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Open Access Publications from the University of California

Scholarly Works (6 results)

  • Thesis
  • Peer Reviewed
UC Davis Electronic Theses and Dissertations (2021)

Lameness imposes concerns for dairy cattle welfare and farmer profitability. After mastitis, lameness is the second most prevalent disease in dairy cattle and is commonly caused by digital dermatitis (DD, also known as foot warts), sole ulcers (SU), and white line disease (WLD). Digital dermatitis is an infectious foot lesion, whereas SU and WLD are noninfectious lesions that arise due to compromised horn production. Genomic selection against these foot lesions and its potential impact on other health traits (mastitis, hypocalcemia, displaced abomasum, ketosis, and metritis) requires the identification of loci associated with these foot lesions and assessment of the genetic correlation of foot lesions with other health traits. To detect susceptibility loci, a genome-wide association study (GWAS) was performed using genotypes from the high density SNP array (777K SNPs) and case/control phenotypes for DD (controls n =129, DD n = 85), SU (controls n = 102, SU n = 152), WLD (controls = 102, WLD n = 117), SU and/or WLD (SU and WLD, controls n = 102, n = 198), and any type of noninfectious foot lesion (controls n = 102, cases = 217). GWAS was performed using linear mixed model (LMM) and random forest (RF) approaches, and effect sizes of top SNPs were estimated using Bayesian regression. For the LMM 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 p-value thresholds of genome-wide statistical significance (p ≤ 0.05/NES) and suggestive significance (p ≤ 0.2/NES). Genetic correlation among foot lesions and health traits was estimated using bivariate genome-based restricted maximum likelihood (GREML) analysis, and a multi-trait GWAS was conducted to identify genomic regions contributing to genetic correlation. Top SNPs identified in the GWAS were in or near genes that were functionally relevant to foot lesion etiology. For DD, both the LMM and RF analyses identified regions of association on Bos taurus autosome (BTA) 1 and 2, with one of the regions on BTA2 containing candidate genes related to immune function. The LMM GWAS revealed an associated region on BTA 8 for SU and BTA13 for WLD, SU and WLD, and noninfectious foot lesions. These associated regions contained genes related to wound healing, skin lesions, bone growth and mineralization, adipose tissue, and keratinization. Furthermore, the region on BTA8 included a SNP previously associated with SU susceptibility. The RF GWAS for SU, WLD, SU and WLD, and noninfectious lesions were overfitted, suggesting that the SNP effects were very small and prevented detection of susceptibility loci using this approach. Estimated effect sizes of top SNPs were small, and though significant genetic correlation was detected among lameness and health traits, the sample size prevented detection of loci contributing to multiple traits. The small effect sizes and the limited ability to detect pleiotropic loci reinforces that the environment plays a nontrivial role in disease susceptibility, and the remaining genetic component is likely governed by many loci. Larger sample sizes are necessary to identify small effect loci and their association with individual or multiple lameness and health traits amidst a strong environmental effect.

