Agriculture, particularly meat and dairy production, is responsible for a large proportion of the annual global nitrogen surplus. Moreover, methane (CH4) production and intensity from cows contributes significantly towards greenhouse gas emissions. Genetic selection on nitrogen use efficiency (NUE, milk N yield / N intake) and CH4 traits offers a permanent and cumulative solution towards reducing emissions from cattle. The main goal of this project is to identify genomic variation linked to NUE and CH4 with regards to diets. Indeed, literature already uncovered genetic variability in NUE and CH4 and estimated their heritability (0.12 for NUE; Chen et al., 2021; and 0.27 for CH4; Pszczola et al., 2018). In fact, genomic regions associated with NUE and CH4 were also discovered (Chen, 2023; Pszczola et al., 2018). This shows that the development of new breeding strategies to produce more efficient and environmentally friendly cows is possible. A total of 1,425 cows between 90 and 250 days in milk were sampled for hair, milk and faeces, on 33 farms from February 2022 to April 2024. Whole-genome low-pass sequencing (1X) was done on DNA extracted from hair roots. Milk and faeces were analysed with infrared spectroscopy (Grelet et al., 2017) to predict NUE and CH4 traits. Diets were sampled to include information about their compositions in the model and make future predictions more accurate. Missing variants in the low-pass sequencing data were imputed using Gencove’s ‘loimpute’ pipeline (Wasik et al., 2021). We expect several million segregating variants that we will use in a genome-wide association study to identify potential genomic variations linked to NUE and CH4 traits.