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

Atlija, Marina; Arranz, Juan-Jose; Martinez-Valladares, María; Gutiérrez-Gil, Beatriz

doi:10.1186/s12711-016-0182-4

Genetics Selection Evolution

Table 2 Chromosome-wise significant results (P_c-value <0.01) from the combined linkage disequilibrium and linkage analysis (LDLA)

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

OAR^a	Trait^b	Pos of max LRT^c (cM)	Significant LDLA interval (cM)^d	P_c-value (P_g-value)^e	TGI (Mb)^f	Positional candidate genes involved in immune response^g
1	LFEC	136.9	136.9–143	<0.05	136.9–143	CXADR, NRIP1
	IgA_t	242.4	–	<0.05	242.1–242.5	–
2	LFEC	78.3	–	<0.05	78.17–78.36	–
	IgA_t	188.3	188.01–188.44	<0.05	188.01–188.44	–
3	IgA_t	159.8	–	<0.05	159.67–160.06	–
		177.7	–	<0.05	177.52–177.89	–
4	LFEC	57.9	54–58	<0.05	54–58	DOCK4, IFRD1, LRRN3
	IgA_t	8.9	–	<0.0019 (<0.05)	8.66–9.49	–
5	LFEC	5.2	–	<0.0019 (<0.05)	5.02–5.43	FCHO1, JAK3, MAP1S, UNC13A
		89.9	–	<0.0019 (<0.05)	89.68–90.14	–
6	LFEC	36	–	<0.05	35.84–36.28	–
		72.5	72.3–77.2	<0.0019 (<0.05)	72.3–77.2	–
		89.9	85–90.2	<0.05	85–90.2	ALB, AMBN, AMTN, ANKRD17, AREG, BTC, EREG, IGJ, IL8, PF4, PPBP, RASSF6
7	LFEC	22.8	12.65–25.5	<0.0019 (<0.05)	12.65–25.5	ACIN1, AJUBA, BBS4, CCNB1IP1, CD276, CDH24, CEBPE, CHD8, CIDEB, CMTM5, DAD1, EFS, EMC4, FEM1B, IL25, IRF9, ITGA11, LRP10, LTB4R, MAP2K1, NEO1, NFATC4, NOX5, NPTN, PIAS1, PSMB5, PSME1, PSME2, RIPK3, RNASE2, RNF31, SMAD3, SMAD6, TRAV16, TRAV21, TRAV24, TRAV27, TRAV36DV7, TRAV39, TRAV4, TRAV41, TRAV5, TRDC, TRDV2, TRDV3, UACA, ZNF219, ZWILCH
		36.8	36.8–37.3	<0.05	36.8–37.3	–
		53.3	–	<0.05	53.08–53.46	UNC13C
8	LFEC	2.3	0.3–12.8	<0.05	0.3–12.8	CD109, COL12A1, IBTK, IRAK1BP1, MYO6, PHIP, SNAP91, TPBG
		38.3	37.7–39.2	<0.05	37.7–39.2	–
		49.8	49.59–50.04	<0.05	49.59–50.04	–
		64.1	61.1–64.1	<0.05	61.1–64.1	BCLAF1, CITED2, IFNGR1, IL20RA, IL22RA2, MAP3K5, PERP, TNFAIP3
		71.4	71.2–73.8	<0.0019 (<0.05)	71.2–73.8	PPIL4, STXBP5
9	LFEC	5.8	–	<0.05	5.64–6.03	PRKAR1A
		16.9	–	<0.05	16.75–17.16	–
		24.5	–	<0.05	24.34–24.78	–
		41.7	–	<0.05	41.56–41.96	–
	IgA_t	56.6	55.9–56.6	<0.05	55.9–56.6	TPD52
		67.8	63.4–67.8	<0.05	63.4–67.8	EBAG9
10	LFEC	71.6	–	<0.05	70.01–71.55	–
	IgA_t	27.2	21.5–27.2	<0.05	21.5–27.2	CKAP2, FOXO1, FREM2, POSTN, SMAD9
		52.9	–	<0.05	52.68–53.06	–
		78.6	–	<0.05	78.39–78.8	SLC10A2
11	LFEC	4.2	4.1–4.27	<0.05	4.1–4.27	–
	IgA_t	51.1	45.4–51.1	<0.05	45.4–51.1	ACE, ARHGDIA, B3GNTL1, CD7, CD79B, DDX42, ERN1, FSCN2, GCGR, ICAM2, ITGB3, MAP3K3, MRC2, MYADML2, PSMC5, PSMD12, SMARCD2, SMURF2
12	LFEC	3.6	–	<0.05	3.34–3.84	IKBKE, IL10, MAPKAPK2
12	IgA_t	1.7	–	<0.05	1.52–1.98	LRRN2, MDM4, NFASC
		17.7	–	<0.05	17.56–17.96	–
		72.3	69.5–75.4	<0.05	69.5–75.4	CAMK1G, CD34, CD46, CFHR5, IRF6, LAMB3, TRAF5
13	IgA_t	3.7	3.7–6.3	<0.05	3.7–6.3	–
15	IgA_t	33.6	33.56–33.93	<0.0019 (<0.05)	33.56–33.93	–
		47	47–53.2	<0.05	47–53.2	ARHGEF17, ARRB1, DNAJB13, FCHSD2, FOLR1, IL18BP, INPPL1, PAAF1, PGAP2, RELT, RPS3, STIM1
		70.2	70.06–70.47	<0.0019 (<0.05)	70.06–70.47	–
16	IgA_t	10.5	–	<0.05	10.29–10.74	–
		64.8	63.8–64.8	<0.0019 (<0.05)	63.8–64.8	SEMA5A
17	IgA_t	18.4	14.6–30.1	<0.0019 (<0.05)	14.6–30.1	ELMOD2, IL15, PCDH10, PCDH18, PLK4, UCP1
		36	–	<0.05	35.8–36.22	–
		46	–	<0.05	45.85–46.27	STX2
		62.3	62–66.8	<0.0019 (<0.05)	62–66.8	CMKLR1, CORO1C, HPS4, PIWIL3, PLA2G1B, PXN, RAB35, SART3, SPPL3, TRIAP1, UNG, WSCD2
20	LFEC	4.8	–	<0.05	4.58–5.04	BMP5
21	LFEC	8.1	8.07–8.35	<0.05	8.07–8.35	–
		31.8	31.7–32.24	<0.05	31.7–32.24	–
		43.9	43.7–44.03	<0.05	43.7–44.03	ACTN3, CTSF, SPTBN2
21	IgA_t	17.5	16.5–17.5	<0.0019 (<0.05)	16.5–17.5	GAB2
		46	45.97–46.25	<0.05	45.97–46.25	FGF19
22	IgA_t	6.7	5.3–7.3	<0.05	5.3–7.3	MBL2, PCDH15
		19.5	–	<0.05	19.26–19.85	NKX2-3
23	IgA_t	8.3	–	<0.05	8.15–8.47	–
		23.3	23.3–28.5	<0.05	23.3–28.5	DSC1, DSC2, DSC3, DSG1, DSG2, DSG3, DSG4,
		33.9	32.8–38	<0.05	32.8–38	ADCYAP1, COLEC12, EMILIN2, GATA6, LAMA3, MIB1, NPC1, ROCK1, THOC1, USP14
		45.8	41.7–48.5	<0.05	41.7–48.5	ATP5A1, CIDEA, PIAS2, PSMG2, RALBP1,SIGLEC15, SKOR2, SLC14A1, SMAD2
		54.9	54.56–55.06	<0.05	54.56–55.06	TCF4
24	LFEC	2.2	1.91–2.65	<0.05	1.91–2.65	CLDN6, CLDN9, HCFC1R1, TNFRSF12A
		17.9	–	<0.05	17.68–18.12	UMOD
25	LFEC	37	36.89–37.21	<0.0019 (<0.05)	36.89–37.21	–

