Animal & Avian Sciences

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Start date: 2022Subject: search.filters.subject.GWAS

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    Phenotypic and Genetic Analysis of Reasons for Disposal in Dairy Cattle
    (2024) Iqbal, Victoria Audrey; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Reasons for disposal are defined as why a cow has left the herd during lactation and are documented as termination codes. Dairy cattle termination codes were collected by Dairy Records Processing Centers and stored in the National Cooperator Database maintained by the Council on Dairy Cattle Breeding for analysis. The list of possible termination codes is as follows: code 0 is cow lactation that ended typically without an abortion, code 1 is locomotion problems, code 2 is female transferred or sold, code 3 is low milk yield, code 4 is reproductive problems, code 5 is unspecified reasons, code 6 is death, code 7 is the presence of mastitis, code 8 is abortion, code 9 is udder problems, code A is an unfavorable phenotype, and lastly code B is undesirable temperament. Understanding termination codes is the key to understanding and improving farm management. Unfortunately, the secondary termination codes are not utilized, despite studies saying one reason is too limited. Heifer termination codes should be more utilized, and studies show that this could improve heifer management. The four processing centers' principal termination codes deviated a little from year to year, but processing center D had the most variation in principal termination codes. There were few records with termination codes 9, A, and B. There was low lameness found for Jersey cattle but more fluctuations for their termination codes 6, 7, and 8. Jersey's main reason for disposal was sold and low milk yield. As for Holstein, the main reasons for disposal were low milk production and death. Recommendations include removing termination code 5 (other reasons) and enforcing a secondary termination code for code 2 (sold). Also, including the percentage of animal records used in traits developed at the CDCB was recommended to encourage farmers to add more records to improve breeding selections. Overall, the top main reasons for disposal were low milk yield, death, and reproduction across breeds from 2011 to 2022. To determine whether health traits correlate to termination codes and how health traits change the probability of survival, a multinomial logistic regression was developed, where twelve health traits, breeds, and other factors were used as an independent variable for the termination code, the dependent variable. The output is a regression coefficient list that conveys the effect of each health trait for each termination code. The results show the apparent impacts of animal breeds on different termination codes, such as dairy crossbreeds negatively affecting termination due to reproductive advantages that follow the literature. Lastly, using termination codes as phenotype, this study focuses on developing a genome-wide association study (GWAS) using the Weighted single-step Genomic Best Linear unbiased prediction (WssGBLUP) model to find significant SNPs related to survival in Holstein cows. In summary, this study provided an understanding of reasons for disposal trends, modeled the reasons for disposal, determined the likelihood of termination post-incidence, and found the heritability and important SNPs of each termination code.
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    Weighted Single-Step GWAS Identifies Genes Influencing Fillet Color in Rainbow Trout
    (MDPI, 2022-07-26) Ahmed, Ridwan O.; Ali, Ali; Al-Tobasei, Rafet; Leeds, Tim; Kenney, Brett; Salem, Mohamed
    The visual appearance of the fish fillet is a significant determinant of consumers’ purchase decisions. Depending on the rainbow trout diet, a uniform bright white or reddish/pink fillet color is desirable. Factors affecting fillet color are complex, ranging from the ability of live fish to accumulate carotenoids in the muscle to preharvest environmental conditions, early postmortem muscle metabolism, and storage conditions. Identifying genetic markers of fillet color is a desirable goal but a challenging task for the aquaculture industry. This study used weighted, single-step GWAS to explore the genetic basis of fillet color variation in rainbow trout. We identified several SNP windows explaining up to 3.5%, 2.5%, and 1.6% of the additive genetic variance for fillet redness, yellowness, and whiteness, respectively. SNPs are located within genes implicated in carotenoid metabolism (β,β-carotene 15,15′-dioxygenase, retinol dehydrogenase) and myoglobin homeostasis (ATP synthase subunit β, mitochondrial (ATP5F1B)). These genes are involved in processes that influence muscle pigmentation and postmortem flesh coloration. Other identified genes are involved in the maintenance of muscle structural integrity (kelch protein 41b (klh41b), collagen α-1(XXVIII) chain (COL28A1), and cathepsin K (CTSK)) and protection against lipid oxidation (peroxiredoxin, superoxide dismutase 2 (SOD2), sestrin-1, Ubiquitin carboxyl-terminal hydrolase-10 (USP10)). A-to-G single-nucleotide polymorphism in β,β-carotene 15,15′-dioxygenase, and USP10 result in isoleucine-to-valine and proline-to-leucine non-synonymous amino acid substitutions, respectively. Our observation confirms that fillet color is a complex trait regulated by many genes involved in carotenoid metabolism, myoglobin homeostasis, protection against lipid oxidation, and maintenance of muscle structural integrity. The significant SNPs identified in this study could be prioritized via genomic selection in breeding programs to improve fillet color in rainbow trout.
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    The Genetic Architecture of Complex Traits and Diseases in Dairy Cattle
    (2022) Freebern, Ellen; Ma, Li; Animal Sciences; Digital Repository at the University of Maryland; University of Maryland (College Park, Md.)
    Genetic architecture refers to the number and locations of genes that affect a trait, as well as the magnitude and the relative contributions of their effects. A better understanding of the genetic architecture of complex traits and diseases will be beneficial for analyzing genetic contributions to disease risk and for estimating genetic values of agricultural importance. In particular, genetic and genomic selection in dairy cattle populations has been well established and exploited through genome-wide association studies, sequencing studies, and functional studies. The objective of this dissertation is to understand the genetic architecture of complex traits and apply the understanding to investigate the biological relationship between genetics and diseases in dairy cattle. First, we performed GWAS and fine-mapping analyses on livability and six health traits in Holstein-Friesian cattle. From our analyses, we reported significant associations and candidate genes relevant to cattle health. Second, we evaluated genome-wide diversity in cattle over a period of time by running GWAS and proposed a gene dropping simulation program. From this study, we identified candidate variants under selection that are associated with biological and economically important traits in cattle. Also, we demonstrated that gene dropping is an applicable method to investigate changes in the cattle genome over time. Third, we investigated the effect of maternal age and temperature on recombination rate in cattle. We provided novel results regarding the plasticity of meiotic recombination in cattle. Additionally, we found a positive correlation between environmental temperature at conception and recombination rate in Holstein-Friesian cows. Collectively, these studies advance our understanding of the genetic architecture and the biological relationship between complex traits and diseases in dairy cattle.