You are here

Protecting genetic diversity

Work Package 2.3 - Agricultural systems and land management

Research Deliverable 
2.3.2 Protecting genetic diversity
Leading Ideas 
Agriculture
Rural Economy

Introduction

Farm animal and plant genetic resources are part of Scotland’s natural capital, underpinning our current productive capacity, encoding our cultural heritage and embodying the resilience for future farming and food security. This RD represent genetic diversity in an economic framework, highlighting market/institutional structures and the costs and benefits (and their distribution) of conserving diversity. 

Proposed research will explore elements of in situ and ex situ diversity in Scotland focussing on selected livestock and crop resources (beef, barley, wheat and potatoes) that demonstrate some of the key conservation values, actions, tools and barriers. Specific breeds and varieties will be identified through stakeholder engagement and data availability.

The research will allow government to be more certain about the value and existence of genetic variability and the impact on rural areas and how effective any interventions from government might be.

Aim of Research

We aim to address a research gap by suggesting how policy can be designed to target maximum diversity conservation (including co-benefits) at minimum cost; where cost and benefits are both financial and social.  Sub-objectives are:

  • demonstrate the extent to which this diversity objective corresponds to (or accommodates) a demand for other socially and culturally relevant objectives that also contribute to resilience such as  maintaining population structures, health/welfare, cultural value of rare breeds and landraces in marginal areas.
  • consider how modern DNA technologies can contribute to enhancing genetic diversity by controlling inbreeding whilst continuing improvement in livestock populations.

Progress

2020 / 2021
2020 / 2021

Research continued to deepen our understanding of genetic diversity in both the livestock and crop sectors.  This year has seen further investigation into the management of and consumer market for genetic diversity. This focus will lead to a better understanding of genetic diversity across the supply chain from both a supply and demand perspective.

A focus of research this year has been further understanding consumer preferences for different potato varieties, and hence the consumer market for genetic diversity.  Building on work in previous years, an online of Scottish consumers surveyed consumers’ perceptions of potatoes and responsiveness to potatoes with increased nutritional benefits.  The survey included a choice experiment in which respondents were asked to make purchasing choices between alternative potato profiles.  The statistical analysis of these choices helped to identify the characteristics of potatoes important in consumers’ purchasing decisions and impact of nutritional information on their preferences.  Most respondents surveyed were satisfied with the diversity in potato varieties available to buy and even thought diversity was high.  With regard to purchasing decisions, colour was found to the be most important factor followed by origin and size.  White fleshed potato were preferred over purple fleshed potatoes, despite the nutritional benefits of the latter.  Information about the health benefits of potatoes significantly impacted consumers’ preferences for and increased their willingness to pay for purple fleshed potatoes. Hence, more information on the health benefits of purple fleshed potatoes would likely raise their profile and in turn support the genetic diversity of potatoes.

Research has continued to build on work in previous years on genetic diversity in the livestock sector.  Computer models developed in previous years were used to estimate inbreeding in ruminants.  This work included the prediction of future progeny inbreeding from specific sire-dam matings.  Different estimates of inbreeding were compared.  Such information is valuable for optimising the management of genetic diversity in livestock populations.  As such, the impact of actual and predicted genomic inbreeding derived in the previous 6 months on important animal traits was assessed.  This work will help to inform how industry can use genomic data to manage inbreeding. The market for genetic diversity from the perspective of a consumer and also the impact of inbreeding policy impacts of support genetic diversity were investigated. 

Highlights:

Some relevant highlights could be pulled from Theme progress reports and then added to.

A representative sample of 660 Scottish consumers answered a choice experiment as well as attitudinal and perception questions. Information related to the health benefits of potato was conveyed to consumers according to 3 different treatments. The survey was analysed using descriptive statistics and econometric technics to estimate a conditional logit model. The report 'Consumers’ preferences and perceptions of genetic diversity and health benefits of potatoes” found that: price, colour, origin and size of potato tubers are key factors in consumers’ choice of potatoes at the purchasing stage. Consumers were generally happy with the diversity of potatoes that is available for them to buy in their usual retail outlet and thought that this diversity was high. They also generally agreed that potatoes could be part of a healthy diet and disagreed that potatoes contribute to weight gain. They were unsure about the advantages of coloured fleshed potatoes from a nutritional point of view but appeared to be responsive to information about the health benefits of purple fleshed potatoes. Detailed health information message based on scientific evidence was twice as efficient as a simple information message.

