ena-STUDY-UNIVERSITA CATTOLICA DEL SACRO CUORE-25-06-2017-23:12:16:084-192
Whole exome sequence data from 18 Italian Holstein bulls sampled from the tails of the distribution of fertility indices.
Deleterious variants contribute to inbreeding depression and have negative effects on reproductive success (individual fitness reduction and, in extreme cases, severe phenotypes such as premature foetal death and abortion). The scope of the project was to identify loss-of-function variants in Italian Holstein breed possible associated to recessive disorders. Whole exome sequence data from 18 Italian Holstein progeny tested bulls sampled from the tails of the distribution of male (ERCR) and female (IAFF) fertility indices. Exome sequences were captured using the “SureSelected All exon Bovine” kit (Agilent Technologies, Santa Clara, California, USA) comprising 225,414 probes (average size 230bp). Mitochondrial and Y chromosome sequences were not included in probe design, which was based on exons, UTRs, and miRNAs predicted by NCBI's database. The over 1.3 billion reads generated were processed with a state of the art bioinformatics pipeline consisting in quality check (FastQC), cleaning (Trimmomatic), and aligning (bwa aln algorithm and Samtools). The probes capture about 53.55Mbp (about 2.2%) of the UMD 3.1 reference cattle genome. The average sequencing depth per subject was 38.2X.The variant calling procedure in GATK identified 254,369 variants. Among these, 147,209 (57.87%) were retained after applying standard variant and genotype filters. The majority of polymorphisms retained after filtering were biallelic SNPs (93.97%), followed by insertions and deletions (InDels; 4.80%), complex variations and multi-allelic SNPs (1.24%).
Deleterious variants contribute to inbreeding depression and have negative effects on reproductive success (individual fitness reduction and, in extreme cases, severe phenotypes such as premature foetal death and abortion). The scope of the project was to identify loss-of-function variants in Italian Holstein breed possible associated to recessive disorders. Whole exome sequence data from 18 Italian Holstein progeny tested bulls sampled from the tails of the distribution of male (ERCR) and female (IAFF) fertility indices. Exome sequences were captured using the “SureSelected All exon Bovine” kit (Agilent Technologies, Santa Clara, California, USA) comprising 225,414 probes (average size 230bp). Mitochondrial and Y chromosome sequences were not included in probe design, which was based on exons, UTRs, and miRNAs predicted by NCBI's database. The over 1.3 billion reads generated were processed with a state of the art bioinformatics pipeline consisting in quality check (FastQC), cleaning (Trimmomatic), and aligning (bwa aln algorithm and Samtools). The probes capture about 53.55Mbp (about 2.2%) of the UMD 3.1 reference cattle genome. The average sequencing depth per subject was 38.2X.The variant calling procedure in GATK identified 254,369 variants. Among these, 147,209 (57.87%) were retained after applying standard variant and genotype filters. The majority of polymorphisms retained after filtering were biallelic SNPs (93.97%), followed by insertions and deletions (InDels; 4.80%), complex variations and multi-allelic SNPs (1.24%).