Bioinformatic analysis of lameness and hoof disease traits in dairy cattle with the emphasis on epistasis

Leader investigator: Joanna Szyda
Period of work: 36 months
Funded: National Science Centre

The aim of the project is a better understanding of genetics underlying hoof diseases and lameness. Traits related to hoof diseases and lameness are called novel traits since their phenotypes have been collected only recently, and thus their genetic background has not yet been extensively studied. Therefore, the objective of the project is to analyze the genetic determinants of traits describing hoof and leg quality in the context of the causes lameness of dairy cattle, with particular emphasis on epistatic effects.

The dataset consists of hoof and leg quality trait values and 76 934 SNP genotypes for 985 cows. Moreover, we also have the information about SNP locations, pedigree and culling of individuals (the number of culled animals ad culling reasons), some additional variables such as the date of birth and the number of finished lactations are available as well. The data set was made available by the courtesy of ZuchtData EDV-Dienstleistungen GmbH.

The preliminary analysis of available data showed that 2.04% all culled cows and 4.80% of cows culled due to health problems or low productivity were removed from herds because of hoof hood or leg disorders. The main causes of culling are age (48.97%), low fertility (24.50%) and udder diseases (13.07%).

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Significant epistatic effects for the number of claw disorders.

 

A,B before removing polymorphisms with the call rate below 95% and polymorphisms with the minor allele frequency below 5%. 

C,D after removing polymorphisms with the call rate below 95% and polymorphisms with the minor allele frequency below 5%