Next generation Sitka spruce breeding informed by predictive and comparative genomics

Lead Research Organisation: University of Edinburgh
Department Name: The Roslin Institute

Abstract

BACKGROUND - Selective breeding has increased Sitka spruce yields by 25% in the UK since 1970 but it takes 30 years to genetically select and mass produce new tree varieties. Genomic prediction methods could shorten the process down to 11 years and thus theoretically increase the rate gain from 0.83% to 1.85% per year. Such an acceleration would also enable more timely responses to new challenges such as emerging pests and climate change. The principle is simple: use DNA markers to predict the genetic worth - also called breeding value - which are the data that breeders need most for effective selection.
GOALS - We propose to develop genomic prediction in Sitka spruce, the UK's third largest crop by area. Research indicates that models developed from DNA markers can predict breeding value in trees but significant knowledge gaps and model development challenges have prevented practical application. We aim to unlock the potential of genomic prediction by improving our understanding of the relationship between prediction accuracy and population structure, modelling several traits simultaneously and optimizing genotype imputation methods.
SPECIFIC OBJECTIVES - We will specifically target productivity and insect resistance traits that we will analyse in a same training population developed from the breeding program and established on two sites, working collaboratively with researchers in the Spruce-up project. The proposed research will develop large-scale genotyping capacity, a genetic linkage map for Sitka spruce and a virtual Pinaceae genome map to support genomic prediction and comparative genomics research.
The RESEARCH OBJECTIVES are:
1. Develop a sequence diversity analysis platform and use it to construct genome maps.
2. Develop a predictive genomics platform to target yield improvements and decreased time to harvest.
3. Develop approaches for insect resistance breeding and genetic diversity management.
Two major PARTNERSHIP OBJECTIVES will support research excellence and impacts.
4. Transfer knowledge and practice to forestry end-users.
5. Develop an international partnership with the Spruce-up project in Canada.
IMPACTS - The methods of predictive genomics and the knowledge developed in this project will benefit the forest industry in three ways: a major acceleration of genetic gains; shorter production time aiming to grow trees and produce the same quality wood in 33% less time; and increased resistance against damaging insect pests. These changes would be transformative for the UK's £2bn per annum forest industry, and lead to more sustainable production, i.e. adapting commercial forests for climate change and mitigating risks of yield losses from newly arrived pests. Our project will link with existing industry networks to translate these changes into benefits for years to come. The impacts could be large in economic terms as commercial Sitka spruce production is valued at around £ 1 billion annually, and in land-use scale as it covers 2.7% of Britain's land area. The novel capacity and know-how from this research will also accelerate developments in other species and will fill gaps in training and expertise of significance to industry and governments globally.
TEAM - The project team is made up of internationally renowned academics in the field of genomics at the Universities of Oxford and Edinburgh together with Britain's conifer breeding and crop quality experts based in Forest Research. It combines a uniquely appropriate set of experiences for developing genomics informed tree breeding in the UK.
INDUSTRY SUPPORT - The industrial partners for this project are BSW Timber Ltd, Maelor Forest Nurseries Ltd, Forestart Ltd, The Sitka Spruce Breeding Cooperative Ltd, and Scottish Woodlands Ltd. Collectively, these organisations encompass nurseries, tree growing and wood processing, representing the key links in the forestry value chain.

Technical Summary

The project aims to develop genomic prediction in Sitka spruce and thus create novel capacity to increase the rates of genetic gain in the UK's breeding of programme. Selective breeding is effective for increasing yields in Sitka spruce but it takes 30 years to select and propagate new varieties. Genomic prediction methods could shorten the breeding process and increase the rate of yield gains from 0.83% per year to 1.85% per year.

The proposed research will develop large-scale genotyping capacity, a genetic linkage map for Sitka spruce, a virtual genome map for the pine family and large training set for predictive genomics model development. We will use this platform to investigate three key issues relevant to prediction in forest trees: i) the accuracy of prediction as a function of training set properties; ii) model development for yield in conjunction with wood quality traits; and iii) development of genotype imputation to enable more cost efficient genotyping methods; iv) resistance traits and candidate genes as relevant to damaging weevils.

The project outputs will include a genetic diversity database and analysis platform. We will also develop statistical models that may be used by breeders to reduce the need for lengthy and costly field evaluations.

