Identification of single-nucleotide variants associated with susceptibility to Salmonella in pigs using a genome-wide association approach

Table 2 The top 15 SNVs ranked by significance (p value) for the GWAS analysis of Salmonella shedding from weaning to end of finisher

SNV ID	SSC^a	Location (bp)^b	Variant type	Gene^c	Gene location^b	p-value^d
rs324041697	2	14,596,159	intron	PTPRJ	2: 14549537–14,726,715	6.6 × 10⁻⁶
rs81476180	6	136,607,113	intergenic	ST6GALNAC3	6: 136633437–137,201,213	9.9 × 10⁻⁶
rs81259485	16	3,248,143	intron	DNAH5	16: 3116189–3,364,956	6.6 × 10^− 5
rs81458700	16	36,370,940	intergenic	ACTBL2	16: 36470503–36,471,633	9.9 × 10^− 5
rs80889714	4	104,920,198	intron	CASQ2	4: 104918501–104,982,852	1.0 × 10^− 4
rs81346930	17	44,032,145	intergenic	LPIN3	17: 43993710–44,006,188	1.2 × 10⁻⁴
rs330624049	15	90,476,754	intergenic	ENSSSCG00000034554	15: 90309385–90,309,702	1.2 × 10⁻⁴
rs81403742	8	117,467,555	intergenic	TACR3	8: 117661792–117,721,591	1.2 × 10⁻⁴
rs80947769	7	19,456,263	upstream	KIAA0319	7: 19386111–19,451,666	1.2 × 10⁻⁴
rs339478050	1	188,917,080	intron	RTN1	1: 188704139–188,926,054	1.9 × 10⁻⁴
rs81237965	3	3,693,136	intron	RADIL	3: 3618093–313,033	1.9 × 10⁻⁴
rs81344023	6	153,022,279	intron	FGGY	6: 152754730–153,213,125	2.1 × 10⁻⁴
rs81349902	1	188,903,236	intron	RTN1	1: 188704139–188,926,054	2.3 × 10⁻⁴
rs318950111	3	43,561,730	downstream	ZNF169	3: 43513397–43,558,613	2.5 × 10⁻⁴
rs81452423	15	32,935,177	intergenic	DLGAP2	15: 33173120–33,264,155	3.0 × 10⁻⁴

^aSSC = Sus scrofa chromosome
^bLocation in Ensembl Sscrofa11.1
^cIf the variant was intergenic, the closest gene within a 1 Mbp window was indicated
^dSNVs under the suggestive significance threshold of 1.0 × 10⁻⁵ in bold [39]

ISSN: 1746-6148