Deleterious muta6ons naturally occur in wild and domes6c animal species. Their des6ny is either to rapidly disappear or to remain at low frequency in the popula6ons. Some may increase in frequency when in linkage with alleles controlling traits under natural or anthropogenic selec6on. This increase may be quick and substan6al when deleterious variants are carried by high gene6c value sires widely use in ar6ficial insemina6on. Here we searched for deleterious variants in the Italian Holstein popula6on combining in a three step approach high density SNP genotyping of 1009 AI bulls and exome sequence data from 18 bulls, selected from opposite tails of the male and female fer6lity EBV distribu6on. In the first step PLINK analysis of high density genotypic data detected 64,215 haplotype blocks of high LD. Among these 261 contained one class of homozygous haplotypes having frequency significantly lower than expected and some6mes completely missing. These were classified as deleterious haplotypes likely carrying deleterious variants in coding or regulatory sequences. In the second step a custom pipeline was developed to trim and align exome sequences. SNPs and InDels were called, filtered and finally annotated using VEP sorware. A total of 9229 muta6ons likely inducing a change in protein func6on (premature stop codons, muta6ons causing frameshirs, alterna6ve splicing sites or changing protein structure) were iden6fied. These were classified as deleterious variants. The third step combined results obtained in the first two steps. A total of 83 deleterious variants in 61 deleterious haplotypes were iden6fied and further inves6gated. Conserva6on across vertebrate species (using phastCons and phyloP score) and concordance between SNP genotype and sequence results were used to filter the co-mapping results. Variants passing these filters are in genes involved in embryonic and postnatal survival or associated to gene6c defects in human and mouse. Their likely deleterious effect is being confirmed in a large popula6on of bulls and cows.
COMBINING HIGH DENSITY GENOTYPING AND EXOME SEQUENCING TO IDENTIFY DELETERIOUS MUTATION IN ITALIAN HOLSTEIN BULLS
CAPOMACCIO, STEFANO;CAPPELLI, Katia;AJMONE MARSAN, PAOLO
2015
Abstract
Deleterious muta6ons naturally occur in wild and domes6c animal species. Their des6ny is either to rapidly disappear or to remain at low frequency in the popula6ons. Some may increase in frequency when in linkage with alleles controlling traits under natural or anthropogenic selec6on. This increase may be quick and substan6al when deleterious variants are carried by high gene6c value sires widely use in ar6ficial insemina6on. Here we searched for deleterious variants in the Italian Holstein popula6on combining in a three step approach high density SNP genotyping of 1009 AI bulls and exome sequence data from 18 bulls, selected from opposite tails of the male and female fer6lity EBV distribu6on. In the first step PLINK analysis of high density genotypic data detected 64,215 haplotype blocks of high LD. Among these 261 contained one class of homozygous haplotypes having frequency significantly lower than expected and some6mes completely missing. These were classified as deleterious haplotypes likely carrying deleterious variants in coding or regulatory sequences. In the second step a custom pipeline was developed to trim and align exome sequences. SNPs and InDels were called, filtered and finally annotated using VEP sorware. A total of 9229 muta6ons likely inducing a change in protein func6on (premature stop codons, muta6ons causing frameshirs, alterna6ve splicing sites or changing protein structure) were iden6fied. These were classified as deleterious variants. The third step combined results obtained in the first two steps. A total of 83 deleterious variants in 61 deleterious haplotypes were iden6fied and further inves6gated. Conserva6on across vertebrate species (using phastCons and phyloP score) and concordance between SNP genotype and sequence results were used to filter the co-mapping results. Variants passing these filters are in genes involved in embryonic and postnatal survival or associated to gene6c defects in human and mouse. Their likely deleterious effect is being confirmed in a large popula6on of bulls and cows.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
