Genome-wide association study for the level of prolificacy in Cameroon’s native goat

Figures & data

Figure 1. QQ plot of the GWAS for prolificacy in CNG.

Figure 2. Manhattan plot of GWAS for prolificacy. The red line is a subjective line at −log10 (p) where p = 3 × 10⁻³.

Table 1. List of the first top 20 SNPs markers and their characteristics ranked according to the p-value from the GWAS output for prolificacy in CNG.

SNP ID	CHR and location	Marker in LD	A1	F_A	F_U	A2	CHISQ	P-value	OR	Gene	Consequence, allele and MAF
rs268285661	5: 7499977	NA (Nonavailable)	A	0.23810	0.066270	B	10.900	0.0009599	4.4030	No	An intergenic variant, G/A |Highest population MAF: 0.38
rs268235169	30: NA	NA	A	0.33330	0.132500	B	9.443	0.0021190	3.2730	NA	NA (This variant has not been mapped), A/G
rs268236449	5: 117202064	2 with 1 (rs667165956 r² = 0.91) and 1 (rs636631477 r² = 0.89)	B	0.09524	0.012050	A	8.281	0.0040070	8.6320	No	Intergenic variant, T/C, Highest population MAF: 0.46
rs268235135	8: 106876093	6 with 1 (r² = 0.949), 1 (r² = 0.928), 1 (r² = 0.891), 2 (r² = 0.845) and 1 (r² = 0.834)	A	0.09524	0.012050	B	8.281	0.0040070	8.6320	No	Intergenic variant,T/C MAF: 0.48
rs268240394	2: 25126120	No	B	0.07143	0.006024	A	7.602	0.0058290	12.6900	SGPP2 sphingosine-1-phosphate phosphatase 2	Intron variant This variant overlaps 2 transcripts, T/C MAF: 0.44
rs268283635	8: 24555691	5 with 1 (rs669900054, r² = 0.88), (rs635913080, r² = 0.90), 1 (rs657282594, r² = 0.87), 1 (rs636067376, r² = 0.84), 1 (rs651661880, r² = 0.85)	A	0.07143	0.006024	B	7.602	0.0058290	12.6900	SLC24A2 (NCKX2) Solute carrier family 24 member 2	Intron variant, G/A MAF: 0.40
rs268251678	9: 67655912	1 (rs640527186, r² = 0.855) located in gene AIG1 see LD plot	B	0.07143	0.006024	A	7.602	0.0058290	12.6900	AIG1, Androgen-Induced Gene 1	Intron variant, C/T, MAF: 0.38
rs268267018	14: 35172825	6 with 1 (r² = 0.984); 1 (r² = 0.983); 2 (r² = 0.968); 1 (r² = 0.951) and 1 (r² = 0.966)	B	0.07143	0.006024	A	7.602	0.0058290	12.6900	No	An intergenic variant, G/A|Highest population MAF: 0.30
rs268239617	15: 69420599	1, rs665520977, (r² = 0.99)	A	0.07143	0.006024	B	7.602	0.0058290	12.6900	No	An intergenic variant, G/A|Highest population MAF: 0.30
rs268281364	30: NA	NA	B	0.07143	0.006024	A	7.602	0.0058290	12.6900	NA	NA (This variant has not been mapped), G/T
rs268273029	12: 66327680	NA	A	0.07143	0.006098	B	7.495	0.0061860	12.5400	No	Intergenic variant, A/G, (MAF: NA)
rs268278194	1: 24717248	28 with 10 (r² = 1), 3 (r² = 0.971–0.986), 2 (r² = 0.928–0.931) and 13 (r² = 0.815–0.819)	A	0.25000	0.487800	B	7.376	0.0066100	0.3500	No	An intergenic variant, G/A|Highest population MAF: 0.45
rs268286941	12: 43032606	No	A	0.62500	0.396300	B	6.820	0.0090160	2.5380	No	An intergenic variant, T/C|Highest population MAF: 0.40
rs268271762	28: 11009847	No	B	0.20000	0.421700	A	6.733	0.0094640	0.3429	No	An intergenic variant, G/A, Highest population MAF: 0.40
rs268236144	12: 52989493	2 with 1 (r² = 0.985) and 1 (r² = 0.971) all located in gene ATP8A2, close to a deletion site at 30 bp	A	0.15000	0.042170	B	6.339	0.0118100	4.0080	ATP8A2 (ATPase phospholipid transporting 8A2)	Intron variant, G/A
rs268244753	3: 49881475	1, rs638895445,r² = 0.965	A	0.00000	0.148100	B	6.069	0.0137600	0.0000	No	Intergenic variant, A/G 0.50
rs268233233	15: 75656786	4, with 3 (r² = 1) and 1 (r² = 0.835)	A	0.16670	0.054220	B	5.969	0.0145600	3.4890	CEP126, (Centrosomal Protein 126)	Intron variant, C/T MAF: 0.47
rs268289122	28: 44019692	NA	B	0.17500	0.378000	A	5.923	0.0149400	0.3490	No	intergenic variant, T/C
rs268286759	26: 44499732	6 with 2 (r² = 1), 2 (r² = 0.976, one in splice region variant) and 2 (r² = 0.975 all in intron except one)	B	0.07500	0.250000	A	5.822	0.0158300	0.2432	PRKG1 (Protein Kinase CGMP-Dependent 1)	Intron variant , T/C|Highest population MAF: 0.45
rs268278159	8: 33816602	8 with 5 (r² = 1), 1 (r² = 0.987), 1 (r² = 0.928) and 1 (r²= 0.908) all intergenic variant	A	0.14290	0.042170	B	5.800	0.0160300	3.7860	No	Intergenic variant, C/T |Highest population MAF: 0.50

CHR = chromosome code, Rs = variant identifier, BP = base-pair coordinate, A1 = allele 1 (usually minor), F_A = allele 1 frequency among cases, F_U = allele 1 frequency among controls, A2 = frequency of allele 2, CHISQ = allelic test Chi-square statistic, OR =   odd ratio.

Figure 3. Study zone. Source: Adapted from PNGE (2009).

Table 2. Evolution of the number of loaded SNPs per chromosome after quality control and pruning.

Chromosome	Initial SNP	SNP after quality control	Pruned SNP	Remaining SNP
1	3238	1271	1159	112
2	2850	1072	979	93
3	2381	955	874	81
4	2415	977	889	88
5	2243	825	757	68
6	2437	934	847	87
7	2192	903	820	83
8	2352	927	867	60
9	1894	749	691	58
10	2098	808	733	75
11	2138	796	730	66
12	1749	622	562	60
13	1649	649	591	58
14	1912	724	657	67
15	1639	628	580	48
16	1592	659	598	61
17	1469	584	534	50
18	1292	468	428	40
19	1229	466	429	37
20	1495	608	571	37
21	1430	549	498	51
22	1169	468	431	37
23	1047	414	372	42
24	1324	509	461	48
25	855	337	302	35
26	1044	414	379	35
27	914	396	364	32
28	929	392	354	38
29	977	347	314	33
30 (X)	1987	629	596	33
Total	51,940	20,080	1,8367	1713

PNGE. 2009. Révision/Opérationnalisation du Plan National de la Gestion de l’Environnement (PNGE) vers un Programme Environnement (PE). Diagnostic de la situation de l’environnement au Cameroun, Diagnostic de la situation de l’environnement au Cameroun. p. 109.

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Data availability statement

All data generated or analysed during this study are included in this published article and its supplementary information files. However, data might be commercially sensitive and any further use will require reasonable request with permission from the corresponding author (KOUAM SIMO).