Genome-Wide Association Study for Response to Eimeria maxima Challenge in Broilers

Use of genetic tools for improvement of host’s response is considered as a promising complementary approach for coccidiosis control. Therefore, we performed genome wide association study (GWAS) for response to Eimeria maxima challenge in broilers. The challenge was done on 2024 Cobb500 broilers. We phenotyped animals on two levels: global phenotyping performed on all animals and deep phenotyping on a subset of 184 extreme animals. The global phenotyping included: body weight gain, hematocrit, plasma coloration and rectal temperature and the deep phenotyping included: blood cell count, plasma proteins profiles, oocyst count and lesion score. GWAS was conducted on 1975 animals which were genotyped using 580K Affymetrix^® Axiom^® HD genotyping array. Quality control procedures involved the following criteria: SNP call rate (<98%), sample call rate (<98%) minor allele frequency (>1%). GWAS was carried out in GEMMA software using standard univariate linear mixed model. The false-discovery rates (FDR) were calculated using the R package q-value and the cut-off of the significant association was set at q-value ≤ 0.05. We identified several genomic regions associated with measured parameters. Among the most promising results, robust associations have been identified between albumin levels and one region on GGA2, alpha 1 globulin and one region on GGA1, alpha 2 globulin and two regions on GGA1 and GGA6 and plasma coloration and one region on GGA6. To our knowledge this is the largest association study that has been conducted in a commercial broiler product to ascertain the genetic components driving the response of chickens to coccidiosis.