. 2020 Nov 20;11(11):1373. doi: 10.3390/genes11111373

Table 2.

Summary of genetic diversity estimates for 24 noug accessions based on 202 single-nucleotide polymorphic (SNP) loci or its subsets, and mean values for different groups and all accessions.

Acc	PPL	I	Ho	He	uHe	F	Theta	EAED₁	EAED₂	EAED₃
NG086 ^a	75.7	0.391	0.238	0.262	0.274	0.105	2.016	0.313	0.554	0.207
NG088 ^a	77.7	0.396	0.242	0.263	0.276	0.092	2.004	0.276	0.468	0.198
NG089 ^a	75.7	0.387	0.248	0.258	0.270	0.042	2.038	0.294	0.528	0.201
NG090 ^a	80.1	0.403	0.244	0.268	0.280	0.084	1.978	0.274	0.489	0.187
NG092 ^a	84.0	0.419	0.235	0.278	0.290	0.165	1.927	0.304	0.541	0.206
NG095 ^a	80.6	0.415	0.256	0.277	0.289	0.087	1.934	0.285	0.497	0.196
NG096 ^a	73.8	0.381	0.259	0.255	0.267	0.017	2.057	0.257	0.454	0.176
NG097 ^a	76.7	0.384	0.224	0.254	0.266	0.122	2.063	0.256	0.430	0.183
NG098 ^a	78.6	0.403	0.256	0.267	0.279	0.060	1.984	0.280	0.436	0.216
NG099 ^a	76.7	0.400	0.261	0.266	0.288	0.011	1.968	n/c	n/c	n/c
NG101 ^a	79.1	0.405	0.259	0.270	0.282	0.047	2.012	0.248	0.396	0.187
NG103 ^a	80.1	0.396	0.245	0.263	0.275	0.067	2.076	0.218	0.380	0.146
NG105 ^a	78.6	0.395	0.259	0.263	0.274	0.057	1.971	0.249	0.386	0.195
NG106 ^a	77.2	0.382	0.227	0.252	0.264	0.103	2.067	0.286	0.548	0.188
NG107 ^a	75.7	0.402	0.246	0.270	0.282	0.086	1.959	0.286	0.496	0.201
NG108 ^a	70.9	0.380	0.237	0.255	0.269	0.081	1.974	0.272	0.484	0.190
NG109 ^a	79.6	0.408	0.244	0.272	0.284	0.115	2.031	0.306	0.465	0.242
NG111 ^a	80.1	0.405	0.234	0.269	0.281	0.134	2.045	0.278	0.568	0.165
NG112 ^a	79.1	0.392	0.233	0.259	0.271	0.110	1.940	0.295	0.532	0.203
NG113 ^a	77.7	0.388	0.237	0.257	0.269	0.073	2.073	0.274	0.453	0.203
NG123 ^a	82.5	0.414	0.256	0.275	0.288	0.090	2.008	0.283	0.462	0.214
NG124 ^b	72.8	0.379	0.217	0.253	0.264	0.133	1.936	0.287	0.493	0.204
Fogera ^c	80.1	0.407	0.253	0.270	0.283	0.072	1.969	0.300	0.519	0.213
Shambu ^c	81.1	0.398	0.238	0.262	0.274	0.091	2.011	0.284	0.487	0.205
Mean_Alt-1	77.8	0.397	0.245	0.264	0.277	0.088	2.005	0.275	0.447	0.205
Mean_Alt-2	77.5	0.397	0.244	0.265	0.277	0.086	2.000	0.289	0.517	0.196
Mean_Alt-3	79.0	0.398	0.245	0.265	0.278	0.075	2.013	0.265	0.470	0.182
Mean_Reg-1	78.8	0.401	0.251	0.266	0.279	0.076	2.006	0.281	0.458	0.211
Mean_Reg-2	73.8	0.382	0.240	0.255	0.267	0.073	2.031	0.262	0.456	0.183
Mean_Reg-3	79.7	0.405	0.244	0.270	0.282	0.100	1.983	0.285	0.495	0.197
Mean_Reg-4	77.4	0.391	0.236	0.260	0.272	0.093	2.010	0.285	0.507	0.199
Mean_Reg-5	80.1	0.396	0.245	0.263	0.275	0.067	2.076	0.218	0.380	0.146
Mean_Reg-6	79.1	0.407	0.250	0.271	0.286	0.077	1.982	0.282	0.533	0.181
Mean_Landrace	78.1	0.397	0.245	0.264	0.277	0.083	2.006	0.277	0.478	0.195
Mean_Cultivar	80.6	0.4025	0.245	0.266	0.278	0.081	1.99	0.292	0.503	0.209
Mean_all	78.1	0.397	0.244	0.264	0.277	0.085	2.002	0.278	0.481	0.197
SE_all	0.006	0.004	0.003	0.003	0.003	0.006	0.050	0.005	0.011	0.004

Acc = accessions (^a landrace populations, ^b breeding population, ^c cultivars); PPL = percent polymorphic loci; I = Shannon’s information index; Ho = observed heterozygosity; He = expected heterozygosity; uHe = unbiased expected heterozygosity; F = fixation index; Theta (H) = Theta from mean heterozygosity under the stepwise mutation model [52]; EAED_1, 2, and 3 = estimates of average evolutionary divergence over sequence pairs within populations for (a) all polymorphic loci, (b) loci with allele frequency of equal or above 0.3 and below or equal 0.7, and (c) loci with allele frequency of below 0.3 and above 0.7, respectively, as estimated based on the Tajima-Nei model [53]. Note: In all cases, genotypes with more than 7% missing data were excluded. The Pearson correlation coefficient of EAED₁ vs. EAED₂, EAED₁ vs. EAED₃, and EAED₂ vs. EAED₃ were 0.79 (p < 0.001), 0.75 (p < 0.001), and 0.20 (p = 0.35). The 21 landrace accessions were grouped into three altitudinal groups and six regional groups (see Table S1).