^a OAR ovine chromosome
^bAnalyzed traits: LFEC log-transformed faecal egg count, IgA _t Box-Cox-transformed optical density ratio (ODR) values of immunoglobulin A activity
^cPosition of the chromosome (in centiMorgans) at which the maximum likelihood ratio test (LRT) is reached in the LDLA
^dA significant LDLA interval (in centiMorgans) was defined by clustering consecutive significant 5 % chromosome-wise LDLA associations on a chromosome (allowing gaps no greater than 5 Mb)
^eP_c-value: chromosome-wise P-value established through 1000 simulations. P_g-value: genome-wise P-value obtained from the P_c-values corrected for the total number of chromosomes analyzed
^f TGI (Mb) Target genomic interval. For each significant LDLA association, target genomic intervals were defined as the genomic region based on the sheep reference genome assembly Oar_v3.1 that corresponded to the defined significant LDLA intervals (for those regions with consecutive significant positions) and a 250-kb long interval centered on each of the significant isolated haplotypes detected by LDLA
^gPositional candidate genes extracted from the LDLA significant associations (within the significant LDLA interval if identified, or within a ±125 kb interval from the position of maximum LRT-value for the significant QTL based on isolated significant haplotypes) that were identified as potential functional candidate genes in the search for immune-related genes

Back to article page

ISSN: 1297-9686

Contact us

Submission enquiries: helene.hayes@inrae.fr
General enquiries: info@biomedcentral.com