Antibiotic treatments and somatic cell count as phenotype to map QTL for mastitis susceptibility in Holstein cattle breed

Figures & data

Table 1. Genome Wide Association Study (GWAS) results: SNPs over the Bonferroni (bold) and False Discovery Rate (FDR) genome wide thresholds (0.05 significance value) together with candidate genes.

QTL n	rs SNP_ID	SNP	Chr	bp	P	-log10 (P)	Gene^a	Tot. N. of SNPs in ± 200,000 bp from significant SNP^b	Upstream gene	Downstream gene
1	rs110002854	BovineHD0100040526	1	140133491	7.79E-06	5.11	DSCAM	13	PCP4
2	rs41255939	BovineHD0100040576	1	140200349	7.79E-06	5.11	DSCAM	14	PCP4
3	rs109241831	BovineHD0400020205	4	72505962	2.37E-06	5.63	intergenic	8	ADAM22, SRI, STEAP4
4	rs43410876	BovineHD0400024205	4	86508557	2.37E-06	5.63	PTPRZ1	9		AASS
5	rs136624841	BovineHD0400024691	4	88411333	1.83E-07	6.74	intergenic	6	SPAM1	TMEM229A
6	rs110017402	ARS-BFGL-NGS-15450	4	104990332	7.79E-06	5.11	WEE2	12	AGK, KIAA1147	SSBP1, TAS2R3, TAS2R4, TAS2R5, PRSS37, OR9A4
7	rs110740218	BovineHD0400033015	4	113478441	7.79E-06	5.11	intergenic	15	TMEM176B, TMEM176A, AOC1	KCNH2, NOS3, ATG9B, ABCB8
8	rs109301545	BovineHD0800022352	8	73389421	1.93E-06	5.71	intergenic	10	EBF2	PPP2R2A
9	rs41257363	Hapmap57092-ss46526915	8	74384468	2.37E-06	5.63	TRIM35	7	STMN4	PTK2B, CHRNA2
10	rs136747884	BovineHD0800022668	8	74425816	2.37E-06	5.63	PTK2B	6	STMN4, TRIM35	CHRNA2, EPHX2
11	rs41668712	Hapmap38552-BTA-99266	8	80228616	7.79E-06	5.11	intergenic	12	GAS1
12	rs134625158	BovineHD1300004878	13	17015829	7.79E-06	5.11	PRKCQ	13
13	rs136055233	BovineHD1300004890	13	17044866	7.79E-06	5.11	PRKCQ	14
14	rs110714783	BovineHD1300009067	13	30887849	7.79E-06	5.11	intergenic	5		PTER, C1QL3, RSU1
15	rs41683068	BovineHD1300009702	13	32964826	7.79E-06	5.11	CACNB2	8		NSUN6, EPC1
16	rs29026933	Hapmap52547-rs29026933	13	33163943	2.37E-06	5.63	EPC1	8	CACNB2	KIF5B
17	rs41568633	BovineHD4100012751	16	74734877	7.79E-06	5.11	intergenic	12
18	rs110512949	BovineHD1600022337	16	75276029	2.03E-11	10.69	PLXNA2	11		CD34
19	rs29017498	BovineHD4100014559	20	16909623	2.37E-06	5.63	IPO11	7		DIMT1, KIF2A
20	rs137039912	BovineHD2300010969	23	38130211	7.79E-06	5.11	intergenic	6	ID4
21	rs43681636	BovineHD2800001676	28	5559644	1.11E-08	7.95	intergenic	10		MAP10
22	rs133891814	BovineHD2800002454	28	8195446	7.79E-06	5.11	B3GALNT2	12	GGPS1, TBCE	GNG4, LYST
23	rs133968650	BovineHD2800002457	28	8199021	7.79E-06	5.11	B3GALNT2	12	GGPS1, TBCE	GNG4, LYST
24	rs137468382	BovineHD2800002736	28	8997685	1.06E-10	9.97	intergenic	4	GPR137B, ERO1B	EDARADD, LGALS8
25	rs133507315	BovineHD2900003304	29	11356071	6.78E-07	6.17	DLG2	8
26	rs137442517	BovineHD2900009666	29	31826445	2.37E-06	5.63	ETS1	9

^aGenes where significative SNPs are located. Intergenic = SNPs located in a genomic region between two genes. ^bList of these SNPs are reported in Table S2.

Figure 1. Experimental design scheme: Susceptible (S1 and S2) and Resistant (R1 and R2) cows in a Selective genotyping and pooling approach.

Figure 2. Graphical representation (Manhattan plot) of Genome Wide Association Study (GWAS) results. Horizontal lines represent the Bonferroni (red line) and the False Discovery Rate (FDR) (blue line) genome wide thresholds, both set at 0.05 significance value.

Figure 3. Scheme of gene functions: underlined genes were those in which significant SNPs mapped (intragenic SNPs – all in intronic positions); the others were nearby-genes (Table 1).

Data availability statement

The data are still under embargo as part of a project still active.