2019 / 2020
2019 / 2020

The value of genetic difference has been explored further with critical investigations on both livestock and crop production sectors. This year has seen further in-depth exploration of several key themes around genetic diversity.  Principally the policy influences towards supporting diversity have been highlighted for both livestock and crops.  With the UK's withdrawal from the EU we have examined the current policy framework for support of genetic diversity and argue that this framework must be strengthened to protect our genetic diversity.  We have also explored the demand and awareness of diversity in consumption.  This leads to understanding of both the supply and consumption perspectives around genetic diversity.

A supply chain level analysis of genetic diversity has been conducted to understand its value within society.  A focus for this year has been developing understanding of consumer and policy influences on promotion or hinderance of genetic diversity.  A set of algorithms and frameworks for understanding the economic effects of loss of genetic diversity have been developed. This has focused on the effect of inbreeding in Scottish blackface sheep, finding the need to apply appropriate mating schemes that avoid increasing inbreeding. We have also engaged with consumers which has identified a desire to understand more diversity within the supply chain.  This supports greater knowledge and understanding between agents within the supply chain to enable protection of genetic diversity.  Consumers’ demand for potatoes genetic diversity has been identified as a leverage for re-introducing diversity in the potato sector. We found that consumers’ understanding of genetic diversity related to the diversity of potatoes varieties encountered at their usual retail points. Consumers were knowledgeable about potato varieties, but ‘variety’ was a criteria they tended to overlook when purchasing as well as a factor they thought they had little leverage of. Their understanding of the health benefits of potatoes was also low. When informed about the health benefits of potatoes though, they reported that if provided with some information about health benefits of potatoes, that would be a criterion they would account for in their future purchases.

A suite of computer programmes was first developed to link inbreeding results from year 3 with animal traits. The software was then applied to a population of Scottish Blackface sheep to assess the impact of inbreeding on the following traits: birth weight, weaning weight, slaughter weight, carcass weight, carcass fat and muscle depth, growth resilience to weather, and faecal egg count. Inbreeding did not have a significant effect on these traits, with the exception of a small effect on carcass fat depth (genomic inbreeding) and faecal egg count (pedigree inbreeding). Thus, current inbreeding levels do not impact in this population, but it is recommended to apply appropriate mating schemes that avoid increasing inbreeding.

Highlights:

A policy brief, 'Conservation of Farm Animal Genetic Resources: Current policies and post-Brexit options'[1] reviewed policies on conservation of genetic resources and potential policy impacts post-Brexit.  We found that the UK’s response, in terms of policies encouraging the conservation of Farm Animal Genetic Resources (FAnGR), has been lacking and support further frameworks and discussion unless this important aspect of future agricultural policy be ignored.

2018 / 2019
2018 / 2019

The value of genetic difference has been explored further with critical investigations on both livestock and crop production sectors. A series of engagement events have allowed empirical testing of models and algorithms, as well as gathering of information towards particular future scenarios for policy planning.  These rely heavily on narratives around Scotland's relationship with the EU in the future and the effects on planning and farm management for both livestock and arable sectors. Moreover, strands devoted to big data analysis have also allowed us to examine decision making and the outcomes of preserving greater diversity.

Policies were further explored and their relationship to supply chain drivers.  Moreover, explorations of how the 'payment for public goods agenda' could fit within post-Brexit agriculture were also explored in order to find opportunities for support to overcome barriers in conservation of genetic resources.

Building on stakeholder workshops conducted in previous phases of the project, supply-chain actors engaged in Scenario Planning, exploring Brexit implications for varietal diversity in potatoes. Researchers canvassed views on important drivers of change at Potatoes in Practice (09.08.18). Three scenarios were developed to promote strategic thinking in the face of future uncertainty. Scenario 1, “Salvation through Science”, envisaged a buoyant market with Britain out of the EU but adapting innovatively with smart solutions. In scenario 2,” Survival of the Fittest”, there are few new potato varieties with conventional breeding techniques still the norm. There is upside, but the cost of production and lack of labour make competing on the world stage tougher. Participants working with Scenario 3, “Potato production in a pesticide free world” visualized an industry struggling with increased incidences of serious disease outbreaks, reduced yields, labour shortages and no subsidies. 

Scenario outcomes include scenario specific strategic recommendations around gene editing, promoting health benefits of potatoes via government social media and breeding for health, developing varieties to cope with weather extremes- especially for export and adopting new pest management technology and crop health (to replace pesticides in line with moves towards a low-carbon economy.)

