Table 1.

Key descriptive analysis of all validated loci on the analyzed international cacao accessions, LG = linkage group, mAF = minor allele frequency, MAF = Major alelel frequency, I = Shannons information index, H_o = observed heterozygosity, H_e = effective heterozygosity, F = fixation index, PIDsib = probability of identity siblings.

Locus	LG	mAF	MAF	Ne	Ho	He	I	F	PIDsib
TcSNP139	8	0.354	0.646	1.843	0.369	0.457	0.650	0.193	0.621
TcSNP144	10	0.408	0.592	1.934	0.323	0.483	0.676	0.331	0.605
TcSNP151	8	0.446	0.554	1.977	0.431	0.494	0.687	0.128	0.597
TcSNP174	4	0.133	0.867	1.299	0.141	0.230	0.392	0.390	0.790
TcSNP193	9	0.414	0.586	1.943	0.391	0.485	0.678	0.195	0.603
TcSNP226	9	0.246	0.754	1.590	0.246	0.371	0.558	0.337	0.681
TcSNP230	10	0.492	0.508	2.000	0.462	0.500	0.693	0.077	0.594
TcSNP364	9	0.146	0.854	1.333	0.200	0.250	0.416	0.199	0.774
TcSNP372	4	0.254	0.746	1.610	0.323	0.379	0.567	0.147	0.675
TcSNP413	3	0.400	0.600	1.923	0.338	0.480	0.673	0.295	0.606
TcSNP448	4	0.192	0.808	1.451	0.138	0.311	0.490	0.554	0.726
TcSNP577	5	0.485	0.515	1.998	0.415	0.500	0.693	0.168	0.594
TcSNP591	1	0.392	0.608	1.911	0.323	0.477	0.670	0.322	0.608
TcSNP602	6	0.215	0.785	1.511	0.277	0.338	0.521	0.181	0.705
TcSNP606	7	0.238	0.762	1.570	0.200	0.363	0.549	0.449	0.686
TcSNP751	5	0.208	0.792	1.491	0.231	0.329	0.511	0.299	0.712
TcSNP786	1	0.046	0.954	1.097	0.062	0.088	0.187	0.301	0.915
TcSNP852	3	0.323	0.677	1.777	0.246	0.437	0.629	0.437	0.634
TcSNP860	2	0.359	0.641	1.853	0.344	0.460	0.653	0.253	0.619
TcSNP872	4	0.446	0.554	1.977	0.277	0.494	0.687	0.440	0.597
TcSNP878	3	0.215	0.785	1.511	0.369	0.338	0.521	−0.092	0.705
TcSNP891	2	0.354	0.646	1.843	0.277	0.457	0.650	0.394	0.621
TcSNP994	6	0.485	0.515	1.998	0.354	0.500	0.693	0.292	0.594
TcSNP1041	10	0.154	0.846	1.352	0.215	0.260	0.429	0.173	0.765
TcSNP1060	2	0.215	0.785	1.511	0.308	0.338	0.521	0.090	0.705
TcSNP1111	5	0.223	0.777	1.531	0.200	0.347	0.531	0.423	0.698
TcSNP1126	7	0.092	0.908	1.201	0.154	0.168	0.308	0.082	0.843
TcSNP1280	1	0.408	0.592	1.934	0.323	0.483	0.676	0.331	0.605
TcSNP1331	10	0.477	0.523	1.996	0.400	0.499	0.692	0.198	0.594
TcSNP1439	9	0.262	0.738	1.629	0.308	0.386	0.575	0.203	0.670
TcSNP1458	1	0.485	0.515	1.998	0.262	0.500	0.693	0.476	0.594
Tcm002s00644224	2	0.446	0.554	1.977	0.338	0.494	0.687	0.315	0.597
Tcm002s29938429	2	0.400	0.600	1.923	0.462	0.480	0.673	0.038	0.606
Tcm002s34015437	2	0.385	0.615	1.899	0.277	0.473	0.666	0.415	0.611
Tcm003s12502217	3	0.438	0.562	1.970	0.415	0.492	0.686	0.156	0.599
Tcm003s20315420	3	0.400	0.600	1.923	0.277	0.480	0.673	0.423	0.606
Tcm003s05554949	3	0.408	0.592	1.934	0.262	0.483	0.676	0.458	0.605
Tcm003s27807955	3	0.485	0.515	1.998	0.354	0.500	0.693	0.292	0.594
Tcm006s26507164	6	0.423	0.577	1.954	0.385	0.488	0.681	0.212	0.601
Tcm008s17168944	8	0.477	0.523	1.996	0.400	0.499	0.692	0.198	0.594
Tcm009s28255143	9	0.438	0.562	1.970	0.262	0.492	0.686	0.469	0.599
Tcm009s41415628	9	0.469	0.531	1.992	0.415	0.498	0.691	0.166	0.595
Mean	—	0.336	0.647	1.726	0.297	0.409	0.591	0.266	3.4 × 10−22*
SE	—	0.127	0.147	0.365	0.100	0.118	0.146	0.143	/

*Accumulated PIDsibs for 42 SNP locus combinations.