Abstract
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.
Highlights
Korean beef producers select for meat yield and quality to increase their income from steer feedlots and sold calves
For region-based annotation of Single Nucleotide Polymorphic (SNP), the ANNOVAR annotates the location of each variant with respect to genes, indicating whether it is exonic, intronic, intergenic, a splicing site, 59/39-UTR, and upstream/downstream of genes. In this genome-wide association study, the 1,011 steers descended from 118 sires were used as a discovery data set to identify the Quantitative Trait Locus (QTL) for carcass traits (CWT, eye muscle area (EMA), marbling score (MAR), and backfat thickness (BF))
The major QTL with large genetic variations for carcass weight (CWT) could be useful for marker-assisted selection to determine animal destiny for feedlots or seed stocks in the Korean beef industry
Summary
Korean beef producers select for meat yield and quality to increase their income from steer feedlots and sold calves. Estimated breeding values (EBVs) for eye muscle area (EMA), carcass weight (CWT), marbling score (MAR), and backfat thickness (BF) after adjustment for age (30 months) are commonly used as selection criteria in attempts to increase meat yield and quality, which determine profitability for the Korean beef industry. More targeted meat production, such as improved genetic gain for EMA and CWT and more desirable MAR, needs to be achieved in Hanwoo beef industry by genetic improvement To this end, investigations have been made for incorporation of DNA information into genetic evaluation models, which may result in improved accuracy of estimated breeding value (EBV) and lead to increased selection response in cattle [1]. Finding causal genes having large effects on quantitative traits has the potential to improve animal selection efficiency and increase understanding of the underlying biology of quantitative traits [2]
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