New genetic identification and characterisation of 12 Algerian sheep breeds by microsatellite markers

Figures & data

Figure 1. Geographic distribution of sheep breeds studied in the Algerian territory.

Table 1. Origin and sample size of 12 sheep breeds raised in Algeria.

Breeds	Abbreviation	N	Origin of samples
Barbarine	BB	21	Oued-Souf, Saïda
Ouled djellal	OJ	36	In the 40 provinces visited
Ifilene	IL	11	Illizi, Tamenrasset, Laghouat, Adrar, Bechar
Srandi	SR	13	All provinces except Southern Algeria (Tindouf, Adrar, Béchar, Ouargla,Illizi, Tamenrasset, Ouargla, OuedSouf, Gharaïa)
Darâa	DR	10	40 provinces visited
Rembi	RB	42	Tiaret, Nâama, Djelfa, Ain-témouchent, Laghouat
Berbere	BR	24	El-Tarf, Souk-Ahras, Skikda, Annaba, Tlemcen
Taâdmit	TD	29	Relizane, Nâama, Djelfa
Hamra	HR	30	Saïda, Nâama, ElBayadh, Souk-Ahras, Tébessa, El-Tarf
Sidaou	SD	30	Illizi, Tamenrasset, Laghouat, Adrar, Bechar
Tazegzawt	TG	30	Béjaia, Tizi-Ouzou, Nâama
D’men	DM	20	Adrar, Bechar, Ouargla
Total		296

Table 2. Details of considered microsatellite loci.

Multiplex group	Primer name	Primer sequence	Chr. no.	Allelic range (bp)		Label
				ISAG	FAO
M1	OarFCB193	TTCATCTCAGACTGGGATTCAGAAAGGC	11		96–136	D3
		GCTTGGAAATAACCCTCCTGCATCCC
	OarFCB304	CCCTAGGAGCTTTCAATAAAGAATCGG	19	148–190	150–188	D3
		CGCTGCTGTCAACTGGGTCAGGG
	INRA0023	GAGTAGAGCTACAAGATAAACTTC		201–219	195–225	D3
		TAACTACAGGGTGTTAGATGAACTC
	OarCP34	GCTGAACAATGTGATATGTTCAGG	3		112–130	D4
		GGGACAATACTGTCTTAGATGCTGC
	INRA0132	AACATTTCAGCTGATGGTGGC	20	152–172		D4
		TTCTGTTTTGAGTGGTAAGCTG
	D5S2	TACTCGTAGGGCAGGCTGCCTG		190–210		D4
		GAGACCTCAGGGTTGGTGATCAG
	BM1818	AGCTGGGAATATAACCAAAGG	20	258–270	248–278	D4
		AGTGCTTTCAAGGTCCATGC
M2	BM8125	CTCTATCTGTGGAAAAGGTGGG	17		110–130	D3
		GGGGGTTAGACTTCAACATACG
	McM0527	GTCCATTGCCTCAAATCAATTC	5	165–179	165–187	D3
		AAACCACTTGACTACTCCCCAA
	CSRD0247	GGACTTGCCAGAACTCTGCAAT	14	209–261	220–247	D3
		CACTGTGGTTTGTATTAGTCAGG
	OarFCB128	ATTAAAGCATCTTCTCTTTATTTCCTCGC	2		96–130	D2
		CAGCTGAGCAACTAAGACATACATGCG
	BM1329	TTGTTTAGGCAAGTCCAAAGTC	6	145–161	160–182	D2
		AACACCGCAGCTTCATCC
	HSC	CTGCCAATGCAGAGACACAAGA	20	267–301		D2
		GTCTGTCTCCTGTCTTGTCATC
	OarJMP29	GTATACACGTGGACACCGCTTTGTAC	24		96–150	D4
		GAAGTGGCAAGATTCAGAGGGGAAG
	MAF214	GGGTGATCTTAGGGAGGTTTTGGAGG	16	181–265	174–282	D4
		AATGCAGGAGATCTGAGGCAGGGACG

Table 3. Thermal cycling conditions according to touchdown PCR.

Loci	Multiplex group	First denaturation	Denaturation	Annealing	Extension	Cycle	Final extension
OarFCB193	1	95 °C (5 min)	95 °C (40 s)	63–54 °C (40 s)	72 °C (60 s)	40	72 °C (10 min)
OarFCB304
INRA0023
OarCP34
INRA0132
D5S2
BM1818
BM8125	2	95 °C (5 min)	95 °C (40 s)	60–50 °C (40 s)	72 °C (60 s)	34	72 °C (10 min)
McM0527
CSRD0247
OarFCB128
BM1329
HSC
OarJMP29
MAF214

Table 4. Genetic polymorphism parameters at 15 microsatellite loci in Algerian sheep population.

