Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle

Area of Science:

• Animal Genetics
• Genomics
• Quantitative Trait Loci

Background:

• Bone weight is a key indicator of cattle conformation and skeletal health.
• Understanding the genetic basis of bone weight is crucial for livestock breeding and disease management.

Purpose of the Study:

• To identify genetic determinants of bone weight in Simmental cattle using a comprehensive genomewide association study (GWAS) strategy.
• To explore the utility of multimarker and rare-marker association approaches for dissecting complex traits.

Main Methods:

• Employed a three-model strategy: traditional linear mixed model (LMM), LMM combined with least absolute shrinkage and selection operator (LMM-Lasso), and gene-based sequence kernel association test (SKAT) for rare variants.
• Analyzed data from 1,217 Simmental cattle genotyped with 770,000 single nucleotide polymorphisms (SNPs).
• Utilized both common and rare SNPs (0.001 < minor allele frequency < 0.05) in the association analyses.

Main Results:

• The traditional LMM identified three genes associated with bone weight.
• The LMM-Lasso approach detected nine candidate genes, encompassing those found by the LMM.
• The gene-based SKAT identified EPHB3 as a significant gene after Bonferroni correction.

Conclusions:

• LCORL, RIMS2, LAP3, PRKAR2B, CHSY1, MAP2K6, and EPHB3 are proposed as candidate genes for bone weight in Simmental cattle.
• The integrated GWAS strategy provides a robust framework for investigating the genetic architecture of economically important traits in livestock.
• This study contributes to a deeper understanding of the genetic factors influencing skeletal development and conformation in cattle.