Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis

Usai, Mario Graziano; Casu, Sara; Sechi, Tiziana; Salaris, Sotero L.; Miari, Sabrina; Sechi, Stefania; Carta, Patrizia; Carta, Antonello

doi:10.1186/s12711-019-0508-0

Genetics Selection Evolution

Table 2 Details of the QTL regions that include SNP positions exceeding the 0.05 genome-wide significance threshold

From: Mapping genomic regions affecting milk traits in Sarda sheep by using the OvineSNP50 Beadchip and principal components to perform combined linkage and linkage disequilibrium analysis

QTL region	OAR	Significant SNP (n)	Highest peak		Significant region (Mb)	Max − log10 (p-value)
QTL region	OAR	Significant SNP (n)	SNP name	Pos. (Mb)	Significant region (Mb)	MY	FY	PY	FC	PC
1	1	1	rs422862154	8.20	8.2–8.2				6.4
2	1	3	rs414745902	16.22	15.6–16.3					6.0
3	1	87	rs399459569	38.46	31.1–63.7				9.7	10.0
4	1	2	rs422745101	100.96	100.9–101.0				6.1
5	1	1	rs402912954	136.40	136.4–136.4	6.0	5.8
6	1	10	rs415285988	145.06	142.1–145.3				8.0
7	1	4	rs424147980	168.06	168.1–168.1					7.4
8	1	2	rs430144352	206.80	206.4–206.8				5.9
9	1	2	rs399774250	253.86	253.9–255.8					5.9
10	1	102	rs426289520	261.02	258.1–275.2				6.6	12.2
11	2	1	rs420740052	13.35	13.4–13.4				5.7
12	2	2	rs420647200	16.66	16.7–22.7					6.5
13	2	5	rs406961044	24.31	24.0–27.2	7.2	7.3	6.5		5.7
14	2	1	rs420043297	33.17	33.2–33.2					5.7
15	2	5	rs428251930	71.40	65.4–71.8				5.9	6.6
16	2	8	rs404690479	131.48	130.1–140.8					7.3
17	2	134	rs403115176	207.86	204.9–223.2				5.8	9.6
18	3	1	rs400767835	4.26	4.3–4.3				5.8
19	3	15	rs426591595	24.64	24.4–57.5				6.2	6.6
20	3	63	rs402979168	92.51	75.4–119.4	7.1	6.7	6.9	9.0	7.3
21	3	145	rs414469986	137.31	133.8–144.8				9.2	14.9
22	3	7	rs400309601	179.14	177.4–179.4				6.8
23	3	39	rs425759731	194.13	193.8–209.9				6.7	9.5
24	4	131	rs421815167	12.34	5.9–24.9				14.9	11.8
25	4	52	rs426895887	55.13	30.6–55.3				8.6	7.3
26	4	7	rs414633478	68.14	66.6–78.1				6.1	6.3
27	5	2	rs419528574	10.52	10.5–10.5	7.3
28	5	10	rs414853728	11.45	11.4–14.2				7.1
29	5	27	rs404931334	86.91	72.6–93.1		7.1	6.1	6.9	6.8
30	5	10	rs405537538	101.53	100.1–106.9	6.6
31	6	1	rs416743517	20.87	20.9–20.9				5.7
32	6	1	rs406594979	22.39	22.4–22.4		5.7
33	6	802	rs423823270	85.35	36.2–105.2				11.6	67.0
34	7	12	rs430671311	73.25	45.3–73.3					6.9
35	8	6	rs411259242	9.71	9.7–13.0				6.9
36	8	24	rs404091172	79.80	52.9–84.6					7.9
37	9	1	rs423933809	13.53	13.5–13.5					6.0
38	9	1	rs422093338	14.86	14.9–14.9				5.9
39	9	2	rs425782463	31.11	30.9–31.1				6.1
40	10	7	rs427168327	19.79	18.3–20.2				7.1
41	10	61	rs401955184	55.91	48.6–72.3	9.5	7.0	9.7		9.1
42	10	1	rs415670587	84.94	84.9–84.9				6.3
43	11	48	rs428923302	9.85	0.7–14.2				6.5	9.6
44	11	104	rs425369179	55.43	43.1–60.3	11.6	9.2	10.7	8.1	8.1
45	12	1	rs423006875	13.91	13.9–13.9		5.9
46	12	2	rs404434178	21.98	22.0–33.8				6.1
47	12	29	rs404821945	68.04	51.3–68.1	6.5				7.8
48	13	223	rs406856069	58.58	36.5–73.8	7.4			10.1	13.1
49	13	2	rs418517103	78.12	78.1–78.1			5.9
50	14	23	rs404164762	26.82	11.0–27.3	6.1	7.5	5.8	7.2
51	14	7	rs425723410	50.19	33.9–50.3				7.4
52	15	5	rs414954821	26.17	26.1–32.7				6.5
53	15	3	rs421695633	61.28	56.4–61.3					6.7
54	15	2	rs421043654	76.61	76.6–76.6				5.9
55	16	9	rs412271633	6.04	5.9–25.3				6.9	6.0
56	16	26	rs412025731	27.93	27.9–37.9	8.2	6.8	6.5		6.6
57	16	80	rs428170809	57.10	38.7–63.7				7.0	10.8
58	16	39	rs419400315	70.14	63.7–70.3				6.9	8.8
59	17	30	rs408602480	26.82	8.1–54.7				7.3	7.6
60	18	12	rs418457958	28.75	25.9–34.9				7.9
61	19	27	rs425457738	13.15	6.7–15.3				7.5	8.8
62	19	1	rs406031789	22.79	22.8–22.8					6.1
63	19	3	rs399225729	23.72	23.7–23.8				6.3
64	19	1	rs402952190	25.06	25.1–25.1			5.9
65	20	28	rs422880779	25.70	4.4–35.3				8.6	6.2
66	21	1	rs400264754	20.17	20.2–20.2				5.7
67	21	8	rs418090277	29.32	29.1–30.6				7.4
68	22	1	rs427327212	10.86	10.9–10.9					5.7
69	22	7	rs161480899	18.07	18.0–24.2					7.7
70	22	6	rs399907821	33.75	31.1–38.9				7.4
71	23	6	rs427932340	59.74	51.5–59.9					8.2
72	24	4	rs416153283	17.58	8.4–17.6					7.8
73	24	8	rs422576401	40.36	37.4–40.4					6.3
74	25	18	rs421872239	16.56	11.1–18.9	7.1	7.1	5.8
75	25	1	rs405225833	31.48	31.5–31.5					6.0

QTL, region identifier; OAR, Ovis aries autosomes; Significant SNP (n) number of SNP positions exceeding the 0.05 genome-wide significance threshold [− log10(p-value) > 5.69] for at least for one trait; Highest peak, the most significant SNP across traits; SNP name, Pos. (Mb), name and position in Mb (from the ovine genome assembly v4.0 of the most significant SNP); Significant region (Mb), position in Mb of the first and last significant SNP of the QTL region; Max − log10 (p-value), highest significance per trait among the SNPs within a QTL region exceeding the genome-wide threshold of 0.05; − log10 (p-value), negative logarithm of the p-value corresponding to the null hypothesis that the effects of principal components that explain 99% of the variability due to the Sarda base gametes (BH^S) are zero; MY, milk yield; FY, fat yield; PY, protein yield; FP, fat content; PP, protein content

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