Progress 10/01/09 to 09/30/14

Outputs
Target Audience: Producers, County Farm Advisors, Cooperative Extension Agents, Scientific Community. Work was published in scientific journals (Journal of Animal Science) and also distributed to producers and the state farm advisors. The work was promoted in Rural News Group, UC Davis media outlets, MilkProduction.Com, Feedstuffs Magazine, Trader's Dispatch, and Hoards Dairyman. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? Several undergraduate students worked as interns on this project inputting data, scouring the database for pedigree information on dairy sires, becoming familiar with the genetic selection side of the dairy industry, developing computational skills, and coordinating sample collection with the producers. Several of these students have pursued a career in genetics and some have enrolled in a veterinary curriculum. Additionally, one graduate student is completing her degree using the genome assessment as the basis of her research thesis. The graduate student will be entering the UC Davis Veterinary School in Fall 2015. How have the results been disseminated to communities of interest? The investigators contacted all of the participating dairies and explained the outcome of the work. Additionally, the county dairy advisor was informed of the findings to broaden the dissemination of the results to more producers. The data was published in a scientific journal (Journal of Dairy Science), presented at national Scientific meetings, and the work highlighted in Western FarmPress, the Agricultural and Natural Resource arm of the University of California Cooperative extension media outlets, and many dairy producer publications. What do you plan to do during the next reporting period to accomplish the goals? Nothing Reported

Impacts
What was accomplished under these goals? Lameness and hoof health is a little studied though significant aspect of dairy management. Lameness impacts dairy producers both as an animal welfare issue as well as being implicated in lowered milk production. Yet genetic improvement selection schemes for dairy cattle focus on milk production with little consideration to the cow's physical structure. In this project, we characterized the prevalence of the predominant hoof lesions detected in California dairy cattle, profiled the occurrence of the lesions during several lactations, and assessed the heritability of those lesions. In addition to improving the welfare and productivity of a dairy herd, reducing lameness will lessen the environmental impact of the dairy industry. All objectives of the study, to determine prevalence of lameness and specific hoof lesions in producing dairy cattle, to determine the genetic parameters of lameness and specific hoof lesions in producing dairy cattle, to characterize management strategies involved in the incidence of lameness, and to undertake a genome wide association analysis to identify the genetic underpinnings of lameness, were all achieved during the period. We identified that the existence of significant genetic contribution to hoof lesions most particularly foot warts and sole ulcers, that will allow a) selection against as sires with a greater likelihood of transmitting risk, and b) exploration of the genome to identify regions underlying the hoof lesions. We identified that other conditions (e.g., foot rot and sole ulcer) that contribute to dairy lameness are more influenced by management practices including facility sanitation. We obtained blood samples from cows that were from sires passing on a predisposition to the genetic conditions as well as control samples from cows with a low likelihood of having the hoof conditions. We have done a genome wide analysis on those samples and identified several chromosomal regions that show significant association to the expression of hoof warts. We have fully sequenced a particularly noteworthy candidate gene in the region but there does not appear to have significant sequence variation to account for the condition. We will continue to explore the indicated regions searching for polymorphism linked to the hoof conditions. Developing markers to aid in selecting against hoof problems to reduce lameness will contribute to overall producer sustainability. Keeping a cow in the herd longer has profound advantages as the greatest investment (both economic and environmental) is in the initial calf/heifer rearing stage when the animals are not producing a marketable product.

Publications

• Type: Theses/Dissertations Status: Submitted Year Published: 2015 Citation: Genome-wide analysis of dairy cattle hoof conditions. Thesis. Alexa Danner, Thomas Famula, Steven Berry, Anita Oberbauer.

