Genetic Variability of Methane Production and Concentration Measured in the Breath of Polish Holstein-Friesian Cattle

SIMPLE SUMMARY: Methane is one of the main contributors to climate change. A potential to reduce emissions by genetic selection exists; however, the genetic architecture of methane production remains largely unknown. We aimed to estimate its heritability and to perform genome-wide association studies for the identification of candidate genes associated with daily methane production and concentration. Methane was measured in the air exhaled by dairy cows during milking in an automated milking system and was analyzed using genomic information that was available for some of the cows. We showed that methane production and concentration are partly controlled by genes; however, no major genes were found. The estimated heritabilities indicate that selection for lower methane emission could be successful. ABSTRACT: The genetic architecture of methane (CH(4)) production remains largely unknown. We aimed to estimate its heritability and to perform genome-wide association studies (GWAS) for the identification of candidate genes associated with two phenotypes: CH(4) in parts per million/day (CH(4) ppm/d) and CH(4) in grams/day (CH(4) g/d). We studied 483 Polish Holstein-Friesian cows kept on two commercial farms in Poland. Measurements of CH(4) and carbon dioxide (CO(2)) concentrations exhaled by cows during milking were obtained using gas analyzers installed in the automated milking system on the farms. Genomic analyses were performed using a single-step BLUP approach. The percentage of genetic variance explained by SNPs was calculated for each SNP separately and then for the windows of neighbouring SNPs. The heritability of CH(4) ppm/d ranged from 0 to 0.14, with an average of 0.085. The heritability of CH(4) g/d ranged from 0.13 to 0.26, with an average of 0.22. The GWAS detected potential candidate SNPs on BTA 14 which explained ~0.9% of genetic variance for CH(4) ppm/d and ~1% of genetic variance for CH(4) g/d. All identified SNPs were located in the TRPS1 gene. We showed that methane traits are partially controlled by genes; however, the detected SNPs explained only a small part of genetic variation—implying that both CH(4) ppm/d and CH(4) g/d are highly polygenic traits.