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Table 3 Combined genotype data for LRRTM4 and CPQ suggests epistatic interactions between these genes for resistance in male REL line birds

From: Identification and validation of quantitative trait loci for ascites syndrome in broiler chickens using whole genome resequencing

Genotype   All   Male   Female
LRRTM4 CPQ n Sus Res P-val. n Sus Res P-val. n Sus Res P-val.
AG TA 23 56.5 43.5 0.375 11 45.5 54.5 3.067 11 63.6 36.4 1.081
AG YM 26 50.0 50.0 6.107 12 44.4 55.6 5.380 12 57.1 42.9 8.443
AG CC 72 36.4 63.6 6.910 36 50.0 50.0 7.575 31 0 100.0 3.449
RR TA 33 33.3 66.7 1.488 18 25.0 75.0 2.340 7 41.7 58.3 3.371
RR YM 31 42.9 57.1 4.935 15 46.7 53.3 2.026 12 27.3 72.7 3.259
RR CC 131 25.8 74.2 0.080 61 14.8 85.2 0.033 53 36.5 63.5 4.818
GA TA 15 38.8 61.2 4.198 8 30.6 69.4 2.488 2 48.4 51.6 2.139
GA YM 14 25.8 74.2 0.620 8 14.8 85.2 0.582 5 36.5 63.5 3.403
GA CC 54 40.0 60.0 6.187 19 44.4 55.6 2.382 26 3.8 69.2 2.661
  1. SNP genotype data for LRRTM4 and CPQ genes were combined and evaluated relative to distribution with respect to ascites phenotype. The CC non-reference homozygote was previously associated with resistance (35). Statistical analyses of association was based on adjusted P-values comparing observed counts vs predicted counts based on HWE. Genotype for LRRTM4 is as described in Table 2. Genotype for CPQ is for SNPs corresponding to bases 127,010,709 and 127,010,716 on chromosome 2 [34]
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