Increasing the sustainability of dairy cattle by providing genetic tools to reduce lameness, improving welfare and production

Project Overview

Project Type: Graduate Student
Funds awarded in 2018: $23,623.00
Projected End Date: 03/31/2020
Grant Recipient: University of California, Davis
Region: Western
State: California
Graduate Student:
Major Professor:
Dr. Anita Oberbauer
University of California, Davis


  • Animals: bovine
  • Animal Products: dairy


  • Animal Production: animal protection and health, genetics, livestock breeding, preventive practices
  • Education and Training: extension, participatory research, workshop
  • Sustainable Communities: quality of life


    Problem: Lameness affects 16% of dairy cows in the US (USDA, 2016) and is associated with
    reduced milk production and premature culling, raising welfare, environmental, and economic concerns.
    Lameness is often caused by foot warts (FW) and sole ulcers (SU), claw lesions that arise from a combination of genetic and environmental factors. Genomic regions identified in this study can be incorporated into selection indices, allowing producers to select for cows genetically protected against FW and SU. These future generations of healthier and more efficient cows will produce milk with a smaller environmental footprint.

    Research approach: To detect susceptibility loci, a genome-wide association study (GWAS) was performed with a mixed linear model in GCTA for each condition using single nucleotide polymorphism (SNP) genotypes from the high density SNP array (777K SNPs) and binary case/control and quantitative (number of lesions divided by the total number of hoof trimming records) phenotypes from cows across five dairies (FW n = 85, SU n = 120, controls n = 129; 23 cows had both FW and SU). For each GWAS, the number of effective SNPs (NES) was calculated as the number of SNPs that were not in linkage disequilibrium and used as the denominator to define Bonferroni-corrected thresholds of significance (p < 0.05/NES) and suggestive significance (p < 1/NES). To assess the predictability of SNP effects estimated from the GWAS while avoiding overfitting, polygenic risk scores were calculated using SNP effects estimated from cross-validated best linear unbiased prediction (cvBLUP).

    Outreach: We have communicated with the producers of the dairies we are working with and the local county advisor.  We will also communicate our findings directly with other local producers at conferences as well as through the extension team in the Animal Science Department at the University of California, Davis. We will also share our findings through trade publications as we did with our initial findings. The goal will be to provide producers with a genetic foundation for the reduction of both FW and SU, thereby reducing lameness.

    Project objectives:

    The broad, long-term goal of this proposal is to reduce the incidence of lameness and
    improve hoof health of Holstein dairy cattle. Thus, the objectives for this proposal are to:

    1. Perform a genome wide association analysis to identify QTL regions contributing to
      genetic susceptibility to FW and SU
      Western SARE.
    2. Utilize the the SNPs of largest effect to develop a predictive model to reduce
      susceptibility to FW or SU that can be used in conjunction with the current selection tools
      for milk production attributes to reduce the prevalence of FW and SU within a herd while
      maintaining overall milk quantity and quality
    Any opinions, findings, conclusions, or recommendations expressed in this publication are those of the author(s) and do not necessarily reflect the view of the U.S. Department of Agriculture or SARE.