  • 1 supplemental ZIP
Cover page: Identifying Loci Associated with Susceptibility to Foot Lesions in Holstein Cattle
  • Article
  • Peer Reviewed
UC Davis Previously Published Works (2018)
Vermifiltration is a biological treatment process during which earthworms (e.g., Eisenia fetida) and microorganisms reduce the organic load of wastewater. To infer microbial pathways responsible for nutrient conversion, past studies characterized the microbiota in vermifilters and suggested that nitrifying and denitrifying bacteria play a significant role during this wastewater treatment process. In contrast to previous studies, which were limited by low-resolution sequencing methods, the work presented here utilized next generation sequencing to survey in greater detail the microbiota of wastewater from a commercial dairy during various stages of vermifiltration. To complement sequence analysis, nitrogenous compounds in and gaseous emissions from the wastewater were measured. Analysis of 16S rRNA gene profiles from untreated wastewater, vermifilter influent, and vermifilter effluent suggested that members of Comamonadaceae, a family of the Betaproteobacteria involved in denitrification, increased in abundance during the vermifiltration process. Subsequent functional gene analysis indicated an increased abundance of nitrification genes in the effluent and suggested that the nitrogen removal during vermifiltration is due to the microbial conversion of ammonia, a finding that was also supported by the water chemistry and emission data. This study demonstrates that microbial communities are the main drivers behind reducing the nitrogen load of dairy wastewater during vermifiltration, providing a valuable knowledge framework for more sustainable and economical wastewater management strategies for commercial dairies.
    Cover page: Profiling of the Microbiome Associated With Nitrogen Removal During Vermifiltration of Wastewater From a Commercial Dairy
    • Article
    • Peer Reviewed
    UC Davis Previously Published Works (2021)
    The Covid-19 pandemic served as the impetus to implement activities designed to engage students in the remote instructional environment while simultaneously developing scientific literacy skills. In a high enrollment general education animal science course, numerous activities were designed to improve scientific literacy. These included specifically developed videos covering strategies for reading published science literature, the utilization of topically relevant scientific articles that captured student interest, and engaging students in a citizen science exercise on whether dogs align themselves to the Earth's magnetic field during excretion behavior. Employing pre- and post-self-perception surveys coupled with tasking students to apply their scientific literacy skills in an assessment scenario demonstrated that students' self-perception of their scientific literacy improved 30% (P < 0.05) with approximately 80% of students accurately applying their literacy skills. The citizen science study on excretory behavior was modeled on previously published findings thereby providing an opportunity to validate the published work which had indicated that dogs align their bodies in a North-South axis during excretion. The present study did not demonstrate preferential alignment to any geomagnetic orientation which emphasized to the students the need for scientific replication. Inclusion of simple activities that were relevant to students' daily lives, and providing interpretive context for those activities, resulted in improved self-perceived scientific literacy.
      Cover page: Enhancing student scientific literacy through participation in citizen science focused on companion animal behavior
      • Article
      • Peer Reviewed
      UC Davis Previously Published Works (2021)
      Lameness is an animal welfare issue that incurs substantial financial and environmental costs. This condition is commonly caused by digital dermatitis (DD), sole ulcers (SU), and white line disease (WLD). Susceptibility to these three foot disorders is due in part to genetics, indicating that genomic selection against these foot lesions can be used to reduce lameness prevalence. It is unclear whether selection against foot lesions will lead to increased susceptibility to other common diseases such as mastitis and metritis. Thus, the aim of this study was to determine the genetic correlation between causes of lameness and other common health disorders to identify loci contributing to the correlation. Genetic correlation estimates between SU and DD and between SU and WLD were significantly different from zero (p < 0.05), whereas estimates between DD and mastitis, DD and milk fever, and SU and metritis were suggestive (p < 0.1). All five of these genetic correlation estimates were positive. Two-trait genome-wide association studies (GWAS) for each of these five pairs of traits revealed common regions of association on BTA1 and BTA8 for pairs that included DD or SU as one of the traits, respectively. Other regions of association were unique to the pair of traits and not observed in GWAS for other pairs of traits. The positive genetic correlation estimates between foot disorders and other health disorders imply that selection against foot disorders may also decrease susceptibility to other health disorders. Linkage disequilibrium blocks defined around significant and suggestive SNPs from the two-trait GWAS included genes and QTL that were functionally relevant, supporting that these regions included pleiotropic loci.
        Cover page: Pleiotropic Loci Associated With Foot Disorders and Common Periparturient Diseases in Holstein Cattle
        • Article
        • Peer Reviewed
        UC Davis Previously Published Works (2020)
        Digital dermatitis (DD) causes lameness in dairy cattle. To detect the quantitative trait loci (QTL) associated with DD, genome-wide association studies (GWAS) were performed using high-density single nucleotide polymorphism (SNP) genotypes and binary case/control, quantitative (average number of FW per hoof trimming record) and recurrent (cases with ≥2 DD episodes vs. controls) phenotypes from cows across four dairies (controls n = 129 vs. FW n = 85). Linear mixed model (LMM) and random forest (RF) approaches identified the top SNPs, which were used as predictors in Bayesian regression models to assess the SNP predictive value. The LMM and RF analyses identified QTL regions containing candidate genes on Bos taurus autosome (BTA) 2 for the binary and recurrent phenotypes and BTA7 and 20 for the quantitative phenotype that related to epidermal integrity, immune function, and wound healing. Although larger sample sizes are necessary to reaffirm these small effect loci amidst a strong environmental effect, the sample cohort used in this study was sufficient for estimating SNP effects with a high predictive value.
          Cover page: Genome-Wide Association Studies Reveal Susceptibility Loci for Digital Dermatitis in Holstein Cattle
          • Article
          • Peer Reviewed
          UC Davis Previously Published Works (2021)
          Sole ulcers (SUs) and white line disease (WLD) are two common noninfectious claw lesions (NICL) that arise due to a compromised horn production and are frequent causes of lameness in dairy cattle, imposing welfare and profitability concerns. Low to moderate heritability estimates of SU and WLD susceptibility indicate that genetic selection could reduce their prevalence. To identify the susceptibility loci for SU, WLD, SU and/or WLD, and any type of noninfectious claw lesion, genome-wide association studies (GWAS) were performed using generalized linear mixed model (GLMM) regression, chunk-based association testing (CBAT), and a random forest (RF) approach. Cows from five commercial dairies in California were classified as controls having no lameness records and ≥6 years old (n = 102) or cases having SU (n = 152), WLD (n = 117), SU and/or WLD (SU + WLD, n = 198), or any type of noninfectious claw lesion (n = 217). The top single nucleotide polymorphisms (SNPs) were defined as those passing the Bonferroni-corrected suggestive and significance thresholds in the GLMM analysis or those that a validated RF model considered important. Effects of the top SNPs were quantified using Bayesian estimation. Linkage disequilibrium (LD) blocks defined by the top SNPs were explored for candidate genes and previously identified, functionally relevant quantitative trait loci. The GLMM and CBAT approaches revealed the same regions of association on BTA8 for SU and BTA13 common to WLD, SU + WLD, and NICL. These SNPs had effects significantly different from zero, and the LD blocks they defined explained a significant amount of phenotypic variance for each dataset (6.1-8.1%, p < 0.05), indicating the small but notable contribution of these regions to susceptibility. These regions contained candidate genes involved in wound healing, skin lesions, bone growth and mineralization, adipose tissue, and keratinization. The LD block defined by the most significant SNP on BTA8 for SU included a SNP previously associated with SU. The RF models were overfitted, indicating that the SNP effects were very small, thereby preventing meaningful interpretation of SNPs and any downstream analyses. These findings suggested that variants associated with various physiological systems may contribute to susceptibility for NICL, demonstrating the complexity of genetic predisposition.
            Cover page: Genome-Wide Association Studies Reveal Susceptibility Loci for Noninfectious Claw Lesions in Holstein Dairy Cattle
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