The microsatelite markers (MSM), the chromosome position of each marker is shown in Table 1. Thirty nine alleles in total were obtained from the eight microsatellite markers used with a size range of 99 to 260 bp detected across the three breeds analyzed. All the eight MSM used in this study belong to the list of microsatellite markers recommended by FAO/ISAG (2011).
The genetic variation among population and individual of the total genetic variance were 2% and 48% respectively, while 51% of the genetic variation was attributed to within population genetic diversity as shown in Table 2.
Table 2
Genetic variation of the Analysis of Molecular Variance
Source | df | SS | MS | Est. Var. | %PV |
Among Pops | 2 | 10.490 | 5.245 | 0.04 | 2% |
Among Indiv | 55 | 208.338 | 3.788 | 1.24 | 48% |
Within Indiv | 58 | 76.000 | 1.310 | 1.31 | 51% |
Total | 115 | 294.828 | | 2.59 | 100% |
Df- degree of freedom; SS- Sum of Squares; MS - mean square: Est. Var. - Estimated variance, %PV -Percentage of Variation |
The observed allele sizes and their frequencies for the microsatellite markers in each breed’s population in Fig. 1 shows the allele frequency ranged from 0.00 to 1.00 from the 39 alleles obtained within the population. Other allele frequency results obtained from the interpretation of Fig. 1 for the microsatellite loci across the three breeds were polymorphic with the exception of S0101 that was monomorphic.
The mean number of alleles (Na) observed in the overall population of the three populations is 3.63 ± 0.36 (Table 3). The mean of Na obtained in this study was higher than black Slovan pigs(ref) but lower than those obtained for Benin pig (8.94 ± 2.64) (Djimènou et al., 2021), Ghanaian Pigs (7.65) (Ayizanga et al., 2016), 4.20 for Philipine pigs (Jay Don Oh et al., 2014) and 14.59 for Thai pigs (Rangusun et al., 2019). In the subpopulation as shown in Table 4, P1 and P2 (Exotic and NP) have the same highest Na of 8, while P3 (Hybrid) had the lowest Na of 6. In Ghanian pig it was 5.48 for Berkshire and 10.6 for Papu indigenous ghanian pig (Ayizanga et al., 2016); 8.23 for Jeju black pig in Korea and 5.03 for Berkshire (Jay Don Oh et al., 2014). High Na has been reported to have high allelic diversity caused by crossbreeding or admixture among the population. The low total means of Na obtained in this study may be as a result of low allelic diversity of the markers used because some can be more polymorphic than others.
Table 3
Parameters | loci 1 S01001 | loci 2 SW026 | loci 3 S009 | Loci 4 SW024 | Loci 5 SW122 | Loci 6 S0226 | Loci 7 S0227 | Loci 8 SW632 | Total Mean |
Na | 1.00 ± 0.00 | 3.00 ± 0.00 | 3.00 ± 0.58 | 4.00 ± 0.00 | 6.67 ± 1.33 | 4.00 ± 0.00 | 3.00 ± 0.00 | 4.33 ± 0.67 | 3.63 ± 0.36 |
