Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species

Dettori, Maria Teresa; Micali, Sabrina; Giovinazzi, Jessica; Scalabrin, Simone; Verde, Ignazio; Cipriani, Guido

doi:10.1186/s40064-015-1098-0

SpringerPlus

Table 5 Population statistics of 26 peach-derived long-core repeat SSR markers developed for five Prunus species

From: Mining microsatellites in the peach genome: development of new long-core SSR markers for genetic analyses in five Prunus species

SSR ID	Pseudo chrom.	N. bases in repeat	N. loci^a	N. alleles^b	Alleles range	N. amplified samples^c	Ho	He	PIC	NE-I	F_IS	f_null	N. amplified species
Almond
RPPG1-017	1	5	1	3	177–188	18	0.444	0.427	0.349	0.408	−0.040	0.0001	5
RPPG1-026	1	3	1	2	239–242	18	0.111	0.108	0.099	0.807	−0.028	0.0038	4
RPPG1-032	1	3	1	1	221	18	–	–	–	–	–	–	4
RPPG1-037	1	3	1	3	230–242	18	0.833	0.684	0.591	0.186	−0.218	0.0011	4
RPPG1-041	1	3	1	8	238–255	18	0.833	0.768	0.712	0.099	−0.085	0.0087	5
RPPG2-011	2	4	>1	12	203–277	18	–	–	–	–	–	–	5
RPPG2-022	2	4	>1	10	208–239	18	–	–	–	–	–	–	5
RPPG3-026	3	4	>1	4	241–253	18	–	–	–	–	–	–	5
RPPG4-059	4	5	1	2	132–161	18	0.056	0.056	0.053	0.896	0	0.0198	3
RPPG4-067	4	5	1	4	261–275	18	0.611	0.662	0.596	0.174	0.077	0.0020	3
RPPG4-077	4	4	1	4	131–151	18	0.611	0.703	0.617	0.167	0.131	0.0159	5
RPPG4-084	4	4	1	5	271–297	18	0.556	0.638	0.545	0.219	0.129	0.0159	5
RPPG4-091	4	5	1	3	245–249	18	0.056	0.500	0.424	0.327	0.888*	0.1512	5
RPPG5-018	5	3	1	8	160–197	18	0.778	0.765	0.707	0.102	−0.017	0.0122	4
RPPG5-022	5	3	>1	7	271–301	18	–	–	–	–	–	–	3
RPPG5-023	5	3	1	2	192–193	18	0.667	0.489	0.362	0.388	−0.364	0.0111	4
RPPG5-025	5	5	>1	5	301–316	18	–	–	–	–	–	–	4
RPPG5-030	5	4	1	2	163–167	18	0.167	0.157	0.141	0.729	−0.064	0.0123	5
RPPG6-009	6	5	1	3	181–191	18	0.333	0.494	0.388	0.362	0.326	0.0335	4
RPPG6-032	6	5	>1	3	141–151	18	–	–	–	–	–	–	4
RPPG6-033	6	4	>1	9	93–130	18	–	–	–	–	–	–	5
RPPG7-015	7	4	>1	8	290–332	18	–	–	–	–	–	–	4
RPPG7-026	7	5	1	2	152–161	18	0.444	0.457	0.346	0.407	0.028	0.0086	5
RPPG7-032	7	3	1	4	186–201	18	0.611	0.575	0.488	0.265	−0.063	0.0025	5
RPPG8-007	8	3	1	3	189–214	18	0.389	0.414	0.363	0.396	0.060	0.0045	5
RPPG8-028	8	5	1	4	192–215	18	0.722	0.660	0.583	0.187	−0.094	0.0020	4
Mean ^d	–	–	–	3.6	–	–	0.474	0.503	0.433	9.48 × 10 ⁻¹⁰	–	–	–
Apricot
RPPG1-017	1	5	1	3	165–169	18	0.500	0.579	0.473	0.281	0.136	0.0080	5
RPPG1-026	1	3	1	2	223–235	18	0.389	0.500	0.368	0.382	0.222	0.0151	4
RPPG1-032	1	3	1	2	227–234	18	0.056	0.056	0.053	0.896	0	0.0131	4
