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Genes Genomics. 2018 Sep;40(9):945-954. doi: 10.1007/s13258-018-0704-2. Epub 2018 May 15.

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

Author information

1
Department of Statistics, Yeungnam University, Gyeongsan-si, Gyeongbuk, 38541, Republic of Korea.
2
Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea.
3
Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea.
4
Department of Biotechnology, College of Agriculture & Life Science, Hankyong National University, Anseong, Gyeonggi, 17579, Republic of Korea.
5
Livestock Research Institute, Gyeongsangbuk-Do, Yeongju, Gyeongbuk, 36052, Republic of Korea. ody1234@korea.kr.
6
Department of Nanobiomedical Science & BK21 PLUS NBM Global Research Center for Regenerative Medicine, Dankook University, Cheonan, 31116, Republic of Korea. kyudong.han@gmail.com.

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 PPARĪ³, 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.

KEYWORDS:

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

PMID:
30155709
DOI:
10.1007/s13258-018-0704-2
[Indexed for MEDLINE]

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