Progress 01/01/13 to 09/30/13

Outputs
Target Audience: We have met with several California Dairy Producers on their farms to describe our findings that certain hoof lesions are prevalent on California commercial dairies: white line disease and foot warts (digital dermatitis) at ~8% and 17% of cows, respectively. Other hoof lesions are less prevalent with many associated with the transition period and farm hygiene suggesting management practices may assist in reducing the incidence. Most importantly, two of the lesions, sole ulcers (having a prevalence of ~4%) and foot warts have significant genetic contributions. This means that hoof-health problems can be reduced through applying selective breeding strategies. Additionally, selecting for reduced hoof lesions would not impact the genetic gain achieved by selecting for milk production. The work was highlighted on the UC Davis news site as well as in several dairy producer publications. Changes/Problems: Nothing Reported What opportunities for training and professional development has the project provided? As noted above, a graduate student is undertaking the research for her graduate degree. She has an undergraduate who is working with her thereby expanding the training. Coordination of the research has required developing communication skills along with organizational skill all on top of mastering the laboratory techniques. How have the results been disseminated to communities of interest? We have met in person with dairy producers as well as dairy veterinarians to discuss our research. We have followed up with written letters to them and providing information on the study to producer publications. What do you plan to do during the next reporting period to accomplish the goals? As noted above, the genomic data derived from cows more genetically susceptible to hoof lesions and those from cows resistant to hoof lesions have been returned from the analyzing lab. The data will be computationally interrogated to identify linkage of genomic regions associated with the lesions. The regions will then be sequenced to determine if there are specific mutations identifiable that contribute to hoof health.

Impacts
What was accomplished under these goals? Identifying a genetic component, will enable producers to broaden selection criteria to include traits associated with herd longevity and improved welfare. The ultimate goal of this research is to generate a molecular diagnostic to apply to dairy sire selection to use sires with qualities of superior milk but also those more or less likely to contribute to hoof lesions. We have identified that there exists significant genetic contribution to hoof lesions that will allow a) selection against as sires with a greater likelihood of transmitting risk, and b) exploration of the genome to identify regions underlying the hoof lesions. This will contribute to overall producer sustainability as the greatest investment (both economic and environmental) is in the initial calf/heifer rearing stage when the animals are not producing a marketable product. We have identified the sires more associated with “at risk” and “resistant” daughters. With that complete, 741 sires used in the data set were ranked as to their genetic propensity to pass on risk or resistance to hoof lesions. We worked with participating commercial dairies and obtained current animal inventories and hoof health records. From appropriate cows blood samples were collected from daughters of sires that do and do not have hoof lesions. DNA was extracted from the blood samples and the purified DNA sent to GeneSeek for genome wide association SNP analyses. Identifying susceptible and control cows took many months as did coordinating with the collection of current health records and blood samples. The DNA was isolated and the final batch of 40 samples sent on October 21 making a total of 228 DNA samples submitted for genome wide analysis at GeneSeek. We were able to negotiate a reduced cost per sample than projected in the original budget permitting us to send additional samples; this is beneficial as some animals do not analyze well. The data has been returned and a graduate student, Alexa Danner, will computationally interrogate the genome to identify linkage. We have continued outreach efforts to dairy producers to inform them of the findings. The local commercial producers have been outstanding in their assistance.

Publications

Progress 01/01/12 to 12/31/12

Outputs
OUTPUTS: The project's goal is to define the genetic contribution to dairy hoof lesions. Associated with this goal is to design selection strategies and highlight management practices that may to improve the welfare and longevity of dairy cows in the milking herd. In addition to improving the welfare and productivity of a dairy herd, will reduce the environmental impact of the dairy industry. The work is collaborative in nature with dairy producers within the state and with other faculty within the department. Dr. Berry although retired, remains one of the principal investigators and maintains contact with farms. Dr. Oberbauer contacted all of the participating dairies to let them know of the results. Additionally, the county dairy advisor has been contacted and the work explained so she too can share the information with producers. The data was recently published and the findings highlighted in Western FarmPress and the ANR UC Cooperative extension media outlets. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Nothing significant to report during this reporting period. PROJECT MODIFICATIONS: Nothing significant to report during this reporting period.

