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8. Additional file 1 of Use of gene expression and whole-genome sequence information to improve the accuracy of genomic prediction for carcass traits in Hanwoo cattle

Author

Heras-Saldana, Sara De Las, Lopez, Bryan Irvine, Moghaddar, Nasir, Woncheoul Park, Jong-Eun Park, Chung, Ki Y., Dajeong Lim, Lee, Seung H., Donghyun Shin, and Werf, Julius H. J. Van Der

Abstract

Additional file 1: Figure S1. Venn diagram with the number of samples that overlap between four sizes of the discovery dataset (D; from 1000 to 4000 animals). Marbling score (MS), eye muscle area (EMA), carcass weight (CWT), and back fat thickness (BFT).

Published
2020
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9. Genome wide association study of fatty acid composition in Duroc swine

Author

Viterbo, Vanessa S., Lopez, Bryan Irvine M., Kang, Hyunsung, Kim, Hoonseop, Song, Choul-won, and Seo, Kang Seok

Subjects
0301 basic medicine, Candidate gene, lcsh:Animal biochemistry, Genome-wide association study, Single-nucleotide polymorphism, Biology, Genome, Article, 03 medical and health sciences, chemistry.chemical_compound, Gene, lcsh:QP501-801, lcsh:SF1-1100, chemistry.chemical_classification, Genetics, Fatty acid, Stearoyl-CoA Desaturase (SCD) Gene, Animal Breeding and Genetics, Stearoyl-CoA Desaturase () Gene, Genome Wide Association Study (GWAS), Duroc, Oleic acid, 030104 developmental biology, chemistry, Animal Science and Zoology, Stearic acid, lcsh:Animal culture, Fatty Acid, Food Science
Abstract

Objective Genome wide association study was conducted to identify and validate candidate genes associated with fatty acid composition of pork. Methods A total of 480 purebreed Duroc pigs were genotyped using IlluminaPorcine60k bead chips while the association test was implemented following genome-wide rapid association using Mixed Model and Regression-Genomic Control (GRAMMAR-GC) approach. Results A total of 25, 29, and 16 single nucleotide polymorphisms (SNPs) were significantly associated with stearic (18:0), oleic (18:1) and saturated fatty acids (SFA), respectively. Genome wide significant variants were located on the same region of swine chromosome 14 (SSC14) that spanned from 120 to 124 Mb. Top SNP ALGA008191 was located at 5 kb near the stearoyl-CoA desaturase (SCD) gene. This gene is directly involved in desaturation of stearic acid into oleic acid. General relationship of significant SNPs showed high linkage disequilibrium thus genome-wide signals was attributed to SCD gene. However, understanding the role of other genes like elongation of very long chain fatty acids-3 (ELOVL3) located on this chromosomal segment might help in further understanding of metabolism and biosynthesis of fatty acids. Conclusion Overall, this study provides evidence that validates SCD gene as strong candidate gene associated with fatty acid composition in Duroc pigs. Moreover, this study confirms significant SNPs near ELOVL3 gene.

Published
2018

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