Genome-wide runs of homozygosity mapping through permutation approaches in Italian Holstein
Contributo in Atti di convegno
Data di Pubblicazione:
2018
Citazione:
Genome-wide runs of homozygosity mapping through permutation
approaches in Italian Holstein / Gaspa, Giustino; Cesarani, Alberto; Milanesi, ; Manca, Elisabetta; Usala, Maria; Paolo Ajmone Marsan, ; Dimauro, Corrado; Macciotta, Nicolò P. P.. - (2018), p. 1. (Intervento presentato al convegno World Congress on Genetics Applied to Livestock Production tenutosi a Auckland, New Zealand nel 11–16 February 2018).
Abstract:
Extended regions of homozygosity (ROH) in the mammalian genomes may be the results of
high level of relatedness in the population or of positive selection for beneficial alleles. ROH
allow estimat the degree of autozygosity at genome-wide level, providing clues for
reconstructing the genetic history of a population. In the present study, a method based on
permutation test for detecting SNP significantly included in ROH is presented. HD genotype
SNP data of 3,009 Italian Holstein bulls were scanned for ROH occurrence. The threshold for
declaring s SNP as significantly included in a ROH was obtained by randomly shuffling
genotypes within animals for each chromosome. The chromosome -wide threshold was the
99th percentile of the distribution of the number of times a SNP occurred in a ROH for a
specific chromosome. Top significant SNP were found mostly on BTAs 6, 7, 14, 21, 26, and
29 in genomic regions known to harbor genes involved in milk traits.
high level of relatedness in the population or of positive selection for beneficial alleles. ROH
allow estimat the degree of autozygosity at genome-wide level, providing clues for
reconstructing the genetic history of a population. In the present study, a method based on
permutation test for detecting SNP significantly included in ROH is presented. HD genotype
SNP data of 3,009 Italian Holstein bulls were scanned for ROH occurrence. The threshold for
declaring s SNP as significantly included in a ROH was obtained by randomly shuffling
genotypes within animals for each chromosome. The chromosome -wide threshold was the
99th percentile of the distribution of the number of times a SNP occurred in a ROH for a
specific chromosome. Top significant SNP were found mostly on BTAs 6, 7, 14, 21, 26, and
29 in genomic regions known to harbor genes involved in milk traits.
Tipologia CRIS:
4.1 Contributo in Atti di convegno
Keywords:
selection signature, runs of homozygosity, Holstein, positive selection
Elenco autori:
Gaspa, Giustino; Cesarani, Alberto; Milanesi, ; Manca, Elisabetta; Usala, Maria; Paolo Ajmone Marsan, ; Dimauro, Corrado; Macciotta, Nicolò P. P.
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Titolo del libro:
Volume electronic poster session - methods and tools - models and computing strategies 1