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Allele substitution and dominance effects of CD166/ALCAM gene polymorphisms for endoparasite resistance and test-day traits in a small cattle population using logistic regression analyses

Abstract

The study investigated the effects of four single-nucleotide polymorphisms (SNPs) in the activated leukocyte cell adhesion molecule (ALCAM) gene on liver fluke (Fasciola hepatica) infections (FH-INF), gastrointestinal nematode infections (GIN-INF) and disease indicator traits [e.g. somatic cell score (SCS), fat-to-protein ratio (FPR)] in German dual-purpose cattle (DSN). A genome-wide association study inferred the chip SNP ALCAMc.73+32791A>G as a candidate for F. hepatica resistance in DSN. Because of the crucial function of ALCAM in immune responses, SNPs in the gene might influence further resistance and performance traits. Causal mutations were identified in exon 9 (ALCAMc.1017T>C) and intron 9 (ALCAMc.1104+10T>A, ALCAMc.1104+85T>C) in a selective subset of 94 DSN cows. We applied logistic regression analyses for the association between SNP genotypes with residuals for endoparasite traits (rINF-FH, rGIN-INF) and estimated breeding values (EBVs) for test-day traits. The probability of the heterozygous genotype was estimated in dependency of the target trait. Allele substitution effects for rFH-INF were significant for all four loci. The T allele of the SNPs ALCAMc.1017T>C and ALCAMc.1104+85T>C was the favourable allele when improving resistance against FH-INF. Significant allele substitution for rGIN-INF was only found for the chip SNP ALCAMc.73+32791A>G. We identified significant associations between the SNPs with EBVs for milk fat%, protein% and FPR. Dominance effects for the EBVs of test-day traits ranged from 0.00 to 0.47 SD and were in the direction of improved resistance for rFH-INF. We estimated favourable dominance effects from same genotypes for rFH-INF and FPR, but dominance effects were antagonistic between rFH-INF and SCS.

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Acknowledgements

This work was financially supported by the German Federal Ministry of Food and Agriculture (BMEL) based on a decision of the Parliament of the Federal Republic of Germany, granted by the Federal Office for Agriculture and Food (BLE; grant number FKZ 2818BM090 and -091). We gratefully thank the H. Wilhelm Schaumann foundation for the provision of a PhD grant to KM.

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May, K., Weimann, C., Scheper, C. et al. Allele substitution and dominance effects of CD166/ALCAM gene polymorphisms for endoparasite resistance and test-day traits in a small cattle population using logistic regression analyses. Mamm Genome 30, 301–317 (2019). https://doi.org/10.1007/s00335-019-09818-z

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Keywords

  • Activated leukocyte cell adhesion molecules
  • Selective genotyping
  • Gene sequences
  • Allele substitution
  • Dominance effects
  • Fasciola hepatica