Superior single nucleotide polymorphisms that contribute to two main routes of the fatty acid synthesis pathway in Korean cattle

Abstract

The fatty acid composition of adipose tissue in livestock has been recognized as an important carcass trait that affects meat quality. To determine the overall positive effect on fatty acid synthesis, we investigated PPARγ, SREBPs, FABP4, SCD, and FASN genes because SNP and/or SNP combinations were strongly affecting each fatty acid synthesis pathway. We screened their SNPs, SNP combinations, and genotype. Furthermore, we studied the economic traits C18:1, monounsaturated fatty acid (MUFA), and marbling score (MS). To enhance the accuracy of the predictive genetic effect, we applied a statistical adjustment model excluding environmental factors. We also selected superior genes, gene combinations, and genotypes for each economic trait by using multifactor dimensionality reduction. Based on the results, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.10153 A>G, g.3977-325 T>C) (AACC, AGCC, GGCC), (g.3690 G>A, g.3977-325 T>C) (GGCC, GACC), (g.3977-325 T>C, g.25670 C>T) (CCCC, CCCT, CCTT) (genotypes of the best SNP combination) was selected as the best gene combination for C18:1 and MUFA. In addition, g.3977-325 T>C (CC) was selected as the best genotype of the SNP and the combination (g.3977-325 T>C, g.6974 G>A) (TTAA, CTAA, CCAA, CCGA, CCGG) as the best SNP combination for MS. We integrated genes that were selected as excellent SNP and SNP combinations affecting two main routes of the fatty acid synthesis pathway and identified the best and final SNP, SNP combination, and superior genotype.

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Acknowledgements

Jea-Young Lee’s work was supported by the 2018 Yeungnam University Research Grant.

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Correspondence to Dong-yep Oh or Kyudong Han.

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Jea-Young Lee, Jaejung Ha, Junkoo Yi, Jieun Jang, Wooseok Lee, Yoonseok Lee, Dong-yep Oh, and Kyudong Han declare that they have no conflict of interest.

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All research protocols and animal experiments in this study were reviewed and approved by the Institutional Animal Care and Use Committee (IACUC) in Gyeongsangbuk-do, Republic of Korea (Gyeongbuk IACUC-87).

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Lee, JY., Ha, J., Yi, J. et al. Superior single nucleotide polymorphisms that contribute to two main routes of the fatty acid synthesis pathway in Korean cattle. Genes Genom 40, 945–954 (2018). https://doi.org/10.1007/s13258-018-0704-2

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Keywords

  • Hanwoo
  • Fatty acid synthesis pathway
  • Single nucleotide polymorphism (SNP)
  • Statistical adjustment model
  • Multifactor dimensionality reduction (MDR)