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Cornell University
1.
Stephan, Christine.
ESTIMATING TECHNICAL, REVENUE, ALLOCATIVE, AND PROFIT EFFICIENCIES OF GENETIC TRAITS FOR DAIRY BULLS.
Degree: M.S., Applied Economics and Management, Applied Economics and Management, 2018, Cornell University
URL: http://hdl.handle.net/1813/59586 
► We estimate technical, revenue, allocative and profit efficiency for the NAABIS list of active AI Dairy Bulls using a FDH output orientation under constant returns.…
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▼ We estimate technical, revenue, allocative and profit efficiency for the NAABIS list of active AI Dairy Bulls using a FDH output orientation under constant returns. The genetic traits used as outputs include, pounds of protein, pounds of fat, somatic cell count, calving ability, daughter pregnancy rate, udder composition, and livability. Empirical results show that most of the bulls were highly technically efficient. That is not the case for allocative efficiency and profit efficiency, especially when genetic characteristics beyond protein and fat are included in the analysis. Given the potential revenue generated by a bull’s trait, some bull’s semen is overpriced. We determine whether this is due to technically inefficiency or allocative inefficiency by decomposing the profit inefficient estimates. We find the reduction in a bull’s semen price that would be necessary to make a bull profit efficient
Advisors/Committee Members: Tauer, Loren William (chair), Huson, Heather Jay (committee member).
Subjects/Keywords: Agriculture economics
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APA (6th Edition):
Stephan, C. (2018). ESTIMATING TECHNICAL, REVENUE, ALLOCATIVE, AND PROFIT EFFICIENCIES OF GENETIC TRAITS FOR DAIRY BULLS. (Masters Thesis). Cornell University. Retrieved from http://hdl.handle.net/1813/59586
Chicago Manual of Style (16th Edition):
Stephan, Christine. “ESTIMATING TECHNICAL, REVENUE, ALLOCATIVE, AND PROFIT EFFICIENCIES OF GENETIC TRAITS FOR DAIRY BULLS.” 2018. Masters Thesis, Cornell University. Accessed April 12, 2021.
http://hdl.handle.net/1813/59586.
MLA Handbook (7th Edition):
Stephan, Christine. “ESTIMATING TECHNICAL, REVENUE, ALLOCATIVE, AND PROFIT EFFICIENCIES OF GENETIC TRAITS FOR DAIRY BULLS.” 2018. Web. 12 Apr 2021.
Vancouver:
Stephan C. ESTIMATING TECHNICAL, REVENUE, ALLOCATIVE, AND PROFIT EFFICIENCIES OF GENETIC TRAITS FOR DAIRY BULLS. [Internet] [Masters thesis]. Cornell University; 2018. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1813/59586.
Council of Science Editors:
Stephan C. ESTIMATING TECHNICAL, REVENUE, ALLOCATIVE, AND PROFIT EFFICIENCIES OF GENETIC TRAITS FOR DAIRY BULLS. [Masters Thesis]. Cornell University; 2018. Available from: http://hdl.handle.net/1813/59586
Cornell University
2.
Stambuk, Cassandra Rae.
GENOTYPIC AND PHENOTYPIC ASSOCIATIONS WITH DIGITAL CUSHION THICKNESS IN DAIRY CATTLE.
