Distribution of functional variants within Runs of Homozygosity in four Italian cattle breeds

Risultato della ricerca: Otherpeer review

Abstract

Several methods have been used to identify genomic regions subjected toselective sweeps. An alternative method can make use of runs ofhomozygosity (ROH), defined as stretches of homozygous regions in agenome. The aim of the present study was to detect selective sweeps usingROH in four cattle breeds. Individuals of Cinisara (71), Modicana (72),Reggiana (168) and Italian Holstein (96) were genotyped with the IlluminaBovine50SNP v2 BeadChip. To identify genomic regions that were mostcommonly associated with ROH within each breed, the percentage ofoccurrences of a single nucleotide polymorphism (SNP) in ROH wascalculated across animals. The genomic regions most commonly associatedwith ROH were identified by selecting the top 1% of the SNPs mostcommonly observed in ROH in each breed. This approach resulted in theidentification of 11 genomic regions in the Cinisara and Italian Holstein,and 8 in Modicana and Reggiana showing increased frequency of ROH.Generally, ROH patterns differed between breeds. There were twocommons genomic regions between breed pairs, and in particular one inBTA6 between Modicana and Reggiana and one in BTA10 between Cinisaraand Italian Holstein. A highly homozygous region (> 45% of individualswith ROH) was found only in Modicana breed in BTA6 (6:37,019,972-39,069,719) within a QTL affecting milk fat and protein concentration. Inthese genomic regions we identified from 126 to 347 genes for each breed.According to Panther and KEGG database, a majority of the genes wasinvolved in multiple signaling and signal transduction pathways in a widevariety of cellular and biochemical processes. Several of these genes werealso comprised in a list of genes related to phenotypes for which cattlebreeds have been subjected to strong positive selection. For most genesassociated with ROH islands, a biological link to traits such as milk yieldand composition, reproduction, immune response, coat colour, geneticdisorders and resistance/susceptibility to infectious and diseases, which areknown to be under selection, can be hypothesized. These results showedthat selective sweeps detected with ROH approach are shared amongbreeds and that scanning the genome for ROH might be an alternative orcomplementary strategy to detect selective sweep related with importanteconomically traits.
Lingua originaleEnglish
Numero di pagine1
Stato di pubblicazionePublished - 2017

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