Fig. 4

Evolution of haplotype frequencies, pedigree analyses, and estimation of haplotype effects on recorded traits. a Evolution of frequency for 13 Holstein haplotypes between 1985 and 2023 (Additional file 1: Table S11). b Representation of the marginal (purple) and raw genetic contribution of the most used sire (more than 1% of raw contribution) in the French Holstein female population born within the period 2019–2022 (3,058,756 animals) based on pedigree information (see “Methods”; Additional file 1: Table S12). c Effects of the heterozygosity for each Holstein, Montbeliarde, and Normande haplotype on 14 traits expressed in genetic standard deviation (GSD; Additional file 1: Table S13). Only significant effects are shown (Benjamini–Hochberg adjusted Student’s t-test p value ≤ 0.01). Note the significant negative effects observed for H11P78/CD on several traits, including chest width and stature (− 0.30 and − 0.23 GSD, respectively), which support reduced growth in heterozygous carriers