Loci	N	Allelic range, bp	Na	Ne	PIC	Ho	He	Ĥ	FIS^a	FIT^a	FST^a	DST	GST	HT	Nm*	HWE	F(Null)
OARFCB193	293	88–138	22	6.29	0.88	0.73	0.89	0.83	0.146	0.210	0.075	0.028	0.038	0.896	3.07	***	0.095
OARFCB304	289	140–192	26	7.08	0.89	0.73	0.90	0.84	0.115	0.162	0.054	0.011	0.016	0.893	4.41	***	0.102
INRA0123	295	191–229	21	8.06	0.91	0.93	0.92	0.86	–0.092	–0.027	0.059	0.024	0.028	0.914	4.00	***	–0.009
OARCP34	293	100–134	19	5.79	0.85	0.83	0.87	0.81	–0.033	0.027	0.058	0.020	0.025	0.866	4.08	***	0.022
INRA0132	294	142–184	21	8.34	0.91	0.86	0.92	0.87	0.01	0.063	0.054	0.020	0.020	0.921	4.38	***	0.029
D5S2	290	160–216	20	6.18	0.88	0.70	0.89	0.82	0.022	0.101	0.081	0.036	0.048	0.897	2.83	***	0.061
BM1818	276	242–296	28	10.25	0.93	0.74	0.94	0.89	0.147	0.196	0.057	0.017	0.015	0.941	4.11	***	0.115
BM8125	295	100–138	20	7.61	0.89	0.89	0.9	0.85	–0.059	–0.012	0.044	0.012	0.013	0.894	5.37	***	0.004
MCM0527	285	151–191	21	6.61	0.87	0.79	0.88	0.84	0.081	0.122	0.044	0.009	0.005	0.884	5.47	***	0.056
CSRD0247	284	199–263	33	6.48	0.9	0.80	0.91	0.81	0.008	0.097	0.089	0.042	0.055	0.897	2.54	***	0.062
OARFCB128	293	94–136	22	6.47	0.88	0.84	0.89	0.83	0.021	0.081	0.061	0.017	0.027	0.887	3.84	***	0.030
BM1329	293	126–194	23	9.67	0.92	0.85	0.93	0.89	0.053	0.096	0.045	0.005	0.009	0.932	5.30	***	0.045
HSC	277	261–311	25	10.02	0.92	0.82	0.93	0.89	0.113	0.153	0.045	0.001	0.003	0.93	5.32	***	0.061
OARJMP29	295	94–162	34	7.76	0.89	0.89	0.90	0.85	–0.042	0.003	0.043	0.004	0.011	0.897	5.57	*	0.006
MAF214	296	179–257	32	5.60	0.84	0.82	0.86	0.80	–0.01	0.044	0.053	0.012	0.02	0.854	4.47	***	0.020
Mean			24.46	7.48	0.89	0.82	0.90	0.85	0.032	0.088	0.057	0.017	0.022	0.90	4.32

BB: Barbarine; OJ: Ouled djellal; IL: Ifilene; SR: Srandi; DR: Darâa; RB: Rembi; BR: Berbere; TD: Taâdmit; HR: Hamra; SD: Sidaou; TG: Tazegzawt; DM: D’men.

^a Wright’s statistics according to Weir and Cockerham (1984).

* p<.05.

*** p<.001.

Nm* gene flow estimated from Nm =0.25(1 – F_ST)/F_ST (Nei 1987).

Table 5. Genetic diversity measure according to breed across 15 loci.

Breeds	MNA	Mean heterozygosity		FIS	HWE	NPA
		Ho, SE	He, SE			Freq. ≥5%	Freq. <%5	Total
BB	14.67	0.84 (0.027)	0.87 (0.012)	0.065**	2	1	5	6
OJ	17.80	0.84 (0.020)	0.90 (0.005)	0.084***	5	–	9	9
IL	9.07	0.83 (0.019)	0.82 (0.014)	0.038	1	1	–	1
SR	10.47	0.83 (0.023)	0.84 (0.014)	0.049	1	–	2	2
DR	8.73	0.75 (0.032)	0.83 (0.012)	0.14**	–	1		1
RB	15.80	0.80 (0.026)	0.88 (0.009)	0.100***	7	–	2	2
BR	13.33	0.81 (0.026)	0.86 (0.012)	0.083**	3	1	3	4
TD	13.20	0.82 (0.025)	0.85 (0.008)	0.056	2	–	2	2
HR	14.60	0.85 (0.023)	0.89 (0.006)	0.062	9	–	2	2
SD	13.67	0.83 (0.027)	0.87 (0.009)	0.063	5	–	4	4
TG	14.87	0.84 (0.027)	0.86 (0.014)	0.046	7	–	5	5
DM	12.87	0.82 (0.029)	0.87 (0.008)	0.082*	4	–	3	3

