Current dairy cattle populations are the result of years of selection that lead to high production levels, but also to a reduction of the within breed genetic diversity. This genomic similarity can be investigated using runs of homozygosity (ROH). Apart from being indicators of inbreeding, ROH are also useful for detecting selection sweeps. In the present study, ROHs were used for GWAS study in dairy cattle production traits. A total of 2,818 Italian Holstein bulls were genotyped with the Illumina HD bead chip. After edits, 609,074 SNPs were retained. Minimum number of SNP and length for a ROH were fixed at 50 and 1Mb, respectively. To account for genotyping/imputation errors one heterozygote was allowed into a ROH. Phenotypes were EBVs for milk yield, fat yield and percentage, protein yield and somatic cell score. A linear model was used to test the effects of ROH presence/absence and year of birth (5 levels according to 7-years interval from 1979 to 2014: 1 = 1979–1986; … 5 = 2007–2014). In the model, only ROHs shared by at least 20 animals were considered. Year of birth affected almost all investigated traits (at least P < 0.00001). The significance threshold was fixed as the negative logarithm of the ratio between 0.05 and the number of ROH tested, which was 1,083. Several genes found to be associated with dairy traits in previous studies have been found in the present work. Examples are the ARHGAP39, CYHR1, CPSF1, DGAT1 and GRINA loci. Results of the present study conforms the usefulness of ROH as indicators of selection sweeps.
A genome-wide analysis using runs of homozygosity in Italian Holstein cattle
G. Gaspa;
2019-01-01
Abstract
Current dairy cattle populations are the result of years of selection that lead to high production levels, but also to a reduction of the within breed genetic diversity. This genomic similarity can be investigated using runs of homozygosity (ROH). Apart from being indicators of inbreeding, ROH are also useful for detecting selection sweeps. In the present study, ROHs were used for GWAS study in dairy cattle production traits. A total of 2,818 Italian Holstein bulls were genotyped with the Illumina HD bead chip. After edits, 609,074 SNPs were retained. Minimum number of SNP and length for a ROH were fixed at 50 and 1Mb, respectively. To account for genotyping/imputation errors one heterozygote was allowed into a ROH. Phenotypes were EBVs for milk yield, fat yield and percentage, protein yield and somatic cell score. A linear model was used to test the effects of ROH presence/absence and year of birth (5 levels according to 7-years interval from 1979 to 2014: 1 = 1979–1986; … 5 = 2007–2014). In the model, only ROHs shared by at least 20 animals were considered. Year of birth affected almost all investigated traits (at least P < 0.00001). The significance threshold was fixed as the negative logarithm of the ratio between 0.05 and the number of ROH tested, which was 1,083. Several genes found to be associated with dairy traits in previous studies have been found in the present work. Examples are the ARHGAP39, CYHR1, CPSF1, DGAT1 and GRINA loci. Results of the present study conforms the usefulness of ROH as indicators of selection sweeps.
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