Genomic diversity and signatures of selection in meat and fancy rabbit breeds based on high-density marker data

Abstract

Background Domestication of the rabbit (Oryctolagus cuniculus) has led to a multi-purpose species that includes many breeds and lines with a broad phenotypic diversity, mainly for external traits (e.g. coat colours and patterns, fur structure, and morphometric traits) that are valued by fancy rabbit breeders. As a consequence of this human-driven selection, distinct signatures are expected to be present in the rabbit genome, defined as signatures of selection or selective sweeps. Here, we investigated the genome of three Italian commercial meat rabbit breeds (Italian Silver, Italian Spotted and Italian White) and 12 fancy rabbit breeds (Belgian Hare, Burgundy Fawn, Champagne d’Argent, Checkered Giant, Coloured Dwarf, Dwarf Lop, Ermine, Giant Grey, Giant White, Rex, Rhinelander and Thuringian) by using high-density single nucleotide polymorphism data. Signatures of selection were identified based on the fixation index (FST) statistic with different approaches, including single-breed and group-based methods, the latter comparing breeds that are grouped based on external traits (different coat colours and body sizes) and types (i.e. meat vs. fancy breeds). Results We identified 309 genomic regions that contained signatures of selection and that included genes that are known to affect coat colour (ASIP, MC1R and TYR), coat structure (LIPH), and body size (LCORL/NCAPG, COL11A1 and HOXD) in rabbits and that characterize the investigated breeds. Their identification proves the suitability of the applied methodologies for capturing recent selection events. Other regions included novel candidate genes that might contribute to the phenotypic variation among the analyzed breeds, including genes for pigmentation-related traits (EDNRA, EDNRB, MITF and OCA2) and body size, with a strong candidate for dwarfism in rabbit (COL2A1). Conclusions We report a genome-wide view of genetic loci that underlie the main phenotypic differences in the analyzed rabbit breeds, which can be useful to understand the shift from the domestication process to the development of breeds in O. cuniculus. These results enhance our knowledge about the major genetic loci involved in rabbit external traits and add novel information to understand the complexity of the genetic architecture underlying body size in mammals.

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

“…The role of this gene is, however, not completely well defined yet. In another study that involved Checkered Giant rabbits (Ballan et al, 2022 ), using F ST parameters we confirmed the signature of selection in this gene region. Therefore, it is quite remarkable that two independent types of analyses (i.e.…”

“…It will be also interesting to compare the results of the two methods that we have applied thus far to identify signatures of selection (i.e. the ROH island method described in this study and the F ST method previously reported; Ballan et al, 2022) with other methods that can be implemented using the same SNP datasets.…”

Genomic, genetic and phylogenetic evidence for a new falcon species using chromosome-level genome assembly of the gyrfalcon and population genomics

“…Moreover, ERVs were found to function as species-specific enhancers in the germline gene expression, influencing spermatogenesis and possibly contributing to speciation ( 48 ). NTRK2 , a gene associated with body weight in humans and mice ( 49 ), was found to have two copies on the gyrfalcon’s W chromosome. While it has gametolog on the Z chromosome, the two W-linked copies may suggest a possible overexpression in females that may contribute to the reverse sexual dimorphism (RSD) known in falcons, where females are larger than males.…”

Selection signatures for fiber production in commercial species: A review

“…Additionally, hair structure can also be used to distinguish distinct rabbit breeds. Ballan et al (2022) conducted selection signature studies using F ST analysis (with single-breed analysis and analysis of the group of breeds) in three commercial and 12 fancy rabbit breeds to explain the phenotypic variability between these breeds. The studies revealed selection signatures in genomic windows containing genes determining coat color (ASIP, MC1R, and TYR) and coat structure (LIPH).…”