The key message of the research (presented through a policy brief) was that constructing an indicator for monitoring rare breed status may support more targeted conservation interventions. Employing multi-criteria decision analysis (MCDA) to differentiate funding for conservation activities may improve the cost effectiveness of investments in preserving rare breed diversity.  We showed that MCDA provides a powerful analytical framework for reporting breed status and developing key performance indicators to benchmark performance. We suggested the method could be adapted to include other livestock species but with some changes to the criteria. With respect to targeted support we concluded that taking account of the multiple factors that may be driving breed extinction risk can support more strategic conservation interventions to improve breed status.

Further analysis has been conducted of the semi-structured interviews conducted in year 2 to examine the governance structure of genetic diversity in the potato sector. More specifically, we examined: i/how genetic resources are managed in the potato sector; ii/ stakeholders’ perceptions of the challenges and opportunities brought about by genetic agrobiodiversity as well as, iii/their perceptions of the role played by genetic agrobiodiversity in the resilience of the sector.

A workshop was held and the findings were: i) Focusing only on conservation grazing was identified as a poor approach and any future incentive schemes must be made more holistic across the main livestock species; ii) Improving the marketability of animal genetic diversity through developing novel products and tapping into niche markets was seen as a major challenge to improve self-sufficiency of breeds; iii) Prioritisation by using more sophisticated approaches such as the approach suggested in this workshop are needed to communicate more effectively with politicians and other stakeholders. Moreover, with an oral presentation we squared these findings with post-Brexit farming to understand how conserving farm animal genetic resources can be considered a public good under the Agriculture Bill.

We investigated challenges and opportunities of conserving rare and native breeds through interviews with enterprises in the sheep meat supply chain and an online survey targeting sheep farmers.   We found that native breeds are mainly kept because of their adaptability, hardiness as well as greater production than average commercial cross bred animals. Our work identified marketability and lack of investment in marketing as an important factor that prevents farmers keeping rare and native breeds.  Furthermore, we investigated the structure of the supply chain with respect to genetic diversity of crops (mainly barley and wheat). It was found that adjustment in current laws and regulations is needed to assure sufficient level of genetic diversity. Also it was found that large companies in the food production chain have the power of controlling the market including entrance, access to distribution channels and ability to set prices and therefore they negatively affect genetic diversity of the producing crops.

We developed a mathematical model to optimise breed conservation choices, and to evaluate alternative scenarios for efficiently re-allocating genetic materials currently stored in different European cryogenic banks, allowing for cross-country gene collection, cost and cryogenic capacity differentials.  We showed how alternative allocations could reduce overall conservation costs, and illustrate the diversity-cost relationship using notional supply curves.  These provide guidance for both policy makers and conservation scientists seeking to define objectives for the design of efficient ex situ conservation.

A suite of algorithms developed in Year 2 were applied to the analysis of bovine genotypic and pedigree data. Data pertained to ca. 250,000 animals with genome-wide genotypes spanning all chromosomes including ca. 50,000 SNPs. These animals are primarily kept for breeding purposes. Results from the analyses include estimates of genomic and pedigree inbreeding of individual animals. Diversity measurements were also derived. These results can be used to inform breeding programmes aiming at both genetic gain and maintenance of genetic diversity.

Highlights:

  • Helping industry value and protecting genetic diversity. SEFARI researchers and students have been working with UK industry stakeholders on the importance of protecting UK native breeds (RD2.3.2) during April. One workshop was hosted by the Rare Breeds Survival Trust (RBST) to discuss the conservation of UK’s native livestock breeds which are at risk. The workshop included participants representing 25 different breed societies and three different institutions including ADHB, RBST and members of Defra’s Farm Animal Genetic Resources Committee. A second workshop, again hosted by RSBT, explored the development of support structures for conservation of the UK’s Native Breeds at Risk post Brexit.
2017 / 2018
2017 / 2018

For livestock, a workshop was held to explore the development of support structures for conservation of the UK’s Native Breeds at Risk post Brexit. The state of rare livestock breeds was studied.  A small-scale survey and semi structural interviews were conducted with sheep farmers in the UK. A mathematical model was developed to optimise ex situ breed conservation choices. Algorithms were developed to identify conserved genomic regions affecting diversity and to control inbreeding. For plants, interviews and stakeholder workshop with representatives of the potato sector were held.