RPPG1-037	1	3	1	5	228–251	18	0.389	0.694	0.633	0.148	0.439*	0.0171	4
RPPG1-041	1	3	1	3	212–214	18	0.056	0.652	0.558	0.21	0.914*	0.1480	5
RPPG2-011	2	4	>1	4	194–218	18	–	–	–	–	–	–	5
RPPG2-022	2	4	>1	7	215–241	18	–	–	–	–	–	–	5
RPPG3-026	3	4	1	2	239–249	18	0.389	0.322	0.264	0.521	−0.208	0.0043	5
RPPG4-059	4	5	1	1	132	18	–	–	–	–	–	–	3
RPPG4-067	4	5	1	1	259	18	–	–	–	–	–	–	3
RPPG4-077	4	4	1	4	136–151	18	0.222	0.257	0.237	0.575	0.136	0.0061	5
RPPG4-084	4	4	1	2	276–285	18	0.333	0.413	0.321	0.439	0.194	0.0068	5
RPPG4-091	4	5	1	2	217–228	18	0.111	0.108	0.099	0.807	−0.028	0.0128	5
RPPG5-018	5	3	1	4	177–197	15	0.333	0.582	0.465	0.288	0.428	0.1536	4
RPPG5-022	5	3	1	3	271–299	18	0.444	0.560	0.445	0.307	0.207	0.0112	3
RPPG5-023	5	3	1	3	181–206	18	0.444	0.541	0.450	0.301	0.179	0.0101	4
RPPG5-025	5	5	1	2	275–283	18	0.056	0.056	0.053	0.896	0	0.0292	4
RPPG5-030	5	4	1	2	154–167	18	0.056	0.056	0.053	0.896	0	0.0210	5
RPPG6-009	6	5	1	1	191	18	–	–	–	–	–	–	4
RPPG6-032	6	5	1	2	151–157	18	0.278	0.246	0.211	0.607	−0.130	0.0048	4
RPPG6-033	6	4	1	6	101–119	18	0.389	0.670	0.609	0.163	0.419*	0.0331	5
RPPG7-015	7	4	1	4	304–322	17	0.471	0.606	0.513	0.245	0.223	0.0768	4
RPPG7-026	7	5	1	2	161–170	18	0.111	0.108	0.099	0.807	−0.028	0.0129	5
RPPG7-032	7	3	1	2	186–189	18	0.333	0.286	0.239	0.560	−0.164	0.0068	5
RPPG8-007	8	3	1	2	184–193	18	0.111	0.108	0.099	0.807	−0.028	0.0172	5
RPPG8-028	8	5	>1	8	192–215	17	–	–	–	–	–	–	4
Mean ^d	–	–	–	2.9	–	–	0.274	0.370	0.312	6.00 × 10 ⁻⁸	–	–	–
Japanese plum
RPPG1-017	1	5	1	5	172–184	18	0.833	0.659	0.593	0.177	−0.264	0.0033	5
RPPG1-026	1	3	1	2	230–235	18	0.056	0.157	0.141	0.729	0.643	0.0401	4
RPPG1-032	1	3	1	2	225–231	18	0.611	0.475	0.355	0.397	−0.286	0.0122	4
RPPG1-037	1	3	1	2	234–237	18	0.167	0.157	0.141	0.729	−0.064	0.0117	4
RPPG1-041	1	3	1	5	219–247	18	0.722	0.616	0.518	0.242	−0.172	0.0053	5
RPPG2-011	2	4	>1	9	196–232	18	–	–	–	–	–	–	5
RPPG2-022	2	4	>1	4	195–265	18	–	–	–	–	–	–	5
RPPG3-026	3	4	1	8	255–355	18	0.889	0.878	0.836	0.039	−0.013	0.0091	5
RPPG4-059	4	5	1	3	155–178	18	0.389	0.338	0.300	0.480	−0.151	0.0148	3
RPPG4-067	4	5	1	2	265–270	18	0.167	0.157	0.141	0.729	−0.064	0.0184	3
RPPG4-077	4	4	1	3	125–136	18	0.056	0.252	0.226	0.589	0.778*	0.0975	5
RPPG4-084	4	4	1	3	285–330	18	0.278	0.675	0.582	0.192	0.588*	0.1501	5
RPPG4-091	4	5	1	4	226–258	18	0.778	0.605	0.522	0.236	−0.286	0.0044	5
RPPG5-018	5	3	1	7	160–197	15	0.467	0.717	0.643	0.144	0.349*	0.2096	4
RPPG5-022	5	3	>1	6	252–299	18	–	–	–	–	–	–	3
