Keeping rare breeds Case studies British Lop project – genomic work complete The completion of a genomic characterisation study has revealed that the British Lop can be clearly defined as distinct from other native pig breeds. By identifying genomic characteristics unique to the breed, the work carried out makes it possible to develop a breed purity test that will carry a number of benefits in ongoing breeding programmes to control inbreeding and ensure genetic diversity. The British Lop Project was launched in 2019 with major funding from the Gerald Fallowes Discretionary Trust with the aim of taking pig genetics’ conservation to a new level. A five-year project, it includes boar semen collection and the latest genomic work. At the outset of the project it was also envisioned that it would also include Gene Bank embryo collections, an aspect that is still being explored. The Genomic Characterisation Project was led by Professor Georgios Banos of Scotland’s Rural College (SRUC) and Dr Enrique Sanchez-Molano of the University of Edinburgh, with the support of Giles Eustice and Celia Upchurch of the British Pig Society who co-ordinated the collection of hair samples for genotyping and the provision of pedigree data. The project set out to achieve three key objectives: An assessment of the British Lop genomic population structure, including levels of genetic diversity and inbreeding. The calculation of the genomic relatedness of British Lops with other pig breeds. The identification of specific genomic (molecular) markers that uniquely characterise and distinguish the British Lop from other pig breeds. The results of the study revealed that there is genetic diversity within the current breeding Lop population, but that levels of inbreeding and the estimated effective population size indicate that prompt measures are needed to safeguard and enhance this diversity. The study also identified 75 Single Nucleotide Polymorphisms (SNPs) – variations in single bases of DNA between organisms which provide useful genetic markers for clinical phenotypes. The combination of these SNP markers is unique to the Lop and can be used to distinguish members of the breed from other breeds. The research was based on analysis of hair samples taken from 190 individual British Lops raised on 40 different farms belonging to members of the British Lop Pig Society, a number that represented a solid cross-section of the current breeding population of registered animals. In addition, all of the available pedigree records were obtained – 2,902 in total (including founders) – spanning between zero and 11 generations per animal. Every hair sample was genotyped and a number of widely accepted quality assurance steps were applied to ensure the quality of those eventually analysed and ultimately the analyses were based on 176 British Lop genotypes. Genomic analyses revealed no population sub-structure and good genomic connections among the farms participating in the study. To assess genetic diversity, including levels of genomic inbreeding, a number of measurements were applied to the genotype data and, in addition to this, pedigree data were also analysed to derive estimates of the standard pedigree inbreeding. In order to compare the Lop with other pig populations, genotypes of individual pigs from 12 other UK pig breeds were obtained from the public domain, together with genotypic data from 29 wild boars and from a number of distinct European breeds. These were compared with thirty-three representative samples from the British Lop. Genetic diversity An analysis of the breed’s historic effective population size revealed that the last 20 generations, theoretically spanning 60 years assuming a typical generational interval of three years, saw a reduction in the effective population size from nearly 70 to 40. This reduction was shown to be practically linear, suggesting that the population did not seem to have passed any severe bottlenecks threatening its diversity in the past. The current estimate of effective population size of the breeding population is 40 to 45; as the value of 40 is borderline critical for breed conservation purposes, this indicates the need for measures to be taken to prevent any further decrease. The study also found that genomic diversity is still present in the population but that estimated genomic inbreeding levels can be considered moderately high. This work demonstrates the genetic uniqueness of the British Lop pig. We used modern technologies and data to derive information that may be used as a practical breed purity test and also inform breeding strategies aiming to safeguard the integrity of the breed. It was a great collaboration with the BPA and RBST. Professor Georgios Banos Lop vs the rest The comparisons of the Lop to other breeds showed that the most closely related were the Welsh and Landrace, followed by Pietrain, Middle White and Large White. However, a Principal Component Analysis offering a closer look at Lop genotypes in relation to the Welsh and Landrace corroborated the Lop’s genetic distinction. All other breeds were much more distant from the British Lop. Unique markers Following repeat data analyses and validations, a set of 75 SNP markers were identified, located on 17 chromosomes, that combined are unique to the British Lop and distinguish it from other breeds. These markers open up the possibility of developing a breed purity test either by constructing a custom-made targeted DNA array or in a breeding programme of continuous genotyping and control of the breed with an existing commercial DNA array. The latter option would mean that these data may then be used to simultaneously perform the breed purity test, to estimate genetic relatedness and inbreeding levels from specific future matings to control inbreeding, and to underpin selective breeding for balanced genetic improvement and managed diversity. This has been a fascinating project to be involved with. I am so pleased with the commitment of our membership to take the necessary hair samples and achieve such a quality result from the samples. To clearly prove the unique traits of the British Lop coupled with proving its evident diversity in such a small population is a resounding success and a credit to all the breeders involved to date. There is work to do in ensuring we better the existing diversity and I have confidence in our breeders commitment to achieve it. The next phase looking into embryos and how we can work with the data will be an exciting time.’ Giles Eustice, Chairman, The British Lop Pig Society Lop project semen collections Working with the British Lop Pig Society, RBST has now collected semen from a total of seven boars: one from each of the Duke, Supreme, Cornishman, Charles and Prince lines and two from the General line. The most recent additions were Blackbush Prince and Blackbush General. Working to the original project target of 15 boars to be added to the Gene Bank, collections will continue through to 2023 and RBST will work with the breed society to identify boars that represent both different boar lines and a diverse range of female lines.