Weighted Single-Step Genome-Wide Association Study Identifies Candidate Genes for Carcass Traits and Primal Cut...

Area of Science:

• Animal Genetics and Genomics
• Quantitative Genetics
• Livestock Production

Background:

• Hanwoo cattle are a valuable breed, and improving carcass traits is economically important.
• Genome-wide association studies (GWAS) are crucial for identifying genetic markers related to complex traits.
• Understanding the genetic architecture of carcass traits and primal cut yields can guide breeding programs.

Purpose of the Study:

• To identify genomic regions associated with carcass traits (weight, eye muscle area, backfat thickness, marbling score) and primal cut yields in Hanwoo cattle.
• To pinpoint candidate genes within these associated regions.
• To explore potential pleiotropic effects of identified genomic regions on multiple traits.

Main Methods:

• Weighted single-step genome-wide association study (WssGWAS) was employed.
• Analysis included 50,227 carcass records and genomic data from 23,573 animals with 45,057 single-nucleotide polymorphisms (SNPs).
• Heritability estimates were calculated for various carcass traits and primal cut yields.

Main Results:

• Significant heritability estimates were found for carcass weight (0.24), eye muscle area (0.22), backfat thickness (0.31), and marbling score (0.36).
• Candidate genes such as XKR4, COBL, LCORL, TGFBR2, ATG7, MYPN, TWIST2, and BMP4 were identified for specific carcass traits.
• Pleiotropic genomic regions on chromosomes 6 (WDR1), 4 (CACNA2D1), and 28 (SIRT1) were associated with multiple primal cut yields, with SIRT1 explaining significant variance for striploin (6.46%).

Conclusions:

• The study successfully identified key genomic regions and candidate genes influencing carcass traits and primal cut yields in Hanwoo cattle.
• The identified pleiotropic regions represent promising targets for genomic selection strategies.
• Implementing genomic selection based on these findings can potentially improve overall production efficiency and enhance the economic value of Hanwoo beef.