BB: Barbarine; OJ: Ouled djellal; IL: Ifilene; SR: Srandi; DR: Daraa; RB: Rembi; BR: Berbere; TD: Taadmit; HR: Hamra; SD: Sidaou; TG: Tazegzawt; DM: D’men; MNA: mean number of alleles; F_IS: within-breed heterozygote deficiency; HWE: number of loci not in the Hardy–Weinberg equilibrium (p < 0.05); NPA: number of private alleles.

Significant p values (*p < .05, **p < .01, ***p < .001).

Figure 2. Dendrogram based on Nei’s minimum genetic distances among 12 breeds (bootstrap resampling methodology (1000 replicates)). BB: Barbarine; OJ: Ouled Djellal; IL: Ifilene; SR: Srandi; DR: Daraa; RB: Rembi; BR: Berbere; TD: Taadmit; HR: Hamra; SD: Sidaou; TG: Tazegzawt; DM: D’men.

Figure 3. The factorial correspondence analysis (FCA) results showing the relationship between 12 breeds. BB: Barbarine; OJ: Ouled Djellal; IL: Ifilene; SR: Srandi; DR: Daraa; RB: Rembi; BR: Berbere; TD: Taadmit; HR: Hamra; SD: Sidaou; TG: Tazegzawt; DM: D’men.

Figure 4. Estimation of the population structure with different K values (assuming K = 2 and 12). BB: Barbarine; OJ: Ouled djellal; IL: Ifilene; SR: Srandi; DR: Daraa; RB: Rembi; BR: Berbere; TD: Taadmit; HR: Hamra; SD: Sidaou; TG: Tazegzawt; DM: D’men.

Table 6. Nei's genetic identity (above diagonal) and genetic distance (below diagonal).

Pop	BB	OJ	IL	SR	DR	RB	BR	TD	HR	SD	TG	DM
BB	–	0.733	0.750	0.697	0.727	0.776	0.770	0.678	0.655	0.663	0.647	0.658
OJ	0.311	–	0.751	0.849	0.783	0.826	0.854	0.767	0.763	0.785	0.729	0.748
IL	0.287	0.287	–	0.829	0.873	0.779	0.807	0.773	0.636	0.738	0.698	0.633
SR	0.361	0.164	0.187	–	0.887	0.832	0.845	0.770	0.634	0.726	0.717	0.590
DR	0.320	0.245	0.136	0.120	–	0.787	0.844	0.806	0.703	0.736	0.779	0.657
RB	0.253	0.191	0.250	0.185	0.240	–	0.875	0.848	0.715	0.727	0.726	0.729
BR	0.261	0.158	0.214	0.168	0.170	0.134	–	0.888	0.698	0.780	0.768	0.747
TD	0.389	0.265	0.257	0.261	0.216	0.166	0.118	–	0.717	0.760	0.746	0.712
HR	0.424	0.270	0.452	0.456	0.352	0.335	0.359	0.333	–	0.802	0.748	0.810
SD	0.411	0.242	0.305	0.321	0.306	0.320	0.249	0.274	0.221	–	0.833	0.753
TG	0.436	0.316	0.359	0.333	0.250	0.321	0.265	0.293	0.290	0.182	–	0.704
DM	0.418	0.291	0.457	0.528	0.420	0.317	0.292	0.340	0.211	0.284	0.351	–

BB: Barbarine; OJ: Ouleddjellal; IL: Ifilene; SR: Srandi; DR: Daraa; RB: Rembi; BR: Berbere; TD: Taâdmit; HR: Hamra; SD: Sidaou; TG: Tazegzawt; DM: D’men.

Table 7. Estimated posterior probabilities [Ln Pr(X|K)] for different numbers of inferred clusters (K) and ΔK statistics.

K	Ln Pr(X|K)	ΔK
2	–22840.215000	–
3	–22641.230000	30.929336*
4	–22718.215000	3.309221
5	–22529.305000	5.836526
6	–22562.610000	1.523554
7	–22759.805000	0.096637
8	–22971.685000	0.006864
9	–23185.810000	0.681015
10	–22941.185000	2.195144
11	–23501.895000	1.021551
12	–23384.780000	0.196768

The asterisks (*) is explained in the text.

Weir BS, Cockerham CC. 1984. Estimating F-statistics for the analysis of population structure. Evolution. 38:1358–1370.

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