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Background  Methane emission by ruminants has contributed considerably to the global warming and understanding the genomic architecture of methane production may help livestock producers to reduce the methane emission from the livestock production system. The goal of our study was to identify genomic regions affecting the predicted methane emission (PME) from volatile fatty acids (VFAs) indicators and VFA traits using imputed whole-genome sequence data in Iranian Holstein cattle.    Results  Based on the significant-association threshold ( p  < 5 × 10 − 8 ), 33 single nucleotide polymorphisms (SNPs) were detected for PME per kg milk ( n  = 2), PME per kg fat ( n  = 14), and valeric acid ( n  = 17). Besides, 69 genes were identified for valeric acid ( n  = 18), PME per kg milk ( n  = 4) and PME per kg fat ( n  = 47) that were located within 1 Mb of significant SNPs. Based on the gene ontology (GO) term analysis, six promising candidate genes were significantly clustered in organelle organization (GO:0004984,  p  = 3.9 × 10 − 2 ) for valeric acid, and 17 candidate genes significantly clustered in olfactory receptors activity (GO:0004984,  p  = 4 × 10 − 10 ) for PME traits. Annotation results revealed 31 quantitative trait loci (QTLs) for milk yield and its components, body weight, and residual feed intake within 1 Mb of significant SNPs.    Conclusions  Our results identified 33 SNPs associated with PME and valeric acid traits, as well as 17 olfactory receptors activity genes for PME traits related to feed intake and preference. Identified SNPs were close to 31 QTLs for milk yield and its components, body weight, and residual feed intake traits. In addition, these traits had high correlations with PME trait. Overall, our findings suggest that marker-assisted and genomic selection could be used to improve the difficult and expensive-to-measure phenotypes such as PME. Moreover, prediction of methane emission by VFA indicators could be useful for increasing the size of reference population required in genome-wide association studies and genomic selection.

Genome-wide association studies for methane emission and ruminal volatile fatty acids using Holstein cattle sequence data