Ne | 1.00 ± 0.00 | 1.99 ± 0.12 | 2.04 ± 0.22 | 3.04 ± 0.09 | 3.43 ± 0.39 | 2.60 ± 0.51 | 1.49 ± 0.08 | 2.16 ± 0.08 | 2.22 ± 0.17 |
I | 0.00 ± 0.00 | 0.81 ± 0.04 | 0.84 ± 0.14 | 1.23 ± 0.02 | 1.44 ± 0.16 | 1.08 ± 0.13 | 0.61 ± 0.06 | 0.94 ± 0.02 | 0.87 ± 0.09 |
Ho | 0.00 ± 0.00 | 0.68 ± 0.10 | 0.55 ± 0.02 | 0.60 ± 0.01 | 0.85 ± 0.09 | 0.69 ± 0.19 | 0.30 ± 0.06 | 0.38 ± 0.05 | 0.51 ± 0.06 |
He | 0.00 ± 0.00 | 0.49 ± 0.03 | 0.50 ± 0.06 | 0.67 ± 0.01 | 0.70 ± 0.03 | 0.59 ± 0.07 | 0.32 ± 0.04 | 0.54 ± 0.02 | 0.48 ± 0.05 |
uHe | 0.00 ± 0.00 | 0.52 ± 0.04 | 0.52 ± 0.06 | 0.72 ± 0.01 | 0.73 ± 0.02 | 0.65 ± 0.11 | 0.33 ± 0.04 | 0.57 ± 0.03 | 0.50 ± 0.05 |
F | | -0.36 ± 0.11 | -0.12 ± 0,11 | 0.10 ± 0.16 | -0.24 ± 0.20 | -0.13 ± 0.21 | 0.06 ± 0.12 | 0.29 ± 0.09 | -0.06 ± 0.06 |
Na = Mean number of alleles; Ne = Effective number of alleles; I = Shannon's Information Index; Ho = Observed Heterozygosity; He = Expected Heterozygosity; uHe = Unbiased Expected Heterozygosity; F = Fixation Index; Mean He = Average He across the populations; Mean Ho = Average Ho across the populations; Ht = Total Expected Heterozygosity. |
Table 4
The Mean (Na ) and Effective (Ne ) Number of Alleles at various Loci Across Population
Pop | | loci 1 S01001 | loci 2 SW26 | loci 3 S009 | Loci 4 SW24 | Loci 5 SW122 | Loci 6 S0226 | Loci 7 S0227 | Loci 8 SW632 |
P1 | Na | 1 | 3 | 4 | 4 | 8 | 4 | 3 | 5 |
| Ne | 1.00 | 2.03 | 2.28 | 2.97 | 3.89 | 2.30 | 1.65 | 2.05 |
| I | 0.00 | 0.78 | 1.01 | 1.21 | 1.60 | 1.02 | 0.72 | 0.94 |
| Ho | 0.00 | 0.71 | 0.56 | 0.46 | 0.88 | 0.73 | 0.35 | 0.33 |
| He | 0.00 | 0.51 | 0.56 | 0.66 | 0.74 | 0.57 | 0.39 | 0.51 |
| uHe | 0.00 | 0.52 | 0.58 | 0.69 | 0.76 | 0.59 | 0.40 | 0.53 |
| F | - | -0.39 | -0.00 | 0.30 | -0.18 | -0.29 | 0.11 | 0.35 |
P2 | Na | 1 | 3 | 3 | 4 | 8 | 4 | 3 | 5 |
| Ne | 1.00 | 1.76 | 2.24 | 3.23 | 3.74 | 1.90 | 1.34 | 2.13 |
| I | 0.00 | 0.74 | 0.94 | 1.28 | 1.58 | 0.88 | 0.50 | 0.97 |
| Ho | 0.00 | 0.50 | 0.57 | 0.55 | 0.68 | 0.33 | 0.19 | 0.47 |
| He | 0.00 | 0.43 | 0.55 | 0.69 | 0.73 | 0.47 | 0.25 | 0.53 |
| uHe | 0.00 | 0.45 | 0.57 | 0.72 | 0.75 | 0.49 | 0.26 | 0.55 |
| F | - | -0.16 | -0.03 | 0.21 | 0.07 | 0.29 | 0.25 | 0.11 |
P3 | Na | 1 | 3 | 2 | 4 | 4 | 4 | 3 | 3 |
| Ne | 1.00 | 2.18 | 1.60 | 2.94 | 2.67 | 3.60 | 1.47 | 2.32 |
| I | 0.00 | 0.89 | 0.56 | 1.22 | 1.13 | 1.33 | 0.60 | 0.92 |
| Ho | 0.00 | 0.83 | 0.50 | 0.80 | 1.00 | 1.00 | 0.38 | 0.33 |
| He | 0.00 | 0.54 | 0.38 | 0.66 | 0.63 | 0.72 | 0.32 | 0.57 |
| uHe | 0.00 | 0.59 | 0.41 | 0.73 | 0.68 | 0.87 | 0.34 | 0.62 |
| F | | -0.54 | -0.33 | -0.21 | -0.60 | -0.39 | -0.17 | 0.42 |
P1− Exotic pigs; P2− NP; P3− Crosses; Na = Mean number of alleles; Ne = Effective number of alleles; I = Shannon's Information Index; Ho = Observed Heterozygosity; He = Expected Heterozygosity; uHe = Unbiased Expected Heterozygosity; F = Fixation Index |
The mean number of effective allele (Ne) was 2.22 ± 0.17. SW122 marker had the highest Ne 3.43 ± 0.39, Sharon index (I) 1.44 ± 0.16, Observed heterozygocity (Ho) 0.85 ± 0.09, expected heterozygosity (He) 0.70 ± 0.03 and uHe 0.73 ± 0.02 as shown in Table 3, while the lowest was S01001 because it was monomorphic. The Ne ranged (1.00 to 3.43) obtained in this study was lower than the one obtained for Brazilian pig that ranged from 1.17 to 8.84 as reported by Sollero et al. (2008), Ghanian pigs ranged from 5.23 to 5.71 (Ayizanga et al., 2016); Thai Pig ranged from 2.62 to 7.15 (Rangusun et al., 2019).
The means obtained in this study for Ho and He were 0.529 and 0.501 respectively. These results were closer to values (0.51 and 0.53) obtained for Berkshire (Jay Don Ho et al., 2014a) and 0.54 and 0.54 (Jay Don Ho et al., 2014b). IThe values are higher than the Philippine pig values of 0.30 and 0.40 (Jay Don Ho et al., 2014b). Higher values were reported for Ghanian pig 0.467 and 0.711 (Ayizanga et al., 2016); 0.68 and 0.67 for Jeju pigs (Jay Don Ho et al., 2014); Thai pigs were 0.679 and 0.710 (Rangsun Charoensook et al., 2019); Portuguese pigs were 0.667 and 0.621 (Vincente et al., 2007); 0.576 and 0.697 for Iberian pigs (Fabuele et al., 2004); 0.534 and 0.696 for Mexican pigs (Chaiwatanasin et al., 2001).
The P1 had the highest Ne, I and He within the three populations, P3 had the highest Ho and uHe. The P2 had the least figures in all with the exception of F as shown in Table 5. The Ne is an important genetic variation parameter that determines alleic diversity among the breeds. It also determines the diversity of the MSM polymorphism. The Ho values were higher than He in 4 loci (SW026, S009, SW122, S0226) while He was higher than Ho in 3 (SW24, S0227 and SW632). It has been reported that He higher than Ho revealed the existence of population structure (Jyoshi et al., 2012). It has also been proved that He had been widely used as most parameters to measure the genetic diversity across and within the populations (Adeoye et al., 2021). Ho and He are one of the parameters used for selection of MSM for pig breed identification (Oh et al., 2014). Takezaki et al. (1996) and Oh et al. (2014) reported that markers can only be useful for measuring genetic variation, when they have an average heterozygosity between 0.3 and 0.8 in the population. Therefore, from this study Ho and He ranged from 0.30 to 0.85 and 0.32 to 0.70 respectively that made the markers good enough for diversity study. The Shannon information index (I) determines the genetic diversity in the populations. The low value range of I show low genetic diversity between the 3 populations.
Table 5
Mean over Loci for the Three Populations
Pn | Na | Ne | I | Ho | He | uHe | F | Private alleles |
P1 | 4.00 ± 0.70 | 2.27 ± 0.31 | 0.91 ± 0.16 | 0.50 ± 0.10 | 0.49 ± 0.08 | 0.51 ± 0.08 | -0.01 ± 0.10 | 6 |
P2 | 3.88 ± 0.72 | 2.17 ± 0.32 | 0.86 ± 0.0.17 | 0.41 ± 0.08 | 0.46 ± 0,08 | 0.47 ± 0.09 | 0.11 ± 0.06 | 6 |
P3 | 3.00 ± 0.38 | 2.22 ± 0.30 | 0.83 ± 0.15 | 0.61 ± 0.13 | 0.48 ± 0.08 | 0.53 ± 0.10 | -0.26 ± 0.12 | 1 |
P1− Exotic pigs; P2− NP; P3− Crosses; Na = Mean number of alleles; Ne = Effective number of alleles; I = Shannon's Information Index; Ho = Observed Heterozygosity; He = Expected Heterozygosity; uHe = Unbiased Expected Heterozygosity; F = Fixation Index |
Departure from Hardy-Weinberg equilibrium (HWE) was tested across the 3 populations within the loci studied. There was significant deviations from HWE observed in Locus S0226, S0227 (P < 0.05) and S0632 (P < 0.001) for P1; SW122, S0632 (P < 0.001) and S0126 (P < 0.05) locus for P2; while others were non-significant as shown in Table 6.
Table 6
Hardy-Weinberg Equilibrium (HWE) at Various Loci Across Population
Pop | Locus | DF | ChiSq | Prob | Signif |
P1 | loci 1 S01001 | Monomorphic | | | |
P1 | loci 2 SW26 | 3 | 3.645 | 0.302 | ns |
P1 | loci 3 S009 | 6 | 3.008 | 0.808 | ns |
P1 | Loci 4 SW24 | 6 | 9.028 | 0.172 | ns |
P1 | Loci 5 SW122 | 28 | 24.802 | 0.639 | ns |
P1 | Loci 6 S0226 | 6 | 13.343 | 0.038 | * |
P1 | Loci 7 S0227 | 3 | 10.721 | 0.013 | * |
P1 | Loci 8 SW632 | 10 | 39.574 | 0.000 | *** |
P2 | loci 1 S01001 | Monomorphic | | | |
P2 | loci 2 SW26 | 3 | 1.880 | 0.598 | ns |
P2 | loci 3 S009 | 3 | 1.074 | 0.783 | ns |
P2 | Loci 4 SW24 | 6 | 7.052 | 0.316 | ns |
P2 | Loci 5 SW122 | 28 | 65.540 | 0.000 | *** |
P2 | Loci 6 S0226 | 6 | 15.169 | 0.019 | * |
P2 | Loci 7 S0227 | 3 | 4.343 | 0.227 | ns |
P2 | Loci 8 SW632 | 10 | 34.723 | 0.000 | *** |
P3 | loci 1 S01001 | Monomorphic | | | |
P3 | loci 2 SW26 | 3 | 3.061 | 0.382 | ns |
P3 | loci 3 S009 | 1 | 0.667 | 0.414 | ns |
P3 | Loci 4 SW24 | 6 | 5.800 | 0.446 | ns |
P3 | Loci 5 SW122 | 6 | 6.000 | 0.423 | ns |
P3 | Loci 6 S0226 | 6 | 4.500 | 0.609 | ns |
P3 | Loci 7 S0227 | 3 | 0.426 | 0.935 | ns |
P3 | Loci 8 SW632 | 3 | 2.907 | 0.406 | ns |
Key: ns = not significant, * P < 0.05, ** P < 0.01, *** P < 0.001; |
P1−Exotic pigs; P2− Nigerian indigenous Pig; P3− Crosses; Pop- Population; DF− Degree of freedom, Chisqd−Chisqare; Proba− Probability; Sign− Significance; |
The F-statistics showed the reduction in heterozygosity at various loci across the population studied i.e Fis, Fit and Fst as shown in Table 7. The mean values for Fis and Fit were − 0.06 ± 0.08 and − 0.02 ± 0.08, respectively. The Fis values ranged from − 0.017 (S0026) to 0.119 (SW24) while the Fit ranged from − 0.034 (SW122) to 0.174 (SW24). The Fst value ranged from 0.01 at locus S0027 and 0.07 at locus SW227 as shown in Table 7. The mean Fst (0.04) can be translated to 4% and 96% for among/inter-population and within/intra-population variation respectively. The FST values up to 0.05 indicate negligible genetic variations, while values greater than 0.25 indicate large genetic differentiation among populations (Weir and Cockerham, 2014; Awobajo et al., 2022). This also show the low genetic variations among the populations studied. The mean level of gene flow (Nm) among the population was estimated to be 9.18 ± 3.59 (Table 7). The pairwise Fst values among the three populations were also ranged from 0.02 to 0.04 (Table 8).
Table 7
Genetic Differentiation by Reduction in Heterozygosity Due to Inbreeding
F-statistics Parameters | Loci 1 S01001 | loci 2 SW026 | loci 3 S009 | Loci 4 SW024 | Loci 5 SW122 | Loci 6 S0226 | Loci 7 S0227 | Loci 8 SW632 | Mean |
Fis | - | -0.38 | -0.10 | 0.10 | -0.22 | -0.17 | 0.06 | 0.29 | -0.06 ± 0.08 |
Fit | - | -0.347 | -0.071 | 0.14 | -0.14 | -0.09 | 0.06 | 0.32 | -0.02 ± 0.08 |
Fst | - | 0.02 | 0.02 | 0.04 | 0.06 | 0.07 | 0.01 | 0.04 | 0.04 ± 0.01 |
Nm | - | 10.98 | 10.26 | 6.25 | 3.78 | 3.29 | 32.70 | 6.20 | 9.18 ± 3.59 |
FIS = reduction in heterozygosity due to inbreeding within each population; FIT = reduction in heterozygosity due to total inbreeding for each locus; FST = Genetic differentiation among the population; Nm = Limited gene flow among the population. |
Table 8
Pairwise Population Fst Values
P1 | P2 | P3 | |
0.00 | | | P1 |
0.02 | 0.00 | | P2 |
0.03 | 0.04 | 0.00 | P3 |
P1− Exotic pigs; P2− Nigerian indigenous Pig; P3− Crosses |
Table 8 shows the pairwise Fst values among the 3 populations ranged from 0.02 to 0.04. These values almost corroborated with mean value of Fst (0.04) result obtained (Table 7).
Table 9 show the Pairwise Population Matrix of Nei Genetic Distance (below diag-onal) and Pairwise Population Matrix of Nei Genetic Identity (above diagonal) among the 3 pig populations. The genetic similar coefficients varied from 0.98 to 1.01 with an average of 0.99. The Genetic distances between the three pigs were 0.02 (Exotic and NIP), 0.01 (NIP and Crosses) and 0.00 (Exotic and crosses) respectively. This shows that the crosses were hybrid of the exotic pigs and not of the NIP.
Table 9
Pairwise population matrix of Nei’s genetic distance and identity
P1 | P2 | P3 | |
0.00 | 0.98 | 1.01 | P1 |
0.02 | 0.00 | 0.99 | P2 |
0.00 | 0.01 | 0.00 | P3 |
P1− Exotic pigs; P2− Nigerian indigenous Pig; P3− Crosses; Upper diagonal - Genetic Identity, Lower diagonal - Genetic Distance |
A phylogenetic tree was estimated based on the equation of Nei et al. (1983), by the distribution of allele sharing by genetic distance (D) using POPTREE2 software. Figure 2 shows that the three pig populations originated from the same ancestor and branched into two where Exotic and crosses clustered together while the NIP clustered alone.
Figure 3 shows the outcome of the PCA conducted among the three pig populations in this study. The principal coordinate plot show clear clustering of Commercial pigs consisting of exotic, hybrids and Southwestern Nigerian indigenous pig. Percentage of variation explained by the first 3 axes were in 33.45, 47.04 and 59.23 percentages respectively. All the breeds dispersed well in all the coordinates as seen in Fig. 3.