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. 2019 Mar 4:10:27.
doi: 10.1186/s40104-019-0322-0. eCollection 2019.

Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle

Zezhao Wang #  1   2 , Bo Zhu #  1 , Hong Niu  1 , Wengang Zhang  1 , Ling Xu  1 , Lei Xu  1   3 , Yan Chen  1 , Lupei Zhang  1 , Xue Gao  1 , Huijiang Gao  1 , Shengli Zhang  2 , Lingyang Xu  1 , Junya Li  1
Affiliations

Genome wide association study identifies SNPs associated with fatty acid composition in Chinese Wagyu cattle

Zezhao Wang et al. J Anim Sci Biotechnol. .

Abstract

Background: Fatty acids are important traits that affect meat quality and nutritive values in beef cattle. Detection of genetic variants for fatty acid composition can help to elucidate the genetic mechanism underpinning these traits and promote the improvement of fatty acid profiles. In this study, we performed a genome-wide association study (GWAS) on fatty acid composition using high-density single nucleotide polymorphism (SNP) arrays in Chinese Wagyu cattle.

Results: In total, we detected 15 and 8 significant genome-wide SNPs for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, respectively. Also, we identified nine candidate genes based on 100 kb regions around associated SNPs. Four SNPs significantly associated with C14:1 cis-9 were embedded with stearoyl-CoA desaturase (SCD), while three SNPs in total were identified for C22:6 n-3 within Phospholipid scramblase family member 5 (PLSCR5), Cytoplasmic linker associated protein 1 (CLASP1), and Chymosin (CYM). Notably, we found the top candidate SNP within SCD can explain ~ 7.37% of phenotypic variance for C14:1 cis-9. Moreover, we detected several blocks with high LD in the 100 kb region around SCD. In addition, we found three significant SNPs within a 100 kb region showing pleiotropic effects related to multiple FA groups (PUFA, n-6, and PUFA/SFA), which contains BAI1 associated protein 2 like 2 (BAIAP2L2), MAF bZIP transcription factor F (MAFF), and transmembrane protein 184B (TMEM184B).

Conclusions: Our study identified several significant SNPs and candidate genes for individual fatty acids and fatty acid groups in Chinese Wagyu cattle, and these findings will further assist the design of breeding programs for meat quality in cattle.

Keywords: Chinese Wagyu cattle; Fatty acids; GWAS; Meat quality; Pleiotropic effects.

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Conflict of interest statement

Animal experiments were approved by the Science Research Department of the Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS) (Beijing, China). There was no use of human participants, data or tissues.Not applicable.The authors declare that they have no competing interests.

Figures

Fig. 1
Fig. 1
a Manhattan plot of association results for C22:0, where the Y-axis was defined as -log10(P) and the genomic position was represented along the X-axis. The green line indicated P = 1.36E-06. b Quantile-quantile plot of 503,579 SNPs in the genome-wide association study for C22:0. c Manhattan plot showing P-values of association for C14:1 cis-9. d Quantile-quantile plot for C14:1 cis-9. e Manhattan plot of association results for C18:1 cis-9. f Quantile-quantile plot for C18:1 cis-9. g Manhattan plot showing P-values of association for C20:1 cis-11. h Quantile-quantile plot of for C20:1 cis-11. i Manhattan plot showing P-values of association for C22:6 n-3. j Quantile-quantile plot for C22:6 n-3
Fig. 2
Fig. 2
a Regional plots of candidate region at 21.05–21.21 Mb on BTA26 for C14:1 cis-9, the top SNP was highlighted by blue solid circles. Different levels of linkage disequilibrium (LD) between the most significant SNP and surrounding SNPs were indicated in different colors. b LD block for the region located at 21.05 Mb - 21.25 Mb on BTA26
Fig. 3
Fig. 3
a Manhattan plot of association results for SFA, where the Y-axis was defined as -log10(P) and the genomic position was represented along the X-axis. The green line indicated P = 1.36E-06. b Quantile-quantile plot of 503,579 SNPs in the genome-wide association study for SFA. c Manhattan plot showing P-values of association for PUFA. d Quantile-quantile plot for PUFA. e Manhattan plot showing P-values of association for MUFA. f Quantile-quantile plot for MUFA. g Manhattan plot showing P-values of association for n-6. h Quantile-quantile plot for n-6. i Manhattan plot showing P-values of association for PUFA/SFA. j Quantile-quantile plot for PUFA/SFA
Fig. 4
Fig. 4
a Regional plot of candidate region at 110.34–110.53 Mb on BTA5 for PUFA. b Regional plot of candidate region at 110.34–110.53 Mb on BTA5 for n-6 group. c Regional plot of candidate region at 110.34–110.53 Mb on BTA5 for PUFA/SFA. d LD block for the region located at 110.34–110.53 Mb on BTA5
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