83	0.81
13	CUPVSiirt115	166–173	6	5.94	0.28	0.83	0.81
14	CUPVSiirt121	106–143	6	2.45	0.10	0.59	0.55
15	CUPVSiirt125^a	167–224	12	6.73	0.57	0.85	0.83
16	CUPVSiirt129^ab	127–172	16	6.76	0.59	0.85	0.84
17	CUPVSiirt131^a	156–175	8	2.96	0.38	0.66	0.62
18	CUPVSiirt140^a	213–235	7	5.10	0.33	0.80	0.78
19	CUPVSiirt149^a	98–136	15	5.25	0.43	0.81	0.79
20	CUPVSiirt151	150–172	9	4.17	0.40	0.76	0.73
21	CUPVSiirt158^a	121–243	9	6.27	0.47	0.84	0.82
22	CUPVSiirt171^a	138–161	4	2.74	0.25	0.64	0.59
23	CUPVSiirt186^a	140–182	15	4.42	0.56	0.77	0.76
24	CUPVSiirt213^a	205–223	7	2.57	0.34	0.61	0.58
25	CUPVSiirt230^a	177–216	12	4.77	0.30	0.79	0.77
26	CUPVSiirt238	171–195	8	3.80	0.37	0.74	0.70
27	CUPVSiirt242^a	129–167	13	6.13	0.49	0.84	0.82
28	CUPVSiirt243^a	137–166	13	4.80	0.41	0.79	0.77
29	CUPVSiirt256^ab	171–199	7	3.20	0.36	0.69	0.63
30	CUPVSiirt259^a	186–218	10	5.33	0.58	0.81	0.79
31	CUPVSiirt265^a	111–200	5	2.97	0.17	0.66	0.62
32	CUPVSiirt271	96–118	10	5.24	0.67	0.81	0.78
33	CUPVSiirt284^ab	220–256	12	6.08	0.39	0.84	0.82
34	CUPVSiirt294^a	114–138	10	6.24	0.34	0.84	0.82
35	CUPVSiirt297^a	136–146	8	5.51	0.30	0.82	0.79
36	CUPVSiirt298	106–198	18	6.86	0.67	0.85	0.84
37	CUPVSiirt308^a	166–175	8	4.62	0.33	0.78	0.76
38	CUPVSiirt312^a	154–172	8	2.27	0.29	0.56	0.54
39	CUPVSiirt316	254–280	7	2.87	0.31	0.65	0.62
40	CUPVSiirt320^a	173–179	2	1.83	0.50	0.45	0.35
41	CUPVSiirt328	181–204	6	2.52	0.40	0.60	0.58
42	CUPVSiirt333^a	127–159	11	5.92	0.51	0.83	0.81
43	CUPVSiirt340^a	125–171	12	6.45	0.48	0.85	0.83
44	CUPVSiirt343	121–127	4	1.96	0.33	0.49	0.43
45	CUPVSiirt349^ab	164–199	13	5.69	0.63	0.82	0.8
46	CUPVSiirt357^a	181–231	14	9.24	0.60	0.89	0.88
47	CUPVSiirt358	215–269	9	5.80	0.27	0.83	0.81
48	CUPVSiirt368	152–188	7	2.49	0.03	0.60	0.57
49	CUPVSiirt415	140–170	6	3.59	0.28	0.72	0.68
50	CUPVSiirt436^ab	91–118	13	6.01	0.68	0.83	0.82
51	CUPVSiirt446^a	221–242	4	1.96	0.36	0.49	0.42
52	CUPVSiirt465^a	112–178	16	9.93	0.45	0.90	0.89
53	CUPVSiirt472^a	172–325	16	4.67	0.44	0.79	0.77
54	CUPVSiirt476^ab	145–171	9	6.01	0.43	0.83	0.82
55	CUPVSiirt479	165–192	5	2.01	0.48	0.50	0.46
56	CUPVSiirt496	158–239	14	3.94	0.26	0.75	0.73
57	CUPVSiirt501	146–171	6	2.26	0.34	0.56	0.52
58	CUPVSiirt505^ab	146–186	13	4.20	0.43	0.76	0.74
59	CUPVSiirt509^ab	162–188	12	3.28	0.36	0.69	0.67
60	CUPVSiirt543^a	111–149	11	6.76	0.63	0.85	0.84
61	CUPVSiirt565^ab	134–174	16	7.49	0.43	0.87	0.85
62	CUPVSiirt568x	100–117	5	2.46	0.21	0.59	0.52
