Avian

Genome-wide association studies on growth and fitness traits of a Pekin duck using imputed genotypes

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Abstract

Global meat consumption is projected to rise significantly by 2050, with a 70% increase from 2010 levels due to factors like population growth and increasing incomes. Ducks, specifically Anas platyrhynchos, play a key economic role in the poultry industry, especially in regions like Asia where duck meat is a staple. While the overall proportion of duck meat in global meat consumption is smaller compared to chicken or beef, it remains important in markets with strong culinary traditions centred around duck. Genome-wide association studies (GWAS) are recognized for detecting QTLs that underlie biological mechanisms for economically important traits. In the present study, we examined growth traits which included average daily gain (ADG), body weight (BW), breast depth (BD). We also included welfare and fitness traits for primary feather length (PRF), foot pads (FP) and gait score (GS) so as to incorporate economically important traits in the breeding programme. We performed variance component analysis and GWAS to provide insight into the genetic mechanism underlying these traits. We used mixed linear models correcting for sex and hatch as fixed effects and animal as a random effect. Ducks with low coverage maker parentage panel data were imputed to a 60K SNP chip panel. This resulted in 13645 animals with total imputed SNPs 63451. We performed quality control of MAF >0.05 and HWE=1.00x10-6 leaving 47156 SNPs for subsequent analyses. The Bonferroni correction for 5 percent genome-wise significance was 1.06x10-6 and the suggestive level was 2.12x10-5 (one false positive per genome scan). We obtained heritability estimates of 0.16±0.01, 0.32±0.02, 0.16±0.01 respectively for ADG, BW and BD; and 0.25±0.01 for both PRF and FP, 0.07±0.01 for GS. The GWAS results identified two genome-wide significant QTL regions with p-8 and 5.63x10-8 respectively for chromosome 8 and 25 for ADG. We also identified QTL regions for BW which were above the suggestive threshold with p -6 and 1.15x10-6 on chromosome 1 and 6 respectively. There was a single SNP on chromosome 15 for BD that was above the suggestive significance level with a p=1.56x10-5. We also found two genome-wide QTL regions for PRF with p-10 and 6.75x10-7 on chromosome 1 and 8 respectively and a single suggestive SNP with p=1.81x10-5 on chromosome 7. We revealed suggestive regions on chromosome 30 for FP (p=1.42x10-5) and chromosome 15 for GS with p-5. All traits analysed were heritable and we identified QTL regions that will add to novel understanding of the underlying genomic regions responsible for Pekin duck traits of economic importance.

Keywords: 2026

How to Cite:

Matika, O., Tarsani, E., Kebede, F., McIntosh, K., Rae, A., Kranis, A. & Watson, K. A., (2026) “Genome-wide association studies on growth and fitness traits of a Pekin duck using imputed genotypes”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285392. doi: https://doi.org/10.31274/wcgalp.23678

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