Detection and replication of QTL underlying resistance to gastrointestinal nematodes in adult sheep using the ovine 50K SNP array

Table 1 Significant chromosome-wise QTL detected by linkage analysis (LA)

Trait^a	OAR^b	Across-family analysis				Within-family analysis
Trait^a	OAR^b	Pos of max LRT (cM)^c	P_c-value^d	CI (cM)^e TGI (Mb)^f	Positional candidate genes involved in immune response^g	Segregating family identifier (Pos of max LRT)^h	CI (cM)ⁱ	Size effect trait units (SD units)^j
LFEC	6	88.1	<0.05	80.8–91.4	AFP, ALB, AMBN, AMTN, AREG, BTC, CXCL1, CXCL10, CXCL11, CXCL9, EREG, GC, IGJ, IL8, MUC7, PF4, PPBP, RASSF6, SCARB2, TMPRSS11D	Fam. 1 (94.9)	70.0–96.8	0.468 ± 0.015 (0.30)
						Fam. 7 (90.6)	80.4–94.8	−0.499 ± 0.012 (0.32)
						Fam. 11 (86.7)	76.4–96.4	−0.777 ± 0.029 (0.50)
	8	2	<0.05	1–3.4	CD109, COL12A1, MYO6	Fam. 4 (31.2)	25.4–35.8	1.218 ± 0.024 (0.78)
						Fam. 11 (1.8)	0–2.9	0.738 ± 0.024 (0.47)
IgA_t	22	3.4	<0.05	0.3–5.8	PCDH15	Fam. 8 (6.4)	0.3–9.9	0.527 ± 0.046 (0.68)

^aAnalyzed traits: LFEC log-transformed faecal egg count, IgA _t Box-Cox-transformed optical density ratio (ODR) values of immunoglobulin A activity
^b OAR ovine chromosome
^{c, h}Position of the chromosome (in centiMorgans) at which the maximum likelihood ratio test of the LA is reached in the analysis involving the 14 half-sib families included in this work (across-family analysis) or the individual analysis of the segregating families (those showing a P_c-value <0.05 in the within-family analysis), respectively
^d P _c -value Chromosome-wise significance P-value established through 1000 permutation analysis
^e,i CI Confidence interval (in cM) estimated from the position of the max LRT for the across-family analysis and the within-family analyses, respectively, following the 1-LOD-drop-off method [38]
^f TGI Target genomic interval (Mb) defined as the corresponding genomic region, according to the sheep reference genome assembly Oar_v3.1, to the CI estimated for the LA significant QTL
^gPositional candidate genes included in the CI of the corresponding QTL that were highlighted by the immune response candidate gene survey performed in the present work as potential functional candidates
^jEstimated size effect of the QTL identified in the within-family analysis expressed in trait units (Yield Deviations of IgA_t) and in phenotypic SD of the trait (in brackets)

ISSN: 1297-9686