Impacts
Identifying a genetic component, will enable producers to broaden selection criteria to include traits associated with herd longevity and improved welfare. The ultimate goal is to generate a molecular diagnostic to apply to dairy sire selection to use sires with qualities of superior milk but also those more or less likely to contribute to hoof lesions. We have identified that there exists significant genetic contribution to hoof lesions that will allow a) selection against as sires with a greater likelihood of transmitting risk, and b) exploration of the genome to identify regions underlying the hoof lesions. This will contribute to overall producer sustainability as the greatest investment (both economic and environmental) is in the initial calf/heifer rearing stage when the animals are not producing a marketable product.

Publications

• Oberbauer AM, Berry SL, Belanger JM, McGoldrick R,Pinos-Rodriquez JM, Famula TR. 2013. Determining the Heritable Component of Dairy Cattle Foot Lesions. J Dairy Sci. 96:605-13.

Progress 01/01/11 to 12/31/11

Outputs
OUTPUTS: The goal of the project is to establish the genetic contribution to dairy hoof health, specifically the inheritance of foot lesions. Associated with this goal is to design selection strategies and highlight management practices that may to improve the welfare and longevity of dairy cows in the milking herd. This in turn will also reduce the environmental impact of the dairy industry. The work is collaborative in nature with dairy producers within the state and with other faculty within the department. Dr. Berry one of the principal investigators is frequently on farm and gives workshops on hoof health within the state to producers. His efforts, along with the presentations of Dr. Oberbauer at scientific and public venues have disseminated the information to the appropriate stakeholders. PARTICIPANTS: Nothing significant to report during this reporting period. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Identifying a genetic component, will enable producers to broaden selection criteria to include traits associated with herd longevity. The ultimate goal is to generate a molecular diagnostic to apply to dairy sire selection to use sires with qualities of superior milk but also those more or less likely to contribute to hoof lesions. This will contribute to overall producer sustainability as the greatest investment (both economic and environmental) is in the initial calf/heifer rearing stage when the animals are not producing a marketable product.

Publications

• Oberbauer AM, TR Famula, S Berry. 2011. Determining the heritable component of dairy cattle foot lesions. J Animal Science 89:E-Suppl 1: 520.

Progress 01/01/10 to 12/31/10

Outputs
OUTPUTS: The goal of the project is to establish the genetic contribution to dairy hoof health, specifically the inheritance of foot lesions. Associated with this goal is to design selection strategies and management practices that would serve to improve the welfare and longevity of dairy cows in the milking herd. This in turn will also reduce the environmental impact of the dairy industry. The work is collaborative in nature with dairy producers within the state and with other faculty within the department. Dr. Berry one of the principal investigators is frequently on farm and gives workshops on hoof health within the state to producers. His efforts, along with the presentations of Dr. Oberbauer at scientific and public venues have disseminated the information to the appropriate stakeholders. PARTICIPANTS: Several undergraduate students worked on this project entering data and gaining firsthand experience in experimental concepts. One student, Rachel McGoldrick, a senior in Animal Science and Management, used this project for her UC Davis MURALS (Mentorships for Undergraduate Research in Agriculture, Letters, and Science) project. TARGET AUDIENCES: Not relevant to this project. PROJECT MODIFICATIONS: Not relevant to this project.

Impacts
Identifying a genetic component, will enable producers to broaden selection criteria to include traits associated with herd longevity. The ultimate goal is to generate a molecular diagnostic to apply to dairy sire selection to use sires with qualities of superior milk but also those more or less likely to contribute to hoof lesions. This will contribute to overall producer sustainability as the greatest investment (both economic and environmental) is in the initial calf/heifer rearing stage when the animals are not producing a marketable product.

Publications

• Abstract submitted to the American Society of Animal Scientists Summer 2011 meeting: Oberbauer AM, SL Berry, JM Belanger, TR Famula. Determining the heritable component of dairy cattle foot lesions.