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Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle

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Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle Animal Science Publications Animal Science 8-18-2021 Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle Muhammad Dawood International Islamic University Luke Matthew Kramer Iowa State University, [email protected] Muhammad Imran Shabbir International Islamic University James Mark Reecy Iowa State University, [email protected] Follow this and additional works at: https://lib.dr.iastate.edu/ans_pubs Part of the Agriculture Commons, Animal Experimentation and Research Commons, Beef Science Commons, and the Genetics and Genomics Commons The complete bibliographic information for this item can be found at https://lib.dr.iastate.edu/ ans_pubs/955. For information on how to cite this item, please visit http://lib.dr.iastate.edu/ howtocite.html. This Article is brought to you for free and open access by the Animal Science at Iowa State University Digital Repository. It has been accepted for inclusion in Animal Science Publications by an authorized administrator of Iowa State University Digital Repository. For more information, please contact [email protected]. Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle Abstract Livestock is an important commodity playing a major role in the global economy. Red meat plays an important role in human life, as it is a good source of animal protein and energy. The fatty acid content of beef has been shown to impact the eating experience and nutritional value of beef. Therefore, this study aimed to identify genomic regions which can account for genetic variation in meat fatty acid content. Genotypes imputed to the Illumina BovineHD 770K BeadChip were used in this study. Thirty-six 1-Mb genomic regions with a posterior probability of inclusion (PPI) greater than 0.90 were identified ot be associated with variation in the content of at least one fatty acid. The genomic regions (1Mb) which were associated with more than one fatty acid trait with high genetic variance and harbored good candidate genes were on Chromosome (Chr) 6 (fatty acid binding protein 2), Chr 19 (thyroid hormone receptor alpha, fatty acid synthase), Chr 26 (stearoyl-CoA desaturase), and Chr 29 (thyroid hormone responsive, fatty acid desaturase 2, and fatty acid desaturase 3). Further studies are required to identify the causal variants within the identified genomic egions.r Findings from the present study will help to increase understanding of the variation in fatty acid content of beef and help to enhance selection for beef with improved fatty acid composition. Keywords fatty acids, beef, GWAS, high density genotyping, Black Angus Disciplines Agriculture | Animal Experimentation and Research | Animal Sciences | Beef Science | Genetics and Genomics Comments This article is published as Dawood, Muhammad, Luke Matthew Kramer, Muhammad Imran Shabbir, and James Mark Reecy. "Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle." Animals 11, no. 8 (2021): 2424. doi:10.3390/ani11082424. Creative Commons License This work is licensed under a Creative Commons Attribution 4.0 International License. This article is available at Iowa State University Digital Repository: https://lib.dr.iastate.edu/ans_pubs/955 animals Article Genome-Wide Association Study for Fatty Acid Composition in American Angus Cattle Muhammad Dawood 1,2 , Luke Matthew Kramer 3, Muhammad Imran Shabbir 1 and James Mark Reecy 3,* 1 Department of Biological Sciences, International Islamic University, Islamabad 44000, Pakistan; [email protected] (M.D.); [email protected] (M.I.S.) 2 Department of Animal Breeding & Genetics, University of Veterinary and Animal Sciences, Lahore 54000, Pakistan 3 Department of Animal Science, Iowa State University, 2255 Kildee Hall, Ames, IA 50011, USA; [email protected] * Correspondence: [email protected] Simple Summary: Almost everybody depends on livestock for various reasons directly or indirectly. Consequently, improving livestock production means improving human life. Meat plays important role in human life, as it is good source of protein and energy. Meat composition depends on breed’s genetics and environmental factors. Fatty acids (FA) play important role in human diet and health. FA add flavor and taste to meat. Fatty acid composition of meat is a complex polygenic trait that is controlled by genetics and environmental factors. Therefore, the objective of the present study was to identify genomic regions associated with FA composition in American Angus. Thirty-six different genomic regions were identified associated with variation in at least one FA. The genomic regions associated with more than one FA and high genetic variance, harbor good candidate genes (e.g., FABP2, FASN, FADS2, FADS3 and SCD). The identified makers could be used to select for altered FA profile and help to increase the understanding of the genetic basis of FA composition. Furthermore, findings from the present study could help to devise effective breeding plans and selection strategies for the improvement of beef FA profile. Citation: Dawood, M.; Kramer, L.M.; Abstract: Livestock is an important commodity playing a major role in the global economy. Red meat Shabbir, M.I.; Reecy, J.M. Genome-Wide Association Study for plays an important role in human life, as it is a good source of animal protein and energy. The fatty Fatty Acid Composition in American acid content of beef has been shown to impact the eating experience and nutritional value of beef. Angus Cattle. Animals 2021, 11, 2424. Therefore, this study aimed to identify genomic regions which can account for genetic variation https://doi.org/10.3390/ani11082424 in meat fatty acid content. Genotypes imputed to the Illumina BovineHD 770K BeadChip were used in this study. Thirty-six 1-Mb genomic regions with a posterior probability of inclusion (PPI) Received: 1 July 2021 greater than 0.90 were identified to be associated with variation in the content of at least one fatty Accepted: 12 August 2021 acid. The genomic regions (1Mb) which were associated with more than one fatty acid trait with Published: 18 August 2021 high genetic variance and harbored good candidate genes were on Chromosome (Chr) 6 (fatty acid binding protein 2), Chr 19 (thyroid hormone receptor alpha, fatty acid synthase), Chr 26 (stearoyl- Publisher’s Note: MDPI stays neutral CoA desaturase), and Chr 29 (thyroid hormone responsive, fatty acid desaturase 2, and fatty acid with regard to jurisdictional claims in desaturase 3). Further studies are required to identify the causal variants within the identified published maps and institutional affil- genomic regions. Findings from the present study will help to increase understanding of the iations. variation in fatty acid content of beef and help to enhance selection for beef with improved fatty acid composition. Keywords: fatty acids; beef; GWAS; high density genotyping; Black Angus Copyright: © 2021 by the authors. Licensee MDPI, Basel, Switzerland. This article is an open access article distributed under the terms and 1. Introduction conditions of the Creative Commons Attribution (CC BY) license (https:// Beef has a high nutritional value, and it is a rich source of minerals, vitamins, and pro- creativecommons.org/licenses/by/ tein. The consumer is becoming more concerned about their health and more conscious 4.0/). about the quality of the meat that they consume. Consumers have been told that beef Animals 2021, 11, 2424. https://doi.org/10.3390/ani11082424 https://www.mdpi.com/journal/animals Animals 2021, 11, 2424 2 of 16 consumption is associated with some serious health issues, such as heart diseases and obesity [1]. However, recent findings have shown that the long-standing belief that beef is associated with cardiovascular disease is incorrect [2–7]. Furthermore, fat is a very im- portant constituent of the human daily diet; it provides energy and also contains essential fatty acids, and adds flavor to food [8]. The fatty acids present in animal tissues can be separated into phospholipid and triacylglyceride fractions [9]. Fatty acid composition and fat content of the beef are associated with the taste, flavor, and sensory properties of the meat [10]. It has been reported that fatty acid composition varies across different breeds and feeding regimes [10,11]. The mechanism that control fatty acid composition of meat is a complex process that is regulated by genetics and environmental factors. There have been several studies published that evaluated the extent to which genetics controlled variation in fatty acid composition in Santa Gertrudis, Brahman, Hereford, Nellore, and Black Angus cattle breeds [12–14]. Identification of genomic markers and regions associated with beef fatty acids could be used to select for an improved fatty acid profile and to alter the saturated to mono- and polyunsaturated fatty acid ratios. The objective of the present study was to identify genomic regions associated with fatty acid composition in American Angus cattle. 2. Materials and Methods 2.1. Animal Selection The purebred American Angus cattle used in the current study were reared according to standard animal care procedures, approved by the Iowa State University Animal Care and Use Committee. All the research animals were raised on Iowa State University research demonstration farms. 2.2. Sampling and DNA Isolation A total of 2177 American Black Angus calves sired by 134 sires were used in this study. Blood samples were collected from the jugular vein. DNA samples were collected as previously described by Garmyn et al. [15]. DNA was stored at -20 degrees Celsius until further processing. 2.3. Genotype Data Animals were originally genotyped with either the BovineSNP50 BeadChip (Illumina, San Diego, CA, USA) or the BovineHD BeadChip (Illumina, San Diego, CA, USA) by Neogen GeneSeek Operations (Lincoln, NE, USA). Animals genotyped with the BovineSNP50 BeadChip were imputed to the BovineHD BeadChip SNP density using FImpute [16] and SNPipeline package (Hailin Su, https://github.com/cbkmephisto/SNPipeline (accessed on 27 February 2017)) by using 820 Angus individuals originally genotyped on the BovineHD BeadChip. These 820 individuals included animals from the ISU herd and external animals.
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