Analysis of genetic diversity and signature of selection in commercial and fancy rabbit breeds

The European rabbit (Oryctolagus cuniculus) is a multi-purpose species used for meat and fur production and considered a fancy animal used for show purposes. For this reason, several commercial and fancy breeds have been developed, mainly over the last century, starting from recently domesticated genetic stocks. Fancy breeds can be mainly distinguished by many different coat colours and patterns, fur structure, and morphometric traits, i.e. body size, shape and position of the ears, the structure of the skull, among other characteristic features. This study aimed to identify signatures of selection in the rabbit genome that could highlight candidate genes whose variability might contribute to explain the diversity of exterior traits that distinguish some commercial and fancy rabbit breeds. A total of 660 rabbits were genotyped using the Affymetrix Axiom OrcunSNP Array, which can analyse 199,692 DNA markers. These animals were from 12 fancy rabbit breeds (Belgian Hare, n. = 24; Burgundy Fawn, 6; Champagne d’Argent, 19; Checkered Giant, 79; Dwarf Colored, 20; Dwarf Lop, 20; Ermine, 20; Giant Grey, 27; Giant White, 20; Rex, 19; Rhinelander, 28; and Thuringian, 9) and three Italian commercial rabbit breeds (Italian d’Argent, 20; Italian Spotted, 93; and Italian White, 256). Fst analyses were performed using sliding genome window methods based on a single-breed approach (i.e. one breed against all other breeds) or by grouping breeds based on common pigmentation or morphometric features. Our results pointed out many genome regions harbouring signatures of selection and including several coat colour genes already described to affect pigmentation in rabbits (ASIP, MC1R, and TYR) and coat structure (LIPH). In addition, several other regions contain genes involved in body structure/stature, fat deposition, growth and reproduction performances. This study added information that can contribute to clarifying the genetic mechanisms determining phenotypic differences among rabbit breeds.