RPPG5-023	5	3	1	2	181–184	18	0.167	0.157	0.141	0.729	−0.064	0.0091	4
RPPG5-025	5	5	1	3	277–285	18	0.667	0.589	0.479	0.277	−0.132	0.0060	4
RPPG5-030	5	4	1	3	154–167	18	0.611	0.475	0.378	0.374	−0.286	0.0103	5
RPPG6-009	6	5	1	2	186–191	18	0.500	0.386	0.305	0.461	−0.295	0.0094	4
RPPG6-032	6	5	1	2	147–152	18	0.444	0.356	0.286	0.488	−0.247	0.0101	4
RPPG6-033	6	4	>1	5	101–119	18	–	–	–	–	–	–	5
RPPG7-015	7	4	>1	9	230–316	18	–	–	–	–	–	–	4
RPPG7–026	7	5	1	4	143–161	18	0.556	0.713	0.638	0.149	0.220	0.0252	5
RPPG7-032	7	3	1	2	186–189	18	0.167	0.246	0.211	0.607	0.321	0.0351	5
RPPG8-007	8	3	1	2	180–194	18	0.056	0.056	0.053	0.896	0	0.0160	5
RPPG8-028	8	5	>1	8	189–224	18	–	–	–	–	–	–	4
Mean ^d	–	–	–	3.3	–	–	0.429	0.433	0.374	6.50 × 10 ⁻¹⁰	–	–	–
Peach
RPPG1-017	1	5	1	4	205–227	18	0.389	0.490	0.437	0.314	0.206	0.0051	5
RPPG1-026	1	3	1	1	239	18	–	–	–	–	–	–	4
RPPG1-032	1	3	1	2	221–225	18	0.056	0.056	0.053	0.896	0	0.0050	4
RPPG1-037	1	3	1	1	242	18	–	–	–	–	–	–	4
RPPG1-041	1	3	1	2	223–231	18	0.333	0.457	0.346	0.407	0.271	0.0050	5
RPPG2-011	2	4	1	2	203–226	18	0.500	0.386	0.305	0.461	−0.295	0.0014	5
RPPG2-022	2	4	1	2	209–214	18	0.222	0.356	0.286	0.488	0.376	0.0069	5
RPPG3-026	3	4	1	2	245–249	18	0.500	0.513	0.374	0.376	0.025	0.0008	5
RPPG4-059	4	5	1	3	176–187	18	0.444	0.589	0.479	0.277	0.246	0.0055	3
RPPG4-067	4	5	1	1	271	18	–	–	–	–	–	–	3
RPPG4-077	4	4	1	2	151–160	18	0.333	0.514	0.375	0.375	0.352	0.0107	5
RPPG4-084	4	4	1	2	279–281	18	0.389	0.513	0.374	0.376	0.242	0.0020	5
RPPG4-091	4	5	1	2	239–245	18	0.444	0.508	0.372	0.378	0.126	0.0049	5
RPPG5-018	5	3	1	2	177–190	18	0.444	0.489	0.362	0.388	0.092	0.0003	4
RPPG5-022	5	3	1	1	301	18	–	–	–	–	–	–	3
RPPG5-023	5	3	1	2	192–196	18	0.333	0.286	0.239	0.560	−0.164	0.0022	4
RPPG5-025	5	5	1	1	301	18	–	–	–	–	–	–	4
RPPG5-030	5	4	1	2	167–169	18	0.056	0.056	0.053	0.896	0.000	0.0044	5
RPPG6-009	6	5	1	2	181–196	18	0.111	0.108	0.099	0.807	−0.028	0.0062	4
RPPG6-032	6	5	1	1	151	18	–	–	–	–	–	–	4
RPPG6-033	6	4	1	2	116–118	18	0.500	0.475	0.355	0.397	−0.053	0.0024	5
RPPG7-015	7	4	1	4	275–303	18	0.611	0.537	0.463	0.287	−0.138	0.0025	4
RPPG7-026	7	5	1	3	157–175	18	0.278	0.541	0.414	0.337	0.486*	0.0044	5
RPPG7-032	7	3	1	2	193–196	18	0.111	0.108	0.099	0.807	−0.028	0.0014	5
RPPG8-007	8	3	1	3	205–214	18	0.056	0.160	0.149	0.719	0.650	0.0082	5
RPPG8-028	8	5	1	2	207–212	18	0.167	0.386	0.305	0.461	0.567	0.0029	4
Mean ^d	–	–	–	2.4	–	–	0.314	0.376	0.297	2.30 × 10 ⁻⁷	–	–	–
Sweet cherry
