Animal Industry Report ASL R2952
AS 661
2015
Fatty Acid SNP Interaction Analysis in Angus Sired
Beef Cattle
Luke M. Kramer
Iowa State University, [email protected]
James E. Koltes
Iowa State University, [email protected]
Eric R. Fritz-Waters
Iowa State University, [email protected]
Mary Sue Mayes
Iowa State University, [email protected]
Alysta Markey
Iowa State University
See next page for additional authors
Recommended Citation
Kramer, Luke M.; Koltes, James E.; Fritz-Waters, Eric R.; Mayes, Mary Sue; Markey, Alysta; Saatchi, Mahdi; Weeks, Nathan T.; and
Reecy, James M. () "Fatty Acid SNP Interaction Analysis in Angus Sired Beef Cattle," Animal Industry Report: AS 661, ASL R2952.
Available at: http://lib.dr.iastate.edu/ans_air/vol661/iss1/15
This Beef is brought to you for free and open access by the Animal Science Research Reports at Digital Repository @ Iowa State University. It has been
accepted for inclusion in Animal Industry Report by an authorized administrator of Digital Repository @ Iowa State University. For more information,
please contact [email protected].
Fatty Acid SNP Interaction Analysis in Angus Sired Beef Cattle
Cover Page Footnote
This research was supported by Zoetis Animal Genetics. This research was supported by NIFA Award
No-2012-3842-19286. This research was supported by the HPC equipment purchased through NSF MRI
grant number CNS 1229081 and NSF CRI grant number 1205413.
Authors
Luke M. Kramer, James E. Koltes, Eric R. Fritz-Waters, Mary Sue Mayes, Alysta Markey, Mahdi Saatchi,
Nathan T. Weeks, and James M. Reecy
This beef is available in Animal Industry Report: http://lib.dr.iastate.edu/ans_air/vol661/iss1/15
Iowa State University Animal Industry Report 2015
Fatty Acid SNP Interaction Analysis in Angus Sired Beef Cattle
A.S. Leaflet R2952 chromatography. These values were collected on forty-four
different TAG fatty acids. All calves were genotype with the
Luke M. Kramer, Graduate Research Assistant; Illumina 54k SNP chip.
James E. Koltes, Postdoctoral Assistant;
Eric R. Fritz-Waters, Research Associate; Statistical analyses were performed to identify
Mary Sue Mayes, Research Associate; interactions between SNPs that exhibited an additive-by-
Alysta Markey, Research Associate; additive, additive-by-dominance or dominance-by-
Mahdi Saatchi, Postdoctoral Assistant; dominance interactions (Table 1). False discovery rate was
Nathan T. Weeks, Systems Analyst; estimated for SNP interactions to account for multiple
testing. Genotype frequency filters were applied to the
James M. Reecy, Professor, Department of Animal Science interactions remaining after FDR analysis, at 5, 10, 20, 50,
and 100 animals per genotype combination. Interactions
Summary and Implications were then plotted for each individual fatty acid in order to
The triacylglyceride (TAG) fatty acid content in meat visualize which chromosomes and which regions are
from Angus-sired cattle was analyzed for non-additive responsible for the interactions discovered (Figure 1).
genetic effects. A total of 11,482 significant DNA marker
interactions (false discovery rate [FDR] < 0.05) were Results and Discussions
detected across thirty-seven different TAG fatty acids. A total of 11,482 significant interactions (FDR < 0.05)
Interactions were not evenly distributed amongst all fatty were detected through our SNP interaction analysis (Table
acids analyzed, and types of interactions (additive-by- 1). A decreasing number of significantly detected
additive, additive-by-dominance, and dominance-by- interactions were seen as the filters became more stringent.
dominance) varied within each individual fatty acid. These Of particular note are TAG fatty acid traits 14:0,
results indicate that it may be possible to account for 18:1t10pt11, and the AI (atherogenic index). These three
additional genetic variance amongst TAG fatty acids over fatty acids had over 500 significant interactions despite
and above individual markers. requiring at minimum 100 animals of each genotype. Traits
were also examined as a broader category such as Saturated
Introduction Fatty Acids (SFA), Monounsaturated Fatty Acids (MUFA),
Increasing awareness of what people are eating has Polyunsaturated Fatty Acids (PUFA), and
brought about a nutritionally minded group of consumers. Ratio/Calculation. The PUFA category of TAG fatty acids
Fatty acid consumption has been associated with some contained the smallest proportion of significant interactions
negative health traits such as cardiovascular disease, and as from this study (0.077) while nearly half the total
such has become an important point of contention amongst interactions discovered (0.483) were associated with
consumers. As such, additional research into how much MUFA.
genetic variance can be accounted for within the various Results for the TAG fatty acids indicate the potential to
fatty acids is an important undertaking in order to better account for additional genetic variation amongst these traits
understand how the traits are controlled and inherited. By in Angus-sired beef cattle. Combined with previous work
better understanding the genetic variance that controls TAG that characterized individual SNP effects, this SNP
fatty acids, we will be better equipped to select for animals interaction study contributed to the total variation that has
with altered fatty acid composition as desired by the been accounted for and will help with selection on various
consumer market. traits as the market demands.
Materials and Methods Acknowledgement
A subset, 1721 head of cattle, was utilized from the This research was supported by Zoetis Animal
beef healthfulness study previously completed. TAG fatty Genetics.
acid fractions of the longissimus dorsi were collected after This research was supported by NIFA Award No-2012-
freeze grinding steaks into a powder. Total lipid fraction 3842-19286.
was extracted from this powder via a chloroform and This research was supported by the HPC equipment
methanol mixture, and then the TAG fraction was separated purchased through NSF MRI grant number CNS 1229081
from the phospholipid fatty acid fraction via thin-layer and NSF CRI grant number 1205413.
chromatography and then quantitated by gas
Iowa State University Animal Industry Report 2015
Table 1. Interaction type breakdown by individual TAG fatty Figure 1: SNP by SNP interactions for TAG fatty acid 18:0
acid at FDR significance and 5-animal filter
Blue lines are significant SNP interactions, Grey blocks
are chromosomes labeled 1 to X. 353 total significant interactions
visualized at FDR < 0.05 and 5 animal filter