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Abstract
In this study we investigated the genetic variability, the inbreeding and allele frequencies of monogenic traits in seven herds of Holstein breed and provided insight to farmers on the value of genomic management of reproduction in their herds. A total of 3,953 Holstein cows were sampled and genotyped with the Neogen GGP Bovine 100K SNP chip within the activities of the Regione Lombardia funded GO-PEI project ‘GENOmic tool for the management of reproduction in dairy cattle and for the control of inbreeding – GENORIP’. Principal component analysis was applied for analysing the genetic variability within and among farms using the SVS software of Golden Helix. Run of Homozygosity (ROH) and the genomic inbreeding were obtained with the detectRUNS package of the R software. Genotype frequencies for mendelian disease, fertility and production traits were also obtained. A total of 458,267 ROH were identified and ROH were distributed on all autosomes with an average length of 2,703,811 bp covering 12.7% of the genome. Several genomic regions appear under selection, while a specific region on BTA4 was identified in one herd, harbouring genes mainly related to the specific selection strategy of the farmer. The FROH values obtained considering ROH greater than 16 Mb, varied from 0.004 to 0.325, with the highest FROH average value of 0.136. Among mendelian heritable diseases, the Haplotype Cholesterol Deficiency was the one with the largest proportion of carrier animals, i.e. 5.6%. A herd-tailored process to assist farmers in genomic management of reproduction was released. The ROH distribution within herd, together with the genotype frequencies for disease, fertility and production mendelian traits, suggest that similar directional selection is occurring across herds. This study released to each farmer the genomic make-up of their herd used jointly with the gEBV estimated by their national breeders’ association (ANAFIBJ) for herd reproductive management.
HIGHLIGHTS
All females of 7 herds have been genotyped with the GGP 100K SNP chip.
Genomic information on all females can be used by farmers in the process to manage reproduction, selection and genetic herd variability.
The availability of genomic information on the whole herd allowed to release to each farmer the genomic make-up of their herd.
The ROH distribution together with the genotype frequencies for disease, fertility and production mendelian traits, made it possible to identify genomic regions under selection according to farmer strategies.
Authors’ contributions
CP: collected the samples; MGS and AB: Conceived and designed the study; RM: performed the experiments, CP and MGS: data analysis; AD and FB: participated to data analysis; CP, MGS and AB: wrote the manuscript. All authors reviewed and approved the final version of the manuscript.
Disclosure statement
No potential conflict of interest was reported by the authors.
Data availability statement
The data supporting the conclusions of this manuscript are included in the Supplementary Materials.