Weighted single-step genome-wide association studies for methane intensity in Chinese Holstein cattle
Abstract
Reducing methane emissions from dairy cows has been a key area of research in recent decades. This study aimed to identify genomic regions associated with methane intensity (MeI) in Chinese Holstein cattle. MeI phenotype was either predicted by mid-infrared spectra (MIRS, R2cv= 0.66) or directly measured by sniffer. Data were collected from eight commercial farms in Beijing between 2017–2020 and 2024. A weighted single-step genome-wide association study (WssGWAS) was performed based on 1,120 genotypes, 4,995 phenotypic records, and pedigree of 10 911 individuals.
The mean MeI was 7.67 ± 1.52 (g/kg milk yield). The estimated heritability of MeI was 0.15±0.04, and the repeatability was 0.42±0.02. Eleven 10-SNP windows harboring 19 protein encoding genes explained 2.17% of the genomic variance, with genomic regions on BTA1, 5, 8, 15, 19, 20, 24, 26, and 27. Five of the windows were also associated with milk production or milk component traits, while one window contained the QTL linked to metabolic body weight. The region explaining the highest proportion of variance (0.34%) was located on BTA15, which included five protein encoding genes. Among them, SCN4B and MPZL3 are proposed as candidate genes.
In total, the preliminary results show that MeI is a heritable, repeatable, and polygenic trait in Chinese Holstein population. The identified MeI-related genomic regions provide an insight for breeding dairy cows with lower methane emissions.
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