Planned Impact

WHO MIGHT BENEFIT? -
This project will impact tree breeding as the proposed predictive genomics methods will be direct applicable to Sitka spruce. With 6640 km2 under cultivation, the UK is the world's largest grower of Sitka spruce. Tee nurseries and growers, forestry operators and management firms, and large wood processors are the industries that profit from its production and are the expected commercial beneficiaries of the research. They are a major source of rural employment and many of them partner within the Sitka Spruce Breeding Cooperative also involving Government (Forest Research). Ireland, France, Scandinavia and North-America also grow 1000s of km2 of Sitka spruce industrially and represent an additional set of potential beneficiaries.
While the proposed research is primarily on Sitka spruce, the impacts will reach beyond this single species and the results will be of interest to diverse beneficiaries. This is because, we will produce an integrated genetic map for species within the Pine family which includes many ecologically significant and economically important trees in the UK and globally. It is also because the project will set up a platform of expertise that is lacking in the UK and this will help broaden the beneficiaries of forest genomics to other species and to uses including multi-purpose forest management, conservation, monitoring, and timber tracking, among others.

HOW MIGHT THEY BENEFIT? -
Genomic Prediction methods from the project have a high likelihood of direct and short term impact, and are expected to have a transformative effect on tree breeding as already realized in livestock. A large SNP database and a genotyping array covering 10,000 SNPs will also become available to industry for further developments. The UK's world leading Sitka spruce breeding program is a logical first target for GP development that is internationally competitive and has commercial impact. The acceleration of breeding that results from GP directly increases rates of genetic gain. The proposed work specifically aims to enable increased wood yields, shorter time to harvest and reduced risks of insect damage. The translation of results to industry is facilitated in the UK by a dynamic value chain from the breeders all the way to the wood processors - turning germplasm improvements into profits.
The expected economic impacts of the anticipated changes in breeding are tangible and could be very large. As the UK only produces 40% of the wood that it consumes and much of its land is under strong pressure for other agricultural and urbanisation uses, there is considerable scope for impact from increased biological efficiency of crops. One study simulating efficiency gains in spruce plantations showed that reducing the time to harvest by 20% would increase the net present value for growers by up to 73%. Applied to the hundreds of km2 that are restocked in Sitka spruce annually, the benefits would reach hundreds of £ millions over several years. Other benefits will result from more rapid development of new varieties and improvements in genetic diversity management as a key to enhancing adaptability to new pests and diseases as well as changing climates.

WHAT WILL BE DONE TO ENGAGE WITH POTENTIAL BENEFICIARIES? -
The commercial environment of the forestry sector involves Industries and Government (Forest Research and Forestry Commission) which we will bring together in our Project Advisory Board. This approach for engaging with end-users will support research co-development with users, improved uptake capacity of research outputs by end-users, and commercial developments. Other actions will include dissemination activities for industry and forestry professionals, a workshop on the transformative effects of genomics and formation of a Research Club in forest genomics. We will also engage with the broader public through public lectures on forest sustainability and press releases.

Publications

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Description This project has only just started and RI direct involvement is in final 2 years. However the Academic partnership with University of Oxford had a very successful kick off meeting with the Sitka Spruce Co-operative which are the industry funders in this IPA, in which we explored the use of genomics in other breeding schemes and developed plans for making the Co-operative more influential in developing science for their objectives. This was delivering the Pathways to Impact as planned in the proposal. We have continued build on the industrial partnership and to help the Sitka Spruce Co-operative develop a research portfolio that is targeted towards a more effective forestry. We have also confirmed an Industry Day to be held at RI in September 2019, in collaboration with our partners.
First Year Of Impact 2018
Sector Agriculture, Food and Drink
Impact Types Cultural,Societal,Economic,Policy & public services

 
Description Next generation Sitka spruce breeding informed by predictive and comparative genomics
Amount £175,351 (GBP)
Funding ID BB/P018653/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 09/2017 
End 09/2020
 
Description Forestart 
Organisation Forestart Ltd
PI Contribution Co PI in project "Next generation Sitka spruce breeding informed by predictive and comparative genomics" (BB/P018653/1). Designing experiment and carrying out quantitative genetic analyses using pedigree and genomic data, establishing imputation protocols.
Collaborator Contribution Funding for IPA.
Impact Early days.
Start Year 2017
 
Description Laval University 
Organisation University of Laval
Country Canada 
Sector Academic/University 
PI Contribution Co PI with Oxford University in project "Next generation Sitka spruce breeding informed by predictive and comparative genomics" (BB/P018653/1). Designing experiment and carrying out quantitative genetic analyses using pedigree and genomic data, establishing imputation protocols.
Collaborator Contribution Making available background IP on conifer genomes, genotyping and sequencing services, bioinformatic analysis of sequence data.
Impact Early days.
Start Year 2017
 
Description University of Oxford 
Organisation University of Oxford
Country United Kingdom 
Sector Academic/University 
PI Contribution Co PI in project "Next generation Sitka spruce breeding informed by predictive and comparative genomics" (BB/P018653/1). Designing experiment and carrying out quantitative genetic analyses using pedigree and genomic data, establishing imputation protocols.
Collaborator Contribution Molecular genetic analysis of conifer genome analysis, comparative genomics, insect resistance expertise, turpene assays, expression arrays.
Impact Early days.
Start Year 2016