63	CUPVSiirt568y	117–145	15	8.50	0.48	0.88	0.87
64	CUPVSiirt569^a	95–109	5	3.99	0.62	0.75	0.71
65	CUPVSiirt598	163–204	14	7.38	0.60	0.86	0.85
66	CUPVSiirt600	225–241	8	5.17	0.54	0.81	0.78
67	CUPVSiirt616	98–204	13	9.88	0.51	0.90	0.89
68	CUPVSiirt617	277–290	4	3.12	0.39	0.68	0.62
69	CUPVSiirt621^a	93–129	9	3.98	0.33	0.75	0.72
70	CUPVSiirt625^a	152–191	15	9.05	0.36	0.89	0.88
71	CUPVSiirt649^a	158–177	4	2.68	0.47	0.63	0.56
72	CUPVSiirt660^ab	129–146	10	3.89	0.62	0.74	0.71
73	CUPVSiirt661	209–288	7	3.28	0.44	0.70	0.67
74	CUPVSiirt674	235–249	6	2.60	0.32	0.61	0.57
75	CUPVSiirt689x	200–210	5	2.10	0.38	0.52	0.50
76	CUPVSiirt689y	306–314	4	2.18	0.49	0.54	0.45
77	CUPVSiirt690	215–221	2	1.40	0.16	0.28	0.24
78	CUPVSiirt712	180–210	9	3.07	0.46	0.67	0.64
79	CUPVSiirt715	139–176	9	2.64	0.25	0.62	0.59
80	CUPVSiirt719^ab	190–234	13	6.99	0.71	0.86	0.84
81	CUPVSiirt724	132–138	3	2.88	0.38	0.65	0.58
82	CUPVSiirt742^a	196–232	14	3.19	0.30	0.69	0.67
83	CUPVSiirt743	159–205	12	6.70	0.39	0.85	0.83
84	CUPVSiirt764^a	161–206	9	6.14	0.56	0.84	0.82
85	CUPVSiirt768^ab	206–220	6	3.43	0.60	0.71	0.67
86	CUPVSiirt782^ab	172–202	10	4.41	0.5	0.77	0.75
87	CUPVSiirt788	205–262	16	6.48	0.43	0.85	0.83
88	CUPVSiirt794	206–244	14	5.90	0.65	0.83	0.81
89	CUPVSiirt796^ab	92–130	17	8.32	0.66	0.88	0.87
90	CUPVSiirt803	202–266	8	3.49	0.36	0.71	0.68
91	CUPVSiirt818^a	165–187	10	5.65	0.48	0.82	0.80
92	CUPVSiirt836^a	144–174	13	2.69	0.23	0.63	0.61
93	CUPVSiirt838^ab	139–181	14	6.21	0.76	0.84	0.82
94	CUPVSiirt841	146–186	14	5.81	0.59	0.83	0.81
95	CUPVSiirt847	226–256	9	6.13	0.50	0.84	0.82
96	CUPVSiirt855^a	237–278	9	4.17	0.43	0.76	0.74
97	CUPVSiirt858^a	167–198	11	4.62	0.63	0.78	0.76
98	CUPVSiirt875	157–190	13	4.23	0.28	0.76	0.74
99	CUPVSiirt876^ab	180–221	16	8.05	0.77	0.88	0.86
100	CUPVSiirt883	172–219	12	3.69	0.28	0.73	0.71
101	CUPVSiirt889^a	168–188	8	4.57	0.40	0.78	0.75
102	CUPVSiirt891^a	130–168	6	3.82	0.28	0.74	0.70
103	CUPVSiirt907	92–98	3	2.86	0.45	0.65	0.58
104	CUPVSiirt924^a	81–89	4	1.49	0.00	0.33	0.31
105	CUPVSiirt929^a	81–105	13	5.66	0.40	0.82	0.81
106	CUPVSiirt931^a	146–340	7	4.59	0.12	0.78	0.75
107	CUPVSiirt932	123–132	7	3.48	0.43	0.71	0.67
108	CUPVSiirt949^a	160–197	9	4.31	0.34	0.77	0.74
109	CUPVSiirt951	154–184	6	1.78	0.08	0.44	0.42
110	CUPVSiirt956^a	105–200	18	6.31	0.42	0.84	0.83
111	CUPVSiirt961^a	177–210	10	5.85	0.33	0.83	0.81
112	CUPVSiirt975^a	139–154	6	3.44	0.30	0.71	0.66
113	CUPVSiirt986^a	146–169	10	3.09	0.41	0.68	0.65