The current UK policies to protect genetic diversity was reviewed and analysed. Also optimisation methods such as multi-criteria decision analysis and diversity maximisation given a limited budget were used to inform future policies to protect genetic diversity.

A second workshop was held and hosted by the Rare Breeds Survival Trust (RBST) to explore the development of support structures for conservation of the UK’s Native Breeds at Risk post Brexit. The workshop included participants representing five different institutions including RBST, SRUC, Natural England, Animal Breeding Europe and the National Trust. The workshop focused on the discussion and weighting of multiple criteria that could be employed to more objectively monitor breed status to provide important information that may allow more targeted policy interventions to improve conservation outcomes.  Data collected at the first RBST workshop, were used to develop a multi-criteria analysis (MCDA) model. The MCDA model was then used in the second RBST workshop to investigate how rare breed incentive schemes can be made more rational. A performance matrix was used to score 19 UK cattle native breeds at risk relative to endangerment, diversity and utility. The workshop was used to assign scores and weights for prioritisation.

For the crop sector:  we undertook interviews and stakeholder workshop with representatives of the potato sector to understand genetic diversity. Using qualitative social network analysis, results show that: i) in the ware sector, the main objectives have been to select varieties for pests and disease resistance while maintaining important yield. Less attention has been paid to organoleptic characteristics of potatoes. ii) main drivers connected to national and global, market and institutional factors e.g. supply chains, education and governance,  iii) Future selection and conservation strategies will need to take into account the evolution of regulations regarding the use of pesticides as well as evolving consumers’ demand.

Barriers and opportunities of conserving livestock genetic resources and protecting genetic diversity was investigated using sheep meat supply chain as an exemplar. A literature review, a small-scale online survey and a number of semi structural interviews were conducted with farmers and other chain players. Also a separate study has been designed and is being conducted to study industrial and supply chain structures and genetic diversity of the crop growing industry in the UK.

The global existential challenges for in situ livestock breed conservation have been a focus of considerable attention, and while ex situ collections may have some limitations, they nevertheless offer the potential to reduce extinction risks, affording option value to society in terms of maintaining future breeding opportunities. In this RD a mathematical model was developed to optimise breed conservation choices, and to evaluate alternative scenarios for efficiently re-allocating genetic materials currently stored in different European cryogenic banks.  The model showed how alternative allocations could reduce overall conservation costs, and illustrates the diversity-cost relationship using notional supply curves. 

Algorithms were developed to (i) identify conserved genomic regions affecting diversity and (ii) underpin simultaneous genetic selection and inbreeding control. End-user input had been considered in the previous year in the design of algorithms. The algorithms were first tested on simulated data mimicking real life scenarios. Subsequently, they were applied to actual livestock data. A report including recommendations was prepared.

Highlights:

  • Supporting and incentivising farm animal genetic resources (FAnGR) Prioritising FAnGR for incentive support under agricultural policies: using a decision support methodology developed in this research, native breeds at risk were investigated relative to diversity, marketability and endangerment. Experts and stakeholders such as rare breed survival trust (RBST) and breed associations contributed to the policy framework in two consecutive workshops. This research reveals employing genetic technologies and simplistic performance recording are major challenges but crucial to realising the option value components of FAnGR diversity. Furthermore, work conducted on the utilisation of animal genomic information for diversity control optimises genetic resource management in livestock production. As a policy implication our model provides a holistic analytical framework to support conservation decision making by considering the multiple factors that may be driving breed extinction risk in addition to the cultural and diversity value attributes. This contributes to the economics of rural areas, enhancing biodiversity and related governmental policies. Further, SEFARI research feeds into the outputs from the national Farm Animal Genetics Resources Group, which gives advice to the government on the conservation and sustainable use of farm animal genetic resources. Key resources developed in the impact period include contingency planning for breeds at risk, technology review related to FAnGR, as well as required national reporting on our National State of Farm Animal Genetic Resources and updating UK Breeds at Risk list.
  • Stakeholder engagement with small potato producers: Greater understanding of the maintenance of varietal diversity for potatoes is achieved through engagement with a broad range of stakeholders. To facilitate this, SEFARI researchers contacted amateur growers including allotment holders throughout Scotland and hosted a workshop in Dundee on 18th January 2018. Their views on varietal diversity within the context of Food and Nutrition Security (FNS) were elicited. Data complemented existing datasets informed by commercial growers and institutional actors with community level insights revealing potato diversity as a cultural asset with particular, associated opportunities and challenges. This data will feed into the Social Network Analysis and Scenario Planning (RD2.3.2) Feedback from the participants was extremely positive and the engagement helped to communicate the science being undertaken to a stakeholder group who were not ‘the usual suspects’ and were appreciative of being included.
2016 / 2017
2016 / 2017