RPPG1-017	1	5	1	3	176–196	17	0.059	0.169	0.157	0.705	0.651	0.1703	5
RPPG1-026	1	3	1	2	274–298	18	0.389	0.437	0.334	0.421	0.110	0.0117	4
RPPG1-032	1	3	1	3	225–231	18	0.833	0.589	0.479	0.277	−0.414*	0.0058	4
RPPG1-037	1	3	1	5	237–265	18	0.444	0.635	0.543	0.220	0.301	0.0209	4
RPPG1-041	1	3	1	6	222–237	17	0.706	0.742	0.682	0.116	0.049	0.0172	5
RPPG2-011	2	4	>1	4	185–224	18	–	–	–	–	–	–	5
RPPG2-022	2	4	1	5	221–234	18	0.889	0.778	0.713	0.102	−0.143	0.0026	5
RPPG3-026	3	4	1	2	239–249	18	0.111	0.108	0.099	0.807	−0.028	0.0183	5
RPPG4-059	4	5	1	1	132	18	–	–	–	–	–	–	3
RPPG4-067	4	5	1	2	260–265	18	0.056	0.056	0.053	0.896	0	0.0204	3
RPPG4-077	4	4	1	3	141–148	18	0.444	0.514	0.449	0.301	0.136	0.0167	5
RPPG4-084	4	4	1	2	287–290	17	0.529	0.515	0.375	0.375	−0.027	0.0312	5
RPPG4-091	4	5	1	4	245–290	18	0.778	0.717	0.649	0.140	−0.085	0.0011	5
RPPG5-018	5	3	1	1	179	18	–	–	–	–	–	–	4
RPPG5-022	5	3	1	1	295	17	–	–	–	–	–	–	3
RPPG5-023	5	3	1	0	–	0	–	–	–	–	–	–	4
RPPG5-025	5	5	1	4	275–289	18	0.722	0.694	0.607	0.173	−0.040	0.0096	4
RPPG5-030	5	4	1	3	163–167	18	0.389	0.522	0.404	0.346	0.255	0.0224	5
RPPG6-009	6	5	1	2	197–207	18	0.556	0.413	0.321	0.439	−0.346	0.0067	4
RPPG6-032	6	5	1	2	147–152	18	0.056	0.056	0.053	0.896	0	0.0125	4
RPPG6-033	6	4	1	3	95–105	17	0.824	0.540	0.414	0.336	−0.526*	0.0123	5
RPPG7-015	7	4	1	0	–	0	–	–	–	–	–	–	4
RPPG7-026	7	5	1	2	175–178	18	0.167	0.157	0.141	0.729	−0.064	0.0052	5
RPPG7-032	7	3	1	3	192–201	18	0.556	0.538	0.412	0.338	−0.033	0.0077	5
RPPG8-007	8	3	1	3	196–208	18	0.389	0.332	0.285	0.496	−0.172	0.0061	5
RPPG8-028	8	5	1	1	201	18	–	–	–	–	–	–	4
Mean ^d	–	–	–	3.1	–	–	0.468	0.448	0.378	2.39 × 10 ⁻⁹	–	–	–

Ho observed heterozygosity, He expected heterozygosity, PIC polymorphic information content, NE-I Probability of Identity, F _IS inbreeding coefficient, fnull frequencies of null alleles.
* value significantly different from zero at α < 0.05.
^aMultilocus markers (N. loci >1) were not used to calculate population parameters.
^bfor multilocus SSRs the number reported refers to the number of fragments.
^cThere are no “missing data” in this matrix. If the number of amplified samples is <18 the sample amplification did not gave a product in at least two repetitions and was thus considered as a null allele (see the main text for details).
^dMeans calculated exluding monomorfic and multilocus SSRs; For NE-I the combined probability of identity is reported.

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