Dataset Information

Identification of Single Nucleotide Polymorphism Marker and Association Analysis of Marbling Score in Fas Gene of Hanwoo.

ABSTRACT: The Fas (APO-1, TNFRSF6) gene known as a member of the tumor necrosis factor receptor superfamily was selected for DNA marker development in Korean cattle. It is a cell membrane protein and mediates programmed cell death (apoptosis). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers related to economical traits at the genomic level. The sequences of whole exon and 1 kb range of both front and back of the gene were determined by direct-sequencing methods using 24 cattle. A total of 55 SNPs were discovered and we selected 31 common polymorphic sites considering their allele frequencies, haplotype-tagging status and linkage disequilibrium (LD) for genotyping in larger-scale subjects. The SNPs were confirmed genotype through the SNaPshot method (n = 274) and were examined for a possible genetic association between Fas polymorphisms and marbling score. So, the SNPs that were identified significant are g.30256G>C, g.31474C>A, g.31940A>G, and g.32982G>A. These results suggest that SNPs of Fas gene were associated with intramuscular fat content of meat quality traits in Korean cattle.

SUBMITTER: Kim SC

PROVIDER: S-EPMC4698685 | biostudies-literature | 2016 Jan

REPOSITORIES: biostudies-literature

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Identification of Single Nucleotide Polymorphism Marker and Association Analysis of Marbling Score in Fas Gene of Hanwoo.

Kim Seung-Chang SC Lee Seung-Hwan SH Lee Ji-Woong JW Kim Tae-Hun TH Choi Bong-Hwan BH

Asian-Australasian journal of animal sciences 20160101 1

The Fas (APO-1, TNFRSF6) gene known as a member of the tumor necrosis factor receptor superfamily was selected for DNA marker development in Korean cattle. It is a cell membrane protein and mediates programmed cell death (apoptosis). We discovered single nucleotide polymorphisms (SNPs) within Fas gene in order to develop novel DNA markers related to economical traits at the genomic level. The sequences of whole exon and 1 kb range of both front and back of the gene were determined by direct-sequ ...[more]

PMID: 26732324

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Project description:Genomic selection using high-density single-nucleotide polymorphism (SNP) markers is used in dairy and beef cattle breeds to accurately estimate genomic breeding values and accelerate genetic improvement by enabling selection of animals with high genetic merit. This genome-wide association study (GWAS) aimed to identify genetic variants associated with beef fatty-acid composition (FAC) traits and to evaluate the accuracy of genomic predictions (GPs) for those traits using genomic best linear unbiased prediction (GBLUP), pedigree BLUP (PBLUP), and BayesR models. Samples of the longissimus dorsi muscle of 965 thirty-month-old Hanwoo steers (progeny of 73 proven bulls) were used to investigate 14 FAC traits. Animals were genotyped or imputed using two bovine SNP platforms (50K and 777K), and after quality control, 38,715 (50K) and 633,448 (777K) SNPs were subjected to GWAS and GP study using a cross-validation scheme. SNP-based heritability estimates were moderate to high (0.25 to 0.47) for all studied traits, with some exceptions for polyunsaturated fatty acids. Association analysis revealed that 19 SNPs in BTA19 (98.7 kb) were significantly associated (P < 7.89 × 10-8) with C14:0 and C18:1n-9; these SNPs were in the fatty-acid synthase (FASN) and coiled-coil domain-containing 57 (CCDC57) genes. BayesR analysis revealed that 0.41 to 0.78% of the total SNPs (n = 2,571 to 4,904) explained almost all of the genetic variance; the majority of the SNPs (>99%) had negligible effects, suggesting that the FAC traits were polygenic. Genome partitioning analysis indicated mostly nonlinear and weak correlations between the variance explained by each chromosome and its length, which also reflected the considerable contributions of relatively few genes. The prediction accuracy of breeding values for FAC traits varied from low to high (0.25 to 0.57); the estimates using the GBLUP and BayesR methods were superior to those obtained by the PBLUP method. The BayesR method performed similarly to GBLUP for most of the studied traits but substantially better for those traits that were controlled by SNPs with large effects; this was supported by the GWAS results. In addition, the predictive abilities of the 50K and 777K SNP arrays were almost similar; thus, both are suitable for GP in Hanwoo cattle. In conclusion, this study provides important insight into the genetic architecture and predictive ability of FAC traits in Hanwoo cattle. Our findings could be used in selection and breeding programs to promote production of meat with enhanced nutritional value.

Dataset Information

Identification of Single Nucleotide Polymorphism Marker and Association Analysis of Marbling Score in Fas Gene of Hanwoo.

Publications

Identification of Single Nucleotide Polymorphism Marker and Association Analysis of Marbling Score in Fas Gene of Hanwoo.

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