Dataset Information

Genetic Analysis of Major Carcass Traits of Korean Hanwoo Males Raised for Thirty Months.

ABSTRACT: Understanding animals' genetic potential for carcass traits is the key to genetic improvements in any beef cattle. In this study, we investigated the genetic merits of carcass traits using Hanwoo males raised in a 30-month production system (PROD30). We achieved this using a dataset comprising 6092 Hanwoo males born between 2005 and 2017 and measures of four carcass traits (carcass weight, CWT; eye muscle area, EMA; backfat thickness, BFT; and marbling score, MS). Genetic parameters were estimated using a multiple-trait animal model through the AIREMLF90 program. According to the multiple-trait model, the h2 of CWT, EMA, BFT, and MS were 0.35 ± 0.04, 0.43 ± 0.05, 0.48 ± 0.05, and 0.56 ± 0.05, respectively. The strongest genetic correlation (rg) was obtained between CWT and EMA (0.49 ± 0.07), whereas it was negligible between CWT and BFT. EMA and MS were also moderately correlated, whereas there was a relatively low negative correlation between EMA and BFT (-0.26 ± 0.08). Our study revealed a consistent indirect genetic improvement in animals from 2005 onwards. Although Hanwoo improvement has mainly focused on males under a 24-month production cycle, we observed PROD30 males to have somewhat similar genetic potential. Our results provide useful insights into the genetic merits of PROD30 males for the first time, which may facilitate future studies on them and their integration into the Hanwoo National Evaluation for genomic selection.

SUBMITTER: Alam M

PROVIDER: S-EPMC8232619 | biostudies-literature | 2021 Jun

REPOSITORIES: biostudies-literature

ACCESS DATA

Publications

Genetic Analysis of Major Carcass Traits of Korean Hanwoo Males Raised for Thirty Months.

Alam Mahboob M Lee Soo Hyun SH Lee Do Hyun DH Cho Chungil C Park Mi Na MN

Animals : an open access journal from MDPI 20210615 6

Understanding animals' genetic potential for carcass traits is the key to genetic improvements in any beef cattle. In this study, we investigated the genetic merits of carcass traits using Hanwoo males raised in a 30-month production system (PROD30). We achieved this using a dataset comprising 6092 Hanwoo males born between 2005 and 2017 and measures of four carcass traits (carcass weight, CWT; eye muscle area, EMA; backfat thickness, BFT; and marbling score, MS). Genetic parameters were estimat ...[more]

PMID: 34203963

Similar Datasets

Project description:This genome-wide association study (GWAS) was conducted to identify major loci that are significantly associated with carcass weight, and their effects, in order to provide increased understanding of the genetic architecture of carcass weight in Hanwoo. This genome-wide association study identified one major chromosome region ranging from 23 Mb to 25 Mb on chromosome 14 as being associated with carcass weight in Hanwoo. Significant Bonferroni-corrected genome-wide associations (P<1.52×10(-6)) were detected for 6 Single Nucleotide Polymorphic (SNP) loci for carcass weight on chromosome 14. The most significant SNP was BTB-01280026 (P = 4.02×10(-11)), located in the 25 Mb region on Bos taurus autosome 14 (BTA14). The other 5 significant SNPs were Hapmap27934-BTC-065223 (P = 4.04×10(-11)) in 25.2 Mb, BTB-01143580 (P = 6.35×10(-11)) in 24.3 Mb, Hapmap30932-BTC-011225 (P = 5.92×10(-10)) in 24.8 Mb, Hapmap27112-BTC-063342 (P = 5.18×10(-9)) in 25.4 Mb, and Hapmap24414-BTC-073009 (P = 7.38×10(-8)) in 25.4 Mb, all on BTA 14. One SNP (BTB-01143580; P = 6.35×10(-11)) lies independently from the other 5 SNPs. The 5 SNPs that lie together showed a large Linkage disequilibrium (LD) block (block size of 553 kb) with LD coefficients ranging from 0.53 to 0.89 within the block. The most significant SNPs accounted for 6.73% to 10.55% of additive genetic variance, which is quite a large proportion of the total additive genetic variance. The most significant SNP (BTB-01280026; P = 4.02×10(-11)) had 16.96 kg of allele substitution effect, and the second most significant SNP (Hapmap27934-BTC-065223; P = 4.04×10(-11)) had 18.06 kg of effect on carcass weight, which correspond to 44% and 47%, respectively, of the phenotypic standard deviation for carcass weight in Hanwoo cattle. Our results demonstrated that carcass weight was affected by a major Quantitative Trait Locus (QTL) with a large effect and by many SNPs with small effects that are normally distributed.

Project description:Quantitative traits are usually controlled by numerous genomic variants with small individual effects, and variances associated with those traits are explained in a continuous manner. However, the relative contributions of genomic regions to observed genetic variations have not been well explored using sequence level single nucleotide polymorphism (SNP) information. Here, imputed sequence level SNP data (11,278,153 SNPs) of 2109 Hanwoo steers (Korean native cattle) were partitioned according to functional annotation, chromosome, and minor allele frequency (MAF). Genomic relationship matrices (GRMs) were constructed for each classified region and fitted in the model both separately and together for carcass weight (CWT), eye muscle area (EMA), backfat thickness (BFT), and marbling score (MS) traits. A genome-wide association study (GWAS) was performed to identify significantly associated variants in genic and exon regions using a linear mixed model, and the genetic contribution of each exonic SNP was determined using a Bayesian mixture model. Considering all SNPs together, the heritability estimates for CWT, EMA, BFT, and MS were 0.57 ± 0.05, 0.46 ± 0.05, 0.45 ± 0.05, and 0.49 ± 0.05, respectively, which reflected substantial genomic contributions. Joint analysis revealed that the variance explained by each chromosome was proportional to its physical length with weak linear relationships for all traits. Moreover, genomic variances explained by functional category and MAF class differed greatly among the traits studied in joint analysis. For example, exon regions had larger contributions for BFT (0.13 ± 0.08) and MS (0.22 ± 0.08), whereas intron and intergenic regions explained most of the total genomic variances for CWT and EMA (0.22 ± 0.09-0.32 ± 0.11). Considering different functional classes of exon regions and the per SNP contribution revealed the largest proportion of genetic variance was attributable to synonymous variants. GWAS detected 206 and 27 SNPs in genic and exon regions, respectively, on BTA4, BTA6, and BTA14 that were significantly associated with CWT and EMA. These SNPs were harbored by 31 candidate genes, among which TOX, FAM184B, PPARGC1A, PRKDC, LCORL, and COL1A2 were noteworthy. BayesR analysis found that most SNPs (>93%) had very small effects and the 4.02-6.92% that had larger effects (10-4 × σA2 , 10-3 × σA2 , and 10-2 × σA2 ) explained most of the total genetic variance, confirming polygenic components of the traits studied.

Dataset Information

Genetic Analysis of Major Carcass Traits of Korean Hanwoo Males Raised for Thirty Months.

Publications

Genetic Analysis of Major Carcass Traits of Korean Hanwoo Males Raised for Thirty Months.

Similar Datasets

OmicsDI is part of the ELIXIR infrastructure

Tweets