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Comparative evaluation of genomic inbreeding parameters in seven commercial and autochthonous pig breeds

Published online by Cambridge University Press:  13 January 2020

G. Schiavo ,
S. Bovo ,
F. Bertolini ,
S. Tinarelli ,
S. Dall’Olio ,
L. Nanni Costa ,
M. Gallo  and
L. Fontanesi Open the ORCID record for L. Fontanesi [Opens in a new window]
G. Schiavo
Affiliation:
Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127Bologna, Italy
S. Bovo
Affiliation:
Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127Bologna, Italy
F. Bertolini
Affiliation:
National Institute of Aquatic Resources, Technical University of Denmark, Kemitorvet, Building 202, 2800Kongens Lyngby, Denmark
S. Tinarelli
Affiliation:
Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127Bologna, Italy Associazione Nazionale Allevatori Suini, Via Nizza 53, 00198Roma, Italy
S. Dall’Olio
Affiliation:
Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127Bologna, Italy
L. Nanni Costa
Affiliation:
Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127Bologna, Italy
M. Gallo
Affiliation:
Associazione Nazionale Allevatori Suini, Via Nizza 53, 00198Roma, Italy
L. Fontanesi*
Affiliation:
Division of Animal Sciences, Department of Agricultural and Food Sciences, University of Bologna, Viale G. Fanin 46, 40127Bologna, Italy
*
†E-mail: luca.fontanesi@unibo.it
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Abstract

Single nucleotide polymorphism (SNP) genotyping tools, which can analyse thousands of SNPs covering the whole genome, have opened new opportunities to estimate the inbreeding level of animals directly using genome information. One of the most commonly used genomic inbreeding measures considers the proportion of the autosomal genome covered by runs of homozygosity (ROH), which are defined as continuous and uninterrupted chromosome portions showing homozygosity at all loci. In this study, we analysed the distribution of ROH in three commercial pig breeds (Italian Large White, n = 1968; Italian Duroc, n = 573; and Italian Landrace, n = 46) and four autochthonous breeds (Apulo-Calabrese, n = 90; Casertana, n = 90; Cinta Senese, n = 38; and Nero Siciliano, n = 48) raised in Italy, using SNP data generated from Illumina PorcineSNP60 BeadChip. We calculated ROH-based inbreeding coefficients (FROH) using ROH of different minimum length (1, 2, 4, 8, 16 Mbp) and compared them with several other genomic inbreeding coefficients (including the difference between observed and expected number of homozygous genotypes (FHOM)) and correlated all these genomic-based measures with the pedigree inbreeding coefficient (FPED) calculated for the pigs of some of these breeds. Autochthonous breeds had larger mean size of ROH than all three commercial breeds. FHOM was highly correlated (0.671 to 0.985) with FROH measures in all breeds. Apulo-Calabrese and Casertana had the highest FROH values considering all ROH minimum lengths (ranging from 0.273 to 0.189 and from 0.226 to 0.152, moving from ROH of minimum size of 1 Mbp (FROH1) to 16 Mbp (FROH16)), whereas the lowest FROH values were for Nero Siciliano (from 0.072 to 0.051) and Italian Large White (from 0.117 to 0.042). FROH decreased as the minimum length of ROH increased for all breeds. Italian Duroc had the highest correlations between all FROH measures and FPED (from 0.514 to 0.523) and between FHOM and FPED (0.485). Among all analysed breeds, Cinta Senese had the lowest correlation between FROH and FPED. This might be due to the imperfect measure of FPED, which, mainly in local breeds raised in extensive production systems, cannot consider a higher level of pedigree errors and a potential higher relatedness of the founder population. It appeared that ROH better captured inbreeding information in the analysed breeds and could complement pedigree-based inbreeding coefficients for the management of these genetic resources.

Keywords

autozygositygenetic resourceruns of homozygositysingle nucleotide polymorphismsSus scrofa
Type
Research Article
Information
animal , Volume 14 , Issue 5 , May 2020 , pp. 910 - 920
Copyright
© The Animal Consortium 2020

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