Identification of genomic regions of recent selection for productive and reproductive traits in Italian Holstein bulls

The impressive genetic improvement of milk production obtained in cosmopolitan dairy breeds during the last 65 years has been accompanied by a reduction in fertility, due to negative genetic correlation between those traits. Aim of this work is to identify genomic regions recently selected for dairy and reproductive traits in 3000 Italian Holstein Bulls born between 1987 and 2007. Illumina BovineSNP50 and BovineHD SNP chip genotype data from SELMOL, PROZOO and INNOVAGEN projects were used. Estimated Breeding Values (EBVs) of the genotyped animals were provided by the Italian Holstein association (ANAFI) for 32 productive, morphological and reproductive traits. Genotypes were quality-checked and medium-density data were imputed to high density using BEAGLE (v.3). The working dataset comprised 2,918 animals and 613,956 SNPs. Contrasting groups of bulls, identified as minus- or plus-variant for each EBV over the 20-year span were previously analyzed to find chromosomes containing genomic regions with the highest differences in allele frequency between groups, and thus supposed to be under strong directional selection. On these chromosomes, runs of homozygosity (ROHs) were investigated on plus- and minus-variant bulls for 13 production and fertility EBVs (bull’s and cow’s calving easiness, body condition score, calving interval, combined longevity, days at first service, somatic cells count, milk, protein and lipid yield, protein and lipid content). Delta ROH (DH) scores for each SNP between plus- and minus-variant groups for each EBV were calculated to detect regions with the highest variation. Genes with the highest differences in allele frequencies between minus and plus variant groups and with the highest DH were identified. About 500 genes on nine chromosomes (BTA 1, 2, 4, 5, 7, 9, 20, 26 and 29) were detected of which 39 showed signals of selection both for dairy and reproductive traits. These signals were classified as discordant (N¼12) or concordant (N¼27) effects on productive and reproductive traits. In addition, these genes are located into QTLs for both dairy and reproduction traits. This approach seems promising for the identification of genomic regions containing genes that show recent selection both for dairy and reproductive traits. In the genomic evaluation of the animals, the SNPs associated with these genes deserve to be weighted for their peculiar effect on EBVs.