114	CUPVSiirt989^a	140–176	13	4.10	0.32	0.76	0.74
115	CUPVSiirt1003^ab	71–112	12	7.87	0.49	0.87	0.86
116	CUPVSiirt1008^a	163–174	6	2.93	0.20	0.66	0.60
117	CUPVSiirt1017^a	203–245	16	6.14	0.50	0.84	0.82
118	CUPVSiirt1021^a	123–143	6	3.03	0.57	0.67	0.63
119	CUPVSiirt1041^a	100–114	7	4.62	0.40	0.78	0.75
120	CUPVSiirt1043^a	89–157	13	3.43	0.30	0.71	0.69
121	CUPVSiirt1047^ab	125–157	11	3.74	0.34	0.73	0.72
122	CUPVSiirt1053^a	145–189	9	4.05	0.40	0.75	0.72
123	CUPVSiirt1055^a	151–180	7	2.83	0.24	0.65	0.62
124	CUPVSiirt1057^a	226–258	12	5.05	0.42	0.8	0.78
125	CUPVSiirt1062^a	138–172	12	3.84	0.56	0.74	0.71
126	CUPVSiirt1071^ab	123–169	16	7.69	0.63	0.87	0.86
127	CUPVSiirt1092^a	136–165	11	6.15	0.56	0.84	0.82
128	CUPVSiirt1095	126–290	11	7.78	0.58	0.87	0.86
129	CUPVSiirt1116^a	151–191	15	5.37	0.57	0.81	0.80
130	CUPVSiirt1117^a	143–172	12	7.74	0.56	0.87	0.86
131	CUPVSiirt1120^ab	193–218	11	4.50	0.39	0.78	0.75
132	CUPVSiirt1122	121–215	7	5.54	0.45	0.82	0.80
133	CUPVSiirt1127	118–142	9	4.74	0.50	0.79	0.77
134	CUPVSiirt1140^a	156–176	8	5.94	0.40	0.83	0.81
135	CUPVSiirt1145^ab	150–174	12	5.98	0.58	0.83	0.81
136	CUPVSiirt1153^a	172–201	8	3.96	0.26	0.75	0.72
137	CUPVSiirt1163	140–166	7	3.80	0.43	0.74	0.70
138	CUPVSiirt1171	229–270	14	3.07	0.38	0.67	0.66
139	CUPVSiirt1182^ab	155–179	8	4.46	0.43	0.78	0.75
140	CUPVSiirt1183	235–250	7	4.48	0.33	0.78	0.75
141	CUPVSiirt1188	116–168	3	2.56	0.31	0.61	0.54
142	CUPVSiirt1189	247–267	5	2.56	0.36	0.61	0.56
143	CUPVSiirt1191	154–190	5	3.19	0.46	0.69	0.65
144	CUPVSiirt1202^ab	174–212	16	4.18	0.50	0.76	0.74
145	CUPVSiirt1214^a	157–182	10	4.56	0.15	0.78	0.76
146	CUPVSiirt1224^ab	257–292	9	6.37	0.53	0.84	0.82
147	CUPVSiirt1238^ab	229–258	11	3.88	0.45	0.74	0.72
148	CUPVSiirt1243^ab	134–164	14	6.64	0.20	0.85	0.84
149	CUPVSiirt1250^a	175–192	10	4.77	0.40	0.79	0.76
150	CUPVSiirt1260^a	151–184	10	3.21	0.36	0.69	0.66
151	CUPVSiirt1267	124–155	9	4.78	0.49	0.79	0.77
152	CUPVSiirt1271^a	203–234	10	3.76	0.23	0.73	0.72
153	CUPVSiirt1273^a	135–160	6	2.53	0.75	0.61	0.55
154	CUPVSiirt1278^a	176–220	11	2.90	0.21	0.66	0.63
155	CUPVSiirt1322^a	218–237	9	3.83	0.40	0.74	0.71
156	CUPVSiirt1326^ab	186–212	17	7.26	0.55	0.86	0.85
157	CUPVSiirt1330	154–201	18	10.58	0.71	0.91	0.90
158	CUPVSiirt1331	97–119	11	4.23	0.34	0.76	0.74
159	CUPVSiirt1345	156–191	7	2.46	0.38	0.59	0.55
160	CUPVSiirt1353	169–197	10	4.70	0.53	0.79	0.76
161	CUPVSiirt1360	127–135	5	3.59	0.34	0.72	0.67
162	CUPVSiirt1372^ab	112–194	11	4.53	0.20	0.78	0.76
