Dataset Information

Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population.

ABSTRACT: Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous genome-wide association study (GWAS) with the four carcass traits in a commercial Hanwoo population. We genotyped 83 SNPs distributed across all 29 autosomes in 867 steers from a Korean Hanwoo feedlot. Six SNPs, namely ARS-BFGL-NGS-22774 (Chr4, Pos:4889229), ARS-BFGL-NGS-100046 (Chr6, Pos:61917424), ARS-BFGL-NGS-39006 (Chr27, Pos:38059196), ARS-BFGL-NGS-18790 (Chr10, Pos:26489109), ARS-BFGL-NGS-43879 (Chr9, Pos:39964297), and BTB-00775794 (Chr20, Pos:20476265), were found to be associated with CW, EMA, BF, and MS. The ARS-BFGL-NGS-22774, BTB-00775794, and ARS-BFGL-NGS-39006 markers accounted for 1.80%, 1.72%, and 1.35% (p<0.01), respectively, of the phenotypic variance in the commercial Hanwoo population. Many genes located in close proximity to the significant SNPs identified in this study were previously reported to have roles in carcass traits. The results of this study could be useful for marker-assisted selection programs.

SUBMITTER: Sudrajad P

PROVIDER: S-EPMC5088372 | biostudies-literature | 2016 Nov

REPOSITORIES: biostudies-literature

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Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population.

Sudrajad Pita P Sharma Aditi A Dang Chang Gwon CG Kim Jong Joo JJ Kim Kwan Suk KS Lee Jun Heon JH Kim Sidong S Lee Seung Hwan SH

Asian-Australasian journal of animal sciences 20160304 11

Four carcass traits, namely carcass weight (CW), eye muscle area (EMA), back fat thickness (BF), and marbling score (MS), are the main price decision parameters used for purchasing Hanwoo beef. The development of DNA markers for these carcass traits for use in a beef management system could result in substantial profit for beef producers in Korea. The objective of this study was to validate the association of highly significant single nucleotide polymorphisms (SNPs) identified in a previous geno ...[more]

PMID: 26954199

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Project description:There has been a growing interest in the genetic improvement of carcass traits as an important and primary breeding goal in the beef cattle industry over the last few decades. The use of correlated traits and molecular information can aid in obtaining more accurate estimates of breeding values. This study aimed to assess the improvement in the accuracy of genetic predictions for carcass traits by using ultrasound measurements and yearling weight along with genomic information in Hanwoo beef cattle by comparing four evaluation models using the estimators of the recently developed linear regression method. We compared the performance of single-trait pedigree best linear unbiased prediction [ST-BLUP and single-step genomic (ST-ssGBLUP)], as well as multi-trait (MT-BLUP and MT-ssGBLUP) models for the studied traits at birth and yearling date of steers. The data comprised of 15,796 phenotypic records for yearling weight and ultrasound traits as well as 5,622 records for carcass traits (backfat thickness, carcass weight, eye muscle area, and marbling score), resulting in 43,949 single-nucleotide polymorphisms from 4,284 steers and 2,332 bulls. Our results indicated that averaged across all traits, the accuracy of ssGBLUP models (0.52) was higher than that of pedigree-based BLUP (0.34), regardless of the use of single- or multi-trait models. On average, the accuracy of prediction can be further improved by implementing yearling weight and ultrasound data in the MT-ssGBLUP model (0.56) for the corresponding carcass traits compared to the ST-ssGBLUP model (0.49). Moreover, this study has shown the impact of genomic information and correlated traits on predictions at the yearling date (0.61) using MT-ssGBLUP models, which was advantageous compared to predictions at birth date (0.51) in terms of accuracy. Thus, using genomic information and high genetically correlated traits in the multi-trait model is a promising approach for practical genomic selection in Hanwoo cattle, especially for traits that are difficult to measure.

Project description:Aim:The present study was performed to assess the association of single-nucleotide polymorphisms (SNPs) in the fatty acid-binding protein 4 (FABP4) gene with birth weight (BW), final weight (FW), and average daily gain (ADG) in three Egyptian sheep breeds. Materials and Methods:Genomic DNA was extracted from the blood samples of 50 male and female individuals representing Ossimi, Rahmani, and Barki sheep breeds. A 407 bp nucleotide (nt) segment from the first intron of FABP4 was amplified by polymerase chain reaction, sequenced, and analyzed in the different samples. Results:Sequence analysis of the determined segment (407 bp) revealed four SNPs (all transition types) at nt position 372 (CP011894.1:g.57605471) A>G, nt position 211 (CP011894.1:g.57605632) A>G, nt position 143 (CP011894.1:g.57605700) T>C, and nt position 111 (CP011894.1:g.57605732) T>C. The allelic and genotypic frequencies for the identified SNPs in the sheep breeds were calculated. At nt positions 372 and 211, two alleles were identified (A and G). Only two genotypes were present at nt position 372 (AA and AG), while three genotypes were present at nt position 211 (AA, AG, and GG). Two alleles (T and C) and three identified genotypes (TT, TC, and CC) were detected at nt positions 143 and 111. Analysis of the results revealed that AA genotype at nt position 372 is associated with higher estimates for BW, FW, and ADG when compared to all the other genotypes. Very high correlation coefficients were found between the genotypes 143-TT and 111-TT and also between 143-TC and 111-TC. The genotypes 372-AG, 211-GG, 211-AA, 143-TT, 143-CC, 111-TT, 111-TC, and 111-CC were associated with negative effects on BW, FW, and ADG. Conclusion:The detection of four SNPs in a partial sequence of the Egyptian ovine FABP4 gene intron 1 reflected that this gene harbors substantial diversity. In addition, a novel SNP at nt position 372 (CP011894.1:g.57605471) A>G was associated with higher estimates for BW, FW, and ADG.

Dataset Information

Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population.

Publications

Validation of Single Nucleotide Polymorphisms Associated with Carcass Traits in a Commercial Hanwoo Population.

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