Prospects and challenges for the conservation of farm animal genomic resources, 2015-2025

Abstract

Livestock conservation practice is changing rapidly in light of policy developments, climate change and diversifying market demands. The last decade has seen a step change in technology and analytical approaches available to define, manage and conserve Farm Animal Genomic Resources (FAnGR). However, these rapid changes pose challenges for FAnGR conservation in terms of technological continuity, analytical capacity and integrative methodologies needed to fully exploit new, multidimensional data. The final conference of the ESF Genomic Resources program aimed to address these interdisciplinary problems in an attempt to contribute to the agenda for research and policy development directions during the coming decade. By 2020, according to the Convention on Biodiversity's Aichi Target 13, signatories should ensure that “…the genetic diversity of …farmed and domesticated animals and of wild relatives …is maintained, and strategies have been developed and implemented for minimizing genetic erosion and safeguarding their genetic diversity.” However, the real extent of genetic erosion is very difficult to measure using current data. Therefore, this challenging target demands better coverage, understanding and utilization of genomic and environmental data, the development of optimized ways to integrate these data with social and other sciences and policy analysis to enable more flexible, evidence-based models to underpin FAnGR conservation. At the conference, we attempted to identify the most important problems for effective livestock genomic resource conservation during the next decade. Twenty priority questions were identified that could be broadly categorized into challenges related to methodology, analytical approaches, data management and conservation. It should be acknowledged here that while the focus of our meeting was predominantly around genetics, genomics and animal science, many of the practical challenges facing conservation of genomic resources are societal in origin and are predicated on the value (e.g., socio-economic and cultural) of these resources to farmers, rural communities and society as a whole. The overall conclusion is that despite the fact that the livestock sector has been relatively well-organized in the application of genetic methodologies to date, there is still a large gap between the current state-of-the-art in the use of tools to characterize genomic resources and its application to many non-commercial and local breeds, hampering the consistent utilization of genetic and genomic data as indicators of genetic erosion and diversity. The livestock genomic sector therefore needs to make a concerted effort in the coming decade to enable to the democratization of the powerful tools that are now at its disposal, and to ensure that they are applied in the context of breed conservation as well as development.

A genomic map of climate adaptation in Mediterranean cattle breeds

“…In addition to the identification of the genetic variants underlying adaptive response of Mediterranean cattle breeds to local climatic variation, characterizing their origin may thus be critical to promote the conservation of genetic resources and the associated traditional herding systems that are threatened by the increasing use of a small number of commercial breeds (Bruford et al, ; Savolainen, Lascoux, & Merila, ). The structuring of genetic diversity of Mediterranean local cattle breeds and their recent post‐domestication history makes it unlikely that locally favourable genetic variants arose by new mutations.…”

Effective population sizes in cattle, sheep, horses, pigs and goats estimated from census and herdbook data

“…Judging by the long lists of authors involved in most publications a wide-ranging, inter-institutional skill set is needed for LD detection, analysis and interpretation. This, the costs of genotyping, and the disappointing track record of molecular methods generally in guiding breed conservation (Bruford et al, 2015) argue for development of a method that can be used by non-specialists, that is dependent only on spreadsheet-type software.…”

“…The extent of genomic linkage disequilibrium (LD), deduced from microsatellite and single-nucleo tide polymorphism (SNP) data, can also indicate effective population size, termed here N e (LD). Another approach is the estimation of N e (ROH) from the extent of runs of homozygosity (ROH), and further genomic approaches are emerging (Bruford et al, 2015). Santiago and Caballero (1995) described from a theoretical basis, coupled with simulations, how N e can be deduced from N c in a population in which every individual is subject to selection.…”

Next‐generation metrics for monitoring genetic erosion within populations of conservation concern

“…Furthermore, due to prolonged and intensive artificial selection, the effective population sizes of major domesticated livestock breeds rarely exceeds a few hundred individuals (Leroy et al., ), despite their often very large census sizes. Thus, many domestic breeds of high heritage value also need management to maintain genetic diversity (Bruford et al., ).…”