We have focused on the difference embodied in rare breeds and have held a workshop with the Rare Breeds Survival Trust (RBST) to explore diversity and difference and how these are measured. We considered endangerment and risk scoring with a view to design of a new (hypothetical) support regime for rare breeds.  A workshop on genetic diversity of potatoes was held in Dundee 29 November 2016.  In addition to three researchers, nine representatives of industry and RESAS (SASA) participated. A research up-date and findings were presented to the Scottish Society for Crop Research Potato Winter meeting 23 March 2017.  For livestock, after the RBST workshop, we have suggested a method (multi criteria weighting) to explore how we can measure the preferences held for different rare livestock breeds. 

A follow-up survey was circulated to participants in the original workshop and Scottish Society for Crop Research Potato winter meeting participants.   The survey involved statements made by participants in the workshop, which were collated and formed into statements, to which to Likert scale (totally agree to totally disagree) responses were requested.

This deliverable is currently a draft paper exploring the metrics linking farm animal genetic diversity and rare breed status.  We consider the public and private objectives being targeted by breed conservation and how these are currently being accommodated in different metrics.  We consider the different national and international institutions for breed conservation and the nature of different incentive structures to promote conservation.  

We hope to develop a limited conservation auction, which is a recommendation.  In the meantime we have been working with Bioversity International to develop conservation contracts for crop land races.  We have written a report on this, which will be published by Bioversity

The work includes a survey of EU wide ex situ gene bank collections for livestock. This survey will be implemented online in 2017; ii) the development of an optimisation model to understand how it might be possible to rationalise (i.e. make more efficient) the potential overlap between in situ and ex situ genetic material held in any jurisdiction. Implementation of this model will depend on data quality (from our survey), but we might envisage an application to Scotland.  A draft model outline exists and this work will be completed by mid-2018. This work is benefitting from our engagement in a related EU project Horizon 2020 (IMAGE) http://www.imageh2020.eu/

A simulation study was developed to combine animal records for productivity and fitness, genomic data and inbreeding, into a breeding programme. Different scenarios were tested placing different emphasis on achieving genetic gain versus maintaining diversity (inbreeding control). The most balanced scenario maximised genetic gain for a pre-defined inbreeding level that remained constant. Breeding programmes can utilise this strategy for inbreeding levels that do not impact negatively on animal performance and diversity.

Highlights:

  • Using genomic information to optimise management of genetic diversity in livestock populations Individual animal records and genomic information can be combined in a way that promotes genetic improvement of livestock while controlling inbreeding and maintaining genetic diversity in the population A simulation study was developed to combine animal records for productivity and fitness, genomic data and inbreeding, into a breeding programme. Different scenarios were tested placing different emphasis on achieving genetic gain versus maintaining diversity (inbreeding control). The most balanced scenario maximised genetic gain for a pre-defined inbreeding level that remained constant. Breeding programmes can utilise this strategy for inbreeding levels that do not impact negatively on animal performance and diversity.
  • Optimising in and ex situ diversity conservation This work considers evidence on genetic and reproductive material conservation ex situ and its role in supporting in situ conservation strategies.  This research involved two strands: i) development of a survey of EU wide ex situ gene bank collections for livestock; and ii) the development of an optimisation model to understand how it might be possible to rationalise (i.e. make more efficient) the potential overlap between in situ and ex situ genetic material held in any jurisdiction.  This work benefitted from our engagement in a related EU project Horizon 2020 (IMAGE).

Future Activities

In year 6 the work will focus on consumer choice, economic modelling, and strategies for and predicting genetic diversity. In particular, research will focus on the differences in consumers’ preferences, characterising the main consumer profiles, their preferences and sensitivity to alternative information campaign strategies.  In the livestock sector, economic modelling will look at the impact of on the economy of the effects of genetic choice on productivity and economic potential.  This includes modelling the impact on the Scottish economy relating to market and disease related disruptions.  In addition, genomic inbreeding information on animal traits will help inform how industry can use genomic data to manage inbreeding.