163	CUPVSiirt1378	83–119	11	4.06	0.30	0.75	0.72
164	CUPVSiirt1388^a	177–201	6	4.67	0.43	0.79	0.75
165	CUPVSiirt1394^a	228–270	9	5.17	0.28	0.81	0.78
166	CUPVSiirt1399	183–216	6	1.95	0.18	0.49	0.46
167	CUPVSiirt1400^ab	155–197	17	5.34	0.77	0.81	0.8
168	CUPVSiirt1402^ab	172–213	9	4.36	0.45	0.77	0.74
169	CUPVSiirt1405^ab	176–223	18	8.85	0.56	0.89	0.88
170	CUPVSiirt1406	172–208	13	3.81	0.23	0.74	0.72
171	CUPVSiirt1413^a	166–202	10	3.74	0.46	0.73	0.70
172	CUPVSiirt1417	134–374	12	4.84	0.31	0.79	0.78
173	CUPVSiirt1418^a	114–159	16	8.24	0.37	0.88	0.87
174	CUPVSiirt1431^a	198–215	8	3.65	0.29	0.73	0.70
175	CUPVSiirt1438^a	265–290	9	4.06	0.14	0.75	0.72
176	CUPVSiirt1442^a	110–138	12	4.12	0.27	0.76	0.74
177	CUPVSiirt1457^a	149–199	12	7.84	0.32	0.87	0.86
178	CUPVSiirt1477^ab	109–126	12	6.27	0.57	0.84	0.83
179	CUPVSiirt1478	84–119	11	4.77	0.46	0.79	0.76
180	CUPVSiirt1517^a	213–225	10	5.13	0.21	0.8	0.79
181	CUPVSiirt1547^a	120–126	2	1.38	0.18	0.28	0.24
182	CUPVSiirt1564	188–222	12	5.94	0.34	0.83	0.81
183	CUPVSiirt1567^ab	181–215	15	5.69	0.52	0.82	0.81
184	CUPVSiirt1599	292–345	11	6.53	0.39	0.85	0.83
185	CUPVSiirt1611^ab	193–215	8	2.68	0.16	0.63	0.6
186	CUPVSiirt1626^a	114–153	12	7.14	0.27	0.86	0.85
187	CUPVSiirt1628	125–155	7	2.98	0.40	0.66	0.61
188	CUPVSiirt1639^a	167–194	7	4.60	0.39	0.78	0.75
189	CUPVSiirt1640^a	134–180	10	3.45	0.17	0.71	0.67
190	CUPVSiirt1652^ab	159–193	13	5.30	0.61	0.81	0.79
191	CUPVSiirt1655^ab	150–213	14	5.77	0.53	0.83	0.81
192	CUPVSiirt1658^a	130–209	13	3.89	0.44	0.74	0.72
193	CUPVSiirt1667^ab	149–186	12	4.58	0.42	0.78	0.76
194	CUPVSiirt1688	160–184	11	5.74	0.63	0.83	0.80
195	CUPVSiirt1705	231–251	3	1.35	0.06	0.26	0.24
196	CUPVSiirt1714	196–208	5	2.13	0.08	0.53	0.50
197	CUPVSiirt1734	168–185	5	3.24	0.50	0.69	0.65
198	CUPVSiirt1740^a	157–192	7	2.88	0.41	0.65	0.61
199	CUPVSiirt1742^a	149–213	15	7.32	0.25	0.86	0.85
200	CUPVSiirt1749^ab	133–164	9	4.44	0.52	0.77	0.74
201	CUPVSiirt1759^ab	137–159	11	5.79	0.62	0.83	0.81
202	CUPVSiirt1764^a	154–178	13	3.59	0.43	0.72	0.71
203	CUPVSiirt1768^a	108–128	8	3.63	0.45	0.72	0.69
204	CUPVSiirt1784^a	177–211	9	5.46	0.43	0.82	0.79
205	CUPVSiirt1788^a	172–189	4	2.44	0.14	0.59	0.51
206	CUPVSiirt1797^a	143–177	13	4.98	0.45	0.8	0.78
	Total		2036	-	-	-	-
	Mean		9.88	4.67	0.41	0.74	0.71

^ahad amplifications in six Pistacia species
^bwere polymorphic in six Pistacia species

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