Degree: PhD, Animal Science, 2019, Cornell University
URL: http://hdl.handle.net/1813/67514
► The bovine digital cushion is a compression pad between the distal phalanx and sole. Digital cushion thickness (DCT) is associated with lameness and claw horn…
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▼ The bovine digital cushion is a compression pad between the distal phalanx and sole. Digital cushion thickness (DCT) is associated with lameness and claw horn disruption lesions (CHDL) and estimated to be moderately heritable. This dissertation focuses on understanding DCT phenotypically and genotypically to evaluate whether DCT has an opportunity to be utilized for indirect selection against lameness and CHDL. To investigate whether DCT varied between digits, across lactation within the cow, or could be a predictor of CHDL or lameness, we collected DCT measurements at 4 time points across lactation for 183 Holstein cows from one farm. Digital cushion thickness varied within primiparous and multiparous cows based on stage in lactation and digit. Parity group and early lactation DCT measurements were predictors of CHDL and lameness during the subsequent lactation. Applying our results, we sampled 502 Holstein cows from 5 farms at 2 time points corresponding to when DCT was thickest and thinnest. The phenotypic results indicated DCT varied by time point, sacral height, parity, claw, farm, body condition score group (BCSG), and wither height. Genome-wide association studies were conducted to explore associations of genetic markers with DCT. From the associated markers, MC4R and DLG2 were identified as putative genes related to fat deposition and bone growth. To characterize DCT across multiple breeds and sexes, we sampled 698 cows and 85 bulls (Holstein and Jersey) from 8 farms. The phenotypic results indicated DCT for cows varied by breed, age, and digit; DCT for bulls varied by breed, age, digit, and BCSG. Genome-wide association studies were conducted on 9 datasets either separating or combining breed and sex. From the associated markers, MC4R, SFRS18, and LRRFIP1 function in fat deposition, DLG2, AHR, BZW2, EFNA5, USP45, and VAV3 in bone remodeling, and SOSTDC1 in epidermal keratinocyte function. Breeding programs can incorporate the markers from this work for marker assisted selection to reduce CHDL and lameness. Producers can apply the phenotypic results to adjust management practices or monitor animals with higher odds of developing CHDL and lameness. The results from this work will hopefully lead to future studies to identify the causal variants of DCT.
Advisors/Committee Members: Huson, Heather Jay (chair), McArt, Jessica Anne Allerton (committee member), Cherney, Debbie Jeannine (committee member).
Subjects/Keywords: claw horn disruption lesion; digital cushion; gene; lameness; marker; Animal sciences; Dairy cattle
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APA (6th Edition):
Stambuk, C. R. (2019). GENOTYPIC AND PHENOTYPIC ASSOCIATIONS WITH DIGITAL CUSHION THICKNESS IN DAIRY CATTLE. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/67514
Chicago Manual of Style (16th Edition):
Stambuk, Cassandra Rae. “GENOTYPIC AND PHENOTYPIC ASSOCIATIONS WITH DIGITAL CUSHION THICKNESS IN DAIRY CATTLE.” 2019. Doctoral Dissertation, Cornell University. Accessed April 12, 2021.
http://hdl.handle.net/1813/67514.
MLA Handbook (7th Edition):
Stambuk, Cassandra Rae. “GENOTYPIC AND PHENOTYPIC ASSOCIATIONS WITH DIGITAL CUSHION THICKNESS IN DAIRY CATTLE.” 2019. Web. 12 Apr 2021.
Vancouver:
Stambuk CR. GENOTYPIC AND PHENOTYPIC ASSOCIATIONS WITH DIGITAL CUSHION THICKNESS IN DAIRY CATTLE. [Internet] [Doctoral dissertation]. Cornell University; 2019. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1813/67514.
Council of Science Editors:
Stambuk CR. GENOTYPIC AND PHENOTYPIC ASSOCIATIONS WITH DIGITAL CUSHION THICKNESS IN DAIRY CATTLE. [Doctoral Dissertation]. Cornell University; 2019. Available from: http://hdl.handle.net/1813/67514
Cornell University
3.
Lima, Svetlana Ferreira.
APPLYING CUTTING EDGE DNA SEQUENCING TECHNOLOGY TO FURTHER OUR UNDERSTANDING ABOUT BOVINE HEALTH.
Degree: PhD, Animal Science, 2017, Cornell University
URL: http://hdl.handle.net/1813/56962
► Technical improvements in high-throughput sequencing technologies have opened new frontiers in microbiome research by allowing cost-effective characterization of complex microbial communities, including that of the…
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▼ Technical improvements in high-throughput sequencing technologies have opened new frontiers in microbiome research by allowing cost-effective characterization of complex microbial communities, including that of the bovine host. Targeted next generation sequencing has been shown to be an efficient approach for detection and identification of microorganisms and is more likely to be implemented in clinical and diagnostic settings due to its lower cost and shorter labor time. Such an approach relies on sequencing of a genetic marker, the 16S rRNA gene, for specific characterization of bacterial communities and bacterial pathogenic agents.
Given the potential role of the microbiome in animal health and disease, the overall objectives of this dissertation were to: 1) identify the most appropriate DNA extraction protocol that efficiently isolates a majority of the heterogeneous bacterial species encountered in non- mastitic and mastitic milk samples for accurate taxonomic profiling and detection of clinical mastitis causative agents (Chapter two); 2) use high-throughput sequencing of the 16S rRNA gene to characterize the bovine microbiome of distinct anatomical sites (mammary gland and upper respiratory tract) and its associations with bovine health (Chapters three and four); and 3) investigate the origin of the bovine microbiome (Chapter five). The present dissertation describes the effective application of the16S rRNA gene amplicon sequencing in clinical science and discovery of new pathogens. The knowledge gained from this research is novel and serves as an anchor for exploring the unfolding frontier of knowledge about the bovine microbiome across various anatomical sites and its effect on animal health.
Advisors/Committee Members: Bicalho, Rodrigo Carvalho (chair), McArt, Jessica Anne Allerton (committee member), Huson, Heather Jay (committee member), Angert, Esther R. (committee member).
Subjects/Keywords: Microbiology; 16S sRNA sequencing; Dairy cattle; High-throughput sequencing technology; Microbiome research; Animal diseases
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APA (6th Edition):
Lima, S. F. (2017). APPLYING CUTTING EDGE DNA SEQUENCING TECHNOLOGY TO FURTHER OUR UNDERSTANDING ABOUT BOVINE HEALTH. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/56962
Chicago Manual of Style (16th Edition):
Lima, Svetlana Ferreira. “APPLYING CUTTING EDGE DNA SEQUENCING TECHNOLOGY TO FURTHER OUR UNDERSTANDING ABOUT BOVINE HEALTH.” 2017. Doctoral Dissertation, Cornell University. Accessed April 12, 2021.
http://hdl.handle.net/1813/56962.
MLA Handbook (7th Edition):
Lima, Svetlana Ferreira. “APPLYING CUTTING EDGE DNA SEQUENCING TECHNOLOGY TO FURTHER OUR UNDERSTANDING ABOUT BOVINE HEALTH.” 2017. Web. 12 Apr 2021.
Vancouver:
Lima SF. APPLYING CUTTING EDGE DNA SEQUENCING TECHNOLOGY TO FURTHER OUR UNDERSTANDING ABOUT BOVINE HEALTH. [Internet] [Doctoral dissertation]. Cornell University; 2017. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1813/56962.
Council of Science Editors:
Lima SF. APPLYING CUTTING EDGE DNA SEQUENCING TECHNOLOGY TO FURTHER OUR UNDERSTANDING ABOUT BOVINE HEALTH. [Doctoral Dissertation]. Cornell University; 2017. Available from: http://hdl.handle.net/1813/56962
Cornell University
4.
Staiger, Elizabeth.
Polymorphic Gait In The Horse: An Interaction Of Genetics, Morphology, And Behavior.
Degree: PhD, Animal Science, 2015, Cornell University
URL: http://hdl.handle.net/1813/39327
► Selection after domestication has primarily focused on performance, conformation and desirable behaviors in the horse, resulting in breeds that are divergent across these traits. An…
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▼ Selection after domestication has primarily focused on performance, conformation and desirable behaviors in the horse, resulting in breeds that are divergent across these traits. An example are the "gaited" breeds, horses with the ability to perform either a lateral or diagonal fourbeat gait without a moment of suspension at intermediate speeds, yet varying in overall size and temperament. To investigate the contribution of genetics to these divergent traits, we collected DNA samples, 35 body measurements, gait information, horse discipline, and a behavior survey from 801 gaited horses. Utilizing previously genotyped horses, an across-breed genome-wide association study (GWA) identified three novel candidate regions associated with gait type on ECA1, ECA11, and EC4. A GWA in a single gaited breed, the Tennessee Walking Horse (TWH) identified two additional candidate regions on ECA19 and ECA11. Polymorphisms from whole-genome sequences have identified several SNPs within these candidate regions. We conducted principle component analysis (PCA) on 33 of the body measures for a subset of TWH. A GWA of the first PC, which describes overall size, identified the LCORL locus, which has previously been implicated with size in horses, cattle, and humans. No causal variant has been discovered yet due to extensive linkage disequilibrium (LD) in the region, but LD in the TWH is much lower, improving the resolution capabilities for fine-mapping and variant discovery. To investigate the contribution of genetics to temperament, we utilized factor analysis (FA) on the questionnaire to identify four temperament factors in TWH: neophobia, trainability, hostility, and independence. These four factors account for 64% of the total trait variance. We ran three separate GWAs using the F1-'neophobia', F2-'trainability', and F3-'hostility' scores as the phenotype and identified candidate markers in genes involved with neurodegeneration, steroidogenesis, brain development, and neuronal cell signaling pathways. The results from this work will hopefully lead to future studies to identify the causal variants of locomotion, size, and behavior traits. This will allow for the development of genetic tests to aid horse owners in their breeding and management decisions and help improve horse welfare as horses are selected for appropriate disciplines.
