Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep

Table 1 Characterisation of QTL influencing parasite resistance traits that exceed the 5% chromosome-wise significance threshold in the commercial population of Spanish Churra sheep analysed in this study

ACROSS-FAMILY ANALYSIS				WITHIIN-FAMILY ANALYSIS
Chr.¹	Trait Position² [95% CI]³	Flanking interval⁴	P_c⁵ ( P_g)⁶	Segregating families P_c⁷	Position⁸ Flanking interval⁹	Size effect¹⁰ (SD units)
1	IgA 35 cM [1-320].	BMS835-ILSTS044	0.038	Family 1 0.005	38 cM BMS835-ILSTS044	0.111 (1.70 SD)
	LFEC ₁ 152 cM [122-374]	INRA006-BMS574	0.016	Family 8 0.013	134 cM INRA006-BMS574	0.129 (1.31 SD)
6	LFEC ₁ 84 cM [49-140]	BM4621-CSN3	0.002 (0.041)	Family 1 0.002 Family 2 0.041 Family 7 0.049	79 cM BM4621-CSN3 113 cM CSRD2158-MCM214 105 cM CSN3-CSRD2158	0.160 (1.63 SD) 0.082 (0.83 SD) 0.117 (1.19 SD)
10	LFEC ₀ 59-60 cM [1-95]	BM4621-CSN3	0.018	Family 7 0.014	65 cM BMS975-TGLA441	0.324 (2.53 SD)
14	LFEC ₀ 1-2 cM [1-125]	TGLA357-CSRD247	0.018	Family 1 0.029 Family 6 0.015	2 cM TGLA357-CSRD247 1-2 cM TGLA357-CSRD247	0.137 (1.07 SD) 0.136 (1.06 SD)

¹ Chromosome number
^2,8 Position (cM Haldane) of the chromosome where the maximum F-statistic value was obtained in the across- and within-family analyses, respectively
³ The 95% confidence interval obtained by bootstrapping analysis [26] is shown in square brackets (cM Haldane)
^4,9 Markers flanking the position of the maximum F-statistic in the across-family and within- analysis, respectively. Markers in bold caps are < 1 cM from the maximum F-statistic
^5,7 P_c = chromosome-wide p-value obtained by permutation test for that position [23]
⁶ P_g= genome-wide p-value for that position obtained by applying the following Bonferroni correction: P_genomewide = 1-(1-P_{chromosomewise})^(1/r), where r indicates the contribution of the chromosome to the total genome length [24]; only indicated for P_g< 0.05
¹⁰ Magnitude of the allelic substitution effect calculated for each segregating family, expressed in units of the trait (egg count/g faeces for LFEC₀ and LFEC₁, D.O ratio for IgA and mUTyr Peps) and in phenotypic SD units of the analysed YDs (value in brackets)

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