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Genome-wide identification of runs of homozygosity islands and associated genes in local dairy cattle breeds

Published online by Cambridge University Press:  26 March 2018

S. Mastrangelo ,
M. T. Sardina ,
M. Tolone ,
R. Di Gerlando ,
A. M. Sutera ,
L. Fontanesi  and
B. Portolano
S. Mastrangelo*
Affiliation:
Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128 Palermo, Italy
M. T. Sardina
Affiliation:
Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128 Palermo, Italy
M. Tolone
Affiliation:
Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128 Palermo, Italy
R. Di Gerlando
Affiliation:
Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128 Palermo, Italy
A. M. Sutera
Affiliation:
Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128 Palermo, Italy
L. Fontanesi
Affiliation:
Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, 40127 Bologna, Italy
B. Portolano
Affiliation:
Dipartimento Scienze Agrarie, Alimentari e Forestali, Università degli Studi di Palermo, 90128 Palermo, Italy
*
†E-mail: salvatore.mastrangelo@unipa.it
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Abstract

Runs of homozygosity (ROH) are widely used as predictors of whole-genome inbreeding levels in cattle. They identify regions that have an unfavorable effect on a phenotype when homozygous, but also identify the genes associated with traits of economic interest present in these regions. Here, the distribution of ROH islands and enriched genes within these regions in four dairy cattle breeds were investigated. Cinisara (71), Modicana (72), Reggiana (168) and Italian Holstein (96) individuals were genotyped using the 50K v2 Illumina BeadChip. The genomic regions most commonly associated with ROHs were identified by selecting the top 1% of the single nucleotide polymorphisms (SNPs) most commonly observed in the ROH of each breed. In total, 11 genomic regions were identified in Cinisara and Italian Holstein, and eight in Modicana and Reggiana, indicating an increased ROH frequency level. Generally, ROH islands differed between breeds. The most homozygous region (>45% of individuals with ROH) was found in Modicana on chromosome 6 within a quantitative trail locus affecting milk fat and protein concentrations. We identified between 126 and 347 genes within ROH islands, which are involved in multiple signaling and signal transduction pathways in a wide variety of biological processes. The gene ontology enrichment provided information on possible molecular functions, biological processes and cellular components under selection related to milk production, reproduction, immune response and resistance/susceptibility to infection and diseases. Thus, scanning the genome for ROH could be an alternative strategy to detect genomic regions and genes related to important economic traits.

Keywords

runs of homozygosity islandsgenomic regionscandidate geneslocal dairy cattlebovine beadchip 50K
Type
Research Article
Information
animal , Volume 12 , Issue 12 , December 2018 , pp. 2480 - 2488
Copyright
© The Animal Consortium 2018 

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