Advisors/Committee Members: Brooks, Samantha A. (chair), Huson, Heather Jay (committee member), Fetcho, Joseph R. (committee member), Cheetham, Jonathan (committee member).
Subjects/Keywords: Genetics; Horses; Gait
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APA ·
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APA (6th Edition):
Staiger, E. (2015). Polymorphic Gait In The Horse: An Interaction Of Genetics, Morphology, And Behavior. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/39327
Chicago Manual of Style (16th Edition):
Staiger, Elizabeth. “Polymorphic Gait In The Horse: An Interaction Of Genetics, Morphology, And Behavior.” 2015. Doctoral Dissertation, Cornell University. Accessed April 12, 2021.
http://hdl.handle.net/1813/39327.
MLA Handbook (7th Edition):
Staiger, Elizabeth. “Polymorphic Gait In The Horse: An Interaction Of Genetics, Morphology, And Behavior.” 2015. Web. 12 Apr 2021.
Vancouver:
Staiger E. Polymorphic Gait In The Horse: An Interaction Of Genetics, Morphology, And Behavior. [Internet] [Doctoral dissertation]. Cornell University; 2015. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1813/39327.
Council of Science Editors:
Staiger E. Polymorphic Gait In The Horse: An Interaction Of Genetics, Morphology, And Behavior. [Doctoral Dissertation]. Cornell University; 2015. Available from: http://hdl.handle.net/1813/39327
Cornell University
5.
Miles, Asha Marie.
Understanding the genetics underlying mastitis using a multi-pronged approach.
Degree: PhD, Animal Science, 2019, Cornell University
URL: http://hdl.handle.net/1813/70122
► This dissertation addresses deficiencies in the existing genetic characterization of mastitis due to granddaughter study designs and selection strategies based primarily on lactation average somatic…
(more)
▼ This dissertation addresses deficiencies in the existing genetic characterization of mastitis due to granddaughter study designs and selection strategies based primarily on lactation average somatic cell score (SCS). Composite milk samples were collected across 6 sampling periods representing key lactation stages: 0-1 day in milk (DIM), 3- 5 DIM, 10-14 DIM, 50-60 DIM, 90-110 DIM, and 210-230 DIM. Cows were scored for front and rear teat length, width, end shape, and placement, fore udder attachment, udder cleft, udder depth, rear udder height, and rear udder width. Independent multivariable logistic regression models were used to generate odds ratios for elevated SCC (≥ 200,000 cells/ml) and farm-diagnosed clinical mastitis. Within our study cohort, loose fore udder attachment, flat teat ends, low rear udder height, and wide rear teats were associated with increased odds of mastitis. Principal component analysis was performed on these traits to create a single new phenotype describing mastitis susceptibility based on these high-risk phenotypes. Cows (N = 471) were genotyped on the Illumina BovineHD 777K SNP chip and considering all 14 traits of interest, a total of 56 genome-wide associations (GWA) were performed and 28 significantly associated quantitative trait loci (QTL) were identified. Special focus was given to the aforementioned mastitis risk traits, and candidate gene investigation revealed both immune function and cell proliferation related genes in the areas surrounding associated QTL, suggesting that selecting for mastitis resistant cows based on these traits would be an effective method for increasing mastitis resiliency in a herd. Tracking the progression of SCS during the study period identified extreme populations of cows that remained “chronic” (SCS ≥ 4) or “healthy” (SCS < 4). Fixation indices were calculated and 2 SNPs identified that demonstrated moderate allelic differentiation of “healthy” from both “chronic” and “average” cows (FST ≥ 0.4). GWAs were performed for SCS at each sampled stage in lactation, area under the SCS curve, and median SCS, and each approach significantly associated unique QTL spanning the genome. This suggests that alternative methods to lactation average SCS must be employed to more efficiently select for mastitis-resistant cows.
Advisors/Committee Members: Huson, Heather Jay (chair), Bicalho, Rodrigo Carvalho (committee member), McArt, Jessica Anne Allerton (committee member), Virkler, Paul Douglas (committee member).
Subjects/Keywords: bovine; genome wide association study; mastitis; somatic cell count; teat conformation; udder conformation
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APA (6th Edition):
Miles, A. M. (2019). Understanding the genetics underlying mastitis using a multi-pronged approach. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/70122
Chicago Manual of Style (16th Edition):
Miles, Asha Marie. “Understanding the genetics underlying mastitis using a multi-pronged approach.” 2019. Doctoral Dissertation, Cornell University. Accessed April 12, 2021.
http://hdl.handle.net/1813/70122.
MLA Handbook (7th Edition):
Miles, Asha Marie. “Understanding the genetics underlying mastitis using a multi-pronged approach.” 2019. Web. 12 Apr 2021.
Vancouver:
Miles AM. Understanding the genetics underlying mastitis using a multi-pronged approach. [Internet] [Doctoral dissertation]. Cornell University; 2019. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1813/70122.
Council of Science Editors:
Miles AM. Understanding the genetics underlying mastitis using a multi-pronged approach. [Doctoral Dissertation]. Cornell University; 2019. Available from: http://hdl.handle.net/1813/70122
Cornell University
6.
Leal Yepes, Francisco Antonio Antonio.
STRATEGIES TO IMPROVE HEALTH AND PRODUCTION OF DAIRY COWS DURING EARLY LACTATION.
Degree: PhD, Animal Science, 2018, Cornell University
URL: http://hdl.handle.net/1813/64892
► The dairy industry directly impacts the socio-economic status of roughly 150 million families worldwide through its contribution to income, food security, and access to protein.…
(more)
▼ The dairy industry directly impacts the socio-economic status of roughly 150 million families worldwide through its contribution to income, food security, and access to protein. One of the most challenging aspects for dairy cows is the transition between the last stage of their pregnancy into a new lactation. The ability of a cow to deal with extensive physiological changes during the late pregnancy and early postpartum periods influences the entire lactation in terms of milk yield, quality, and health status. Observational and interventional studies are key to understanding the complexity of physiological changes during this transition in dairy cows. For example, the identification of genomic regions associated with the development of hyperketonemia will enhance our ability to identify the most susceptible animals to these metabolic diseases. Supplementation of diets with rumen-protected branched-chain amino acids during early postpartum may be a functional strategy to prevent adverse effects of excessive negative energy balance. Utilization of these studies and future applied research will be crucial to ensure the sustainability of the dairy industry worldwide.
Advisors/Committee Members: Nydam, Daryl Van (chair), McArt, Jessica Anne Allerton (committee member), Overton, Thomas R. (committee member), Wakshlag, Joseph J. (committee member), Huson, Heather Jay (committee member).
Subjects/Keywords: BCAA; GWAS; Dairy cows; Hyperketonemia; Genetics; Molecular biology; Epidemiology
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APA ·
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APA (6th Edition):
Leal Yepes, F. A. A. (2018). STRATEGIES TO IMPROVE HEALTH AND PRODUCTION OF DAIRY COWS DURING EARLY LACTATION. (Doctoral Dissertation). Cornell University. Retrieved from http://hdl.handle.net/1813/64892
Chicago Manual of Style (16th Edition):
Leal Yepes, Francisco Antonio Antonio. “STRATEGIES TO IMPROVE HEALTH AND PRODUCTION OF DAIRY COWS DURING EARLY LACTATION.” 2018. Doctoral Dissertation, Cornell University. Accessed April 12, 2021.
http://hdl.handle.net/1813/64892.
MLA Handbook (7th Edition):
Leal Yepes, Francisco Antonio Antonio. “STRATEGIES TO IMPROVE HEALTH AND PRODUCTION OF DAIRY COWS DURING EARLY LACTATION.” 2018. Web. 12 Apr 2021.
Vancouver:
Leal Yepes FAA. STRATEGIES TO IMPROVE HEALTH AND PRODUCTION OF DAIRY COWS DURING EARLY LACTATION. [Internet] [Doctoral dissertation]. Cornell University; 2018. [cited 2021 Apr 12].
Available from: http://hdl.handle.net/1813/64892.
Council of Science Editors:
Leal Yepes FAA. STRATEGIES TO IMPROVE HEALTH AND PRODUCTION OF DAIRY COWS DURING EARLY LACTATION. [Doctoral Dissertation]. Cornell University; 2018. Available from: http://hdl.handle.net/1813/64892
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