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.
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).
Genome-wide runs of homozygosity mapping through permutation approaches in Italian Holstein
Giustino Gaspa;MANCA, Elisabetta;USALA, Maria;Corrado Dimauro;Nicolò P. P. Macciotta
2018-01-01
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.I documenti in IRIS sono protetti da copyright e tutti i diritti sono riservati, salvo diversa indicazione.
