Genomic analysis of the rare British Lop pig and identification of distinctive genomic markers

Concentration of production on a few commercial pig breeds has led to the marginalization of many native, numerically small breeds, increasing their risk of endangerment. In the UK, one such rare breed is the British Lop, a lop-eared breed, of similar origin to the Welsh breed. The objective of the present study was to address the genomic status of the British Lop and its relationship with other breeds and identify a small set of genomic markers that uniquely characterize and distinguish British Lop animals. Results have shown that the British Lop is a relatively distinct population with reduced genomic diversity and effective size consistent with its status as a rare breed. Furthermore, we demonstrated the genetic closeness of the British Lop to phenotypically similar breeds such as Landrace and Welsh as well Large White, Middle White and Pietrain. Finally, a set of 75 Single Nucleotide Polymorphisms distributed across multiple chromosomes were identified and validated as markers that can consistently distinguish British Lops from other closely related breeds. Results may inform breeding and management strategies aiming to enhance diversity as well as the development of a breed purity test

British Lop Pig genotypes

This dataset contains genotypes for 190 British Lop Pig samples genotyped with the Illumina PorcineSNP60v2 BeadChip, comprising 61,565 Single Nucleotide Polymorphisms (SNPs) spread throughout the entire genome. Genotypes are reported according to the Forward strand in the 10.2 Porcine assembly, but map positions were updated to the Sus Scrofa assembly 11.1.Molano, Enrique; Banos, Georgios; Talenti, Andrea; Chatziplis, Dimitris. (2022). British Lop Pig genotypes, [dataset]. British Lop Pig Society, The Roslin Institute and Scotland‘s Rural College (SRUC). https://doi.org/10.7488/ds/3479

A genetic linkage map of the hermaphrodite teleost fish Sparus aurata L.

The gilthead sea bream (Sparus aurata L.) is a marine fish of great importance for fisheries and aquaculture. It has also a peculiar sex-determination system, being a protandrous hermaphrodite. Here we report the construction of a first-generation genetic linkage map for S. aurata, based on 204 microsatellite markers. Twenty-six linkage groups (LG) were found. The total map length was 1241.9 cM. The ratio between sex-specific map lengths was 1:1.2 (male:female). Comparison with a preliminary radiation hybrid (RH) map reveals a good concordance, as all markers located in a single LG are located in a single RH group, except for Ad-25 and CId-31. Comparison with the Tetraodon nigroviridis genome revealed a considerable number of evolutionary conserved regions (ECRs) between the two species. The mean size of ECRs was 182 bp (sequence identity 60–90%). Forty-one ECRs have a known chromosomal location in the pufferfish genome. Despite the limited number of anchoring points, significant syntenic relationships were found. The linkage map presented here provides a robust comparative framework for QTL analysis in S. aurata and is a step toward the identification of genetic loci involved both in the determination of economically important traits and in the individual timing of sex reversal