A strategy to exploit genomic selection for achieving higher genetic gains in groundnut

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

Abstract

This project will develop the technology for genomic selection in legume and oilseed crops by applying the research tools developed at Roslin for computational genetics and breeding programme design in livestock to groundnut breeding programmes. Genomic selection has revolutionised livestock breeding programmes worldwide because animals are selected for breeding on the basis of genotype information - which can be collected from very young animals - instead of accurate phenotype information (inherited characteristics) which may not be available until several years after birth.
Genomic selection is now widely and successfully used in dairy cattle, pigs, sheep, and poultry and it offers new opportunities to increase the efficiency, effectiveness and sustainability of plant breeding programmes. Genomic selection promises the same benefits in pulse breeding as it has already delivered in livestock. Rates of genetic improvement in a breeding programme are determined by four factors: selection intensity, selection accuracy, breeding cycle time, and the amount of genetic diversity to be selected upon. The first three of these factors would be improved by genomic selection. In this discussion, we take the groundnut as an example but very similar limitations apply in other oilseed and pulse crops.
Selection intensity is low and breeding cycle time is long because traits such as X, Y, yield and disease resistance, as well as genotype by environment interactions, can only be selected upon late in the breeding cycle, by which point most of the candidates have been eliminated on crude visual criteria. Genomic selection would allow all traits to be estimated in very large numbers of plants once low-cost genotyping technologies have been developed. We need low cost genotyping technologies to increase selection intensity.
Selection accuracy is limited because selection in the early years of the breeding cycle is limited to the few traits that can be measured at the seedling stage. Important factors such as yield, X, genotype by environment interactions and Y cannot be evaluated in seedlings. Genomic selection would allow breeding values for all traits of importance to be estimated in young seedlings with a high degree of accuracy once an appropriate training population has been created and the necessary phenotype and genotype data collected. We need optimal designs for training populations to increase selection accuracy.
Breeding cycle time in groundnut is a minimum of four years because of the time it takes from crossing to advance generation from F1 to F6 to achieve homozygosity from where phenotyping can be done in plots. Genomic selection could reduce the breeding cycle time to a year or even six months because genomic selection can be carried out on immature seedlings and so the new cycle can be initiated as soon as the selection candidates reach maturity through rapid generation advancement. Additionally, genomic selection also help to reduce the size from F3 generation onwards thus optimizing the resources. This reduction in generation interval represents the most obvious advantage of genomic selection in comparison to traditional groundnut breeding as it gives a potential tenfold increase in the rate of genetic improvement. We need optimised breeding programme designs and transition strategies to reduce breeding cycle time in an affordable way that minimizes risks, hence the need for the proposed research.
To deliver this project we need to develop genotyping and sequencing technologies, algorithms and strategies to enable sufficient genomic data to be generated within the economic constraints of groundnut breeding programs. We need to develop a genomic selection training set. We need to develop and optimise the population improvement and product development components of the proposed redesigