Genetic diversity and phylogenetic relationship estimation of Shanxi indigenous goat breeds using microsatellite markers

Figures & data

Table 1. Primer sequence information of 15 microsatellite loci.

Loci	Chromosome	Primer sequence (5′–3′)	Tm (°C)	FS (bp)	LM
SRCRSP5	21	F: GGACTCTACCAACTGAGCTACAAG R: TGAAATGAAGCTAAAGCAATGC	55	156–178	FAM
OarFCB48	17	F: GAGTTAGTACAAGGATGACAAGAGGCAC R: GACTCTAGAGGATCGCAAAGAACCAG	58	149–173	HEX
CSRD247	14	F: GGACTTGCCAGAACTCTGCAAT R: CACTGTGGTTTGTATTAGTCAGG	58	220–247	FAM
TGLA53	16	F: GCTTTCAGAAATAGTTTGCATTCA R: ATCTTCACATGATATTACAGCAGA	55	126–160	HEX
BM6526	26	F: CATGCCAAACAATATCCAGC R: TGAAGGTAGAGAGCAAGCAGC	56	155–185	HEX
ILSTS087	6	F: AGCAGACATGATGACTCAGC R: CTGCCTCTTTTCTTGAGAG	58	149–165	FAM
INRA063	14	F: GACCACAAAGGGATTTGCACAAGC R: AAACCACAGAAATGCTTGGAAG	58	164–186	FAM
OarFCB20	2	F: GGAAAACCCCCATATATACCTATAC R: AAATGTGTTTAAGATTCCATACATGTG	58	93–112	HEX
BMS1788	4	F: ACGTCCAGATTCAGATTTCTTG R: GGAGAGGAATCTTGCAAAGG	56	80–121	HEX
MCM527	5	F: GTCCATTGCCTCAAATCAATTC R: AAACCACTTGACTACTCCCCAA	59	165–187	FAM
OarHH35	4	F: AATTGCATTCAGTATCTTTAACATCTGGC R: ATGAAAATATAAAGAGAATGAACCACACGG	52	105–146	HEX
OarAE54	25	F: TACTAAAGAAACATGAAGCTCCCA R: GGAAACATTTATTCTTATTCCTCAGTG	58	115–138	HEX
MAF065	15	F: AAAGGCCAGAGTATGCAATTAGGAG R: CCACTCCTCCTGAGAATATAACATG	58	116–158	HEX
BM3412	——	F: GTCCCAGCAGACATCACATG R: ACAAAGAATATGTGCAGCAAGC	58	136–168	FAM
INRA023	3	F: GAGTAGAGCTACAAGATAAACTTC R: TAACTACAGGGTGTTAGATGAACT	58	196–215	FAM

Tm: Annealing temperature; FS: Fragment size; LM: label marker.

Table 2. Genetic diversity of 15 microsatellite locus across five the goat populations in Shanxi province.

Loci	NA	NE	HO	HE	PIC	HWE	F(Null)
BMS1788	11	4.1124	0.7005	0.7578	0.727	NS	0.0394
ILSTS087	13	8.2112	0.9109	0.8793	0.866	NS	−0.0187
OarFCB20	12	3.9616	0.7761	0.7485	0.713	NS	−0.0135
BM3412	20	9.5210	0.9109	0.8961	0.886	NS	−0.0081
OarHH35	17	3.7493	0.8163	0.7342	0.697	**	−0.0629
INRA063	7	4.2549	0.7596	0.7660	0.725	NS	0.0023
OarAE54	13	3.1417	0.5612	0.6826	0.655	***	0.0946
SRCRSP5	18	6.0691	0.7954	0.8363	0.816	NS	0.0253
MAF065	25	8.1871	0.8342	0.8790	0.867	***	0.0253
MCM527	12	3.9517	0.7513	0.7479	0.709	NS	−0.0047
TGLA53	11	4.8993	0.7092	0.7969	0.770	***	0.0593
INRA023	24	9.4391	0.8750	0.8952	0.885	***	0.0094
OarFCB48	12	7.9316	0.8295	0.8750	0.861	***	0.0282
CSRD247	13	6.8858	0.8376	0.8559	0.838	NS	0.0109
BM6526	22	9.1566	0.8808	0.8919	0.881	NS	0.0059
Mean	15.3	6.2315	0.7966	0.8162	0.793	——	——

N_A: mean number of alleles; N_E: effective number of alleles; H_O: observed heterozygosity; H_E: expected heterozygosity; PIC: polymorphic information content; HWE: Hardy-Weinberg equilibrium test; F(Null): Estimated null allele frequency; ** = significant at the 1% level, *** = significant at the 0.1% level, NS: not significant.

Table 3. Genetic diversity of the five goat populations.

	NA	NE	HO	HE	PIC
LCBG	11.13 ± 3.48	5.81 ± 2.39	0.82 ± 0.15	0.80 ± 0.09	0.77 ± 0.10
LLBG	11.27 ± 3.9	5.87 ± 1.88	0.83 ± 0.10	0.82 ± 0.06	0.79 ± 0.07
YCWG	9.93 ± 3.33	5.68 ± 2.29	0.81 ± 0.11	0.80 ± 0.09	0.77 ± 0.10
LQGB	10.47 ± 3.27	5.45 ± 2.22	0.81 ± 0.10	0.80 ± 0.06	0.77 ± 0.07
JLCG	10.07 ± 3.47	4.93 ± 1.65	0.76 ± 0.13	0.78 ± 0.08	0.74 ± 0.09

N_A: mean number of alleles; N_E: effective number of alleles; H_O: observed heterozygosity; H_E: expected heterozygosity; PIC: polymorphic information content.

Table 4. Wilcoxon sign rank test to evaluate five populations for mutation drift equilibrium under different models.

Population	p_IAM	p_SMM	p_TPM
LCBG	0.001678	0.98233	0.906189
LLBG	0.000015	0.984924	0.915588
YCWG	0.000031	0.932312	0.532959
LQGB	0.000107	0.98233	0.906189
JLCG	0.000015	0.98233	0.939728

IAM: infinite allele model; SMM: stepwise mutation model; TPM: two-phase model.

Figure 1. Allele frequency distribution of the 15 microsatellite loci.

Table 5. Genetic diversity of the five goat populations.

Loci	FIS	FST	Nm
BMS1788	0.0126	0.0326	7.4161
ILSTS087	−0.0716	0.0266	9.1650
OarFCB20	−0.1144	0.0336	7.1812
BM3412	−0.0734	0.0295	8.2216
OarHH35	−0.1295	0.0257	9.4724
INRA063	−0.0521	0.0255	9.5529
OarAE54	0.1215	0.0323	7.4983
SRCRSP5	0.0410	0.0220	11.0963
MAF065	0.0059	0.0498	4.7668
MCM527	−0.0213	0.0191	12.8283
TGLA53	0.0903	0.0305	7.9380
INRA023	0.0097	0.0357	6.7489
OarFCB48	−0.0243	0.0431	5.5552
CSRD247	−0.0146	0.0311	7.7866
BM6526	−0.0184	0.0178	13.8294
Mean	−0.0159	0.0303	8.6038
SE	0.01770	0.0022	0.6426

F_IS: Inbreeding coefficient within individuals; F_ST: Inbreeding coefficient within subpopulations; Nm: Gene flow.

Table 6. Pairwise differences of F_ST in the five goat populations.

LCBG	LLBG	YCWG	LQGB	JLCG
					LCBG
0.015*					LLBG
0.029*	0.022*				YCWG
0.019*	0.018*	0.030*			LQGB
0.048*	0.044*	0.046*	0.036*		JLCG

Figure 2. UPGMA phylogenetic tree of five sheep populations based on nei’s genetic distance (D_A).

Table 7. Nei’s unbiased measures (1978) of genetic identity and genetic distance.

Pop ID	LCBG	LLBG	YCWG	LQGB	JLCG
LCBG		0.9130	0.8623	0.9113	0.8065
LLBG	0.0910		0.8912	0.9086	0.8133
YCWG	0.1482	0.1151		0.8628	0.8127
LQGB	0.0929	0.0959	0.1475		0.8511
JLCG	0.2151	0.2067	0.2074	0.1612

Nei’s genetic identity (above diagonal) and genetic distance (below diagonal).

Figure 3. Population structure analysis of five goat populations using model-based clustering method. the abscissa value 1, 2, 3, 4 and 5 in Fig. 3(b) represent LCBG, LLBG, YCWG, LQGB, and JLCG, respectively.