Comparative analysis of genomic inbreeding parameters and runs of homozygosity islands in several fancy and meat rabbit breeds

Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Arra...

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Bibliographic Details
Published in:Animal genetics 2022-12, Vol.53 (6), p.849-862
Main Authors: Ballan, Mohamad, Schiavo, Giuseppina, Bovo, Samuele, Schiavitto, Michele, Negrini, Riccardo, Frabetti, Andrea, Fornasini, Daniela, Fontanesi, Luca
Format: Article
Language:English
Subjects:
Animals
Body length
Body size
Comparative analysis
Deoxyribonucleic acid
DNA
Genetic resources
genetic variability
Genomes
Genomic analysis
Genomic islands
Genomics
Genotype
Homozygosity
Homozygote
Inbreeding
Information management
Islands
Meat
Mustela erminea
Oryctolagus cuniculus
Parameter identification
Pigmentation
Polymorphism, Single Nucleotide
Rabbits
ROH
signature of selection
Single-nucleotide polymorphism
SNP
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Summary:Runs of homozygosity (ROH) are defined as long stretches of DNA homozygous at each polymorphic position. The proportion of genome covered by ROH and their length are indicators of the level and origin of inbreeding. In this study, we analysed SNP chip datasets (obtained using the Axiom OrcunSNP Array) of a total of 702 rabbits from 12 fancy breeds and four meat breeds to identify ROH with different approaches and calculate several genomic inbreeding parameters. The highest average number of ROH per animal was detected in Belgian Hare (~150) and the lowest in Italian Silver (~106). The average length of ROH ranged from 4.001 ± 0.556 Mb in Italian White to 6.268 ± 1.355 Mb in Ermine. The same two breeds had the lowest (427.9 ± 86.4 Mb, Italian White) and the highest (921.3 ± 179.8 Mb, Ermine) average values of the sum of all ROH segments. More fancy breeds had a higher level of genomic inbreeding (as defined by ROH) than meat breeds. Several ROH islands contain genes involved in body size, body length, pigmentation processes, carcass traits, growth, and reproduction traits (e.g.: AOX1, GPX5, IFRD1, ITGB8, NELL1, NR3C1, OCA2, TRIB1, TRIB2). Genomic inbreeding parameters can be useful to overcome the lack of information in the management of rabbit genetic resources. ROH provided information to understand, to some extent, the genetic history of rabbit breeds and to identify signatures of selection in the rabbit genome.
ISSN:0268-9146
1365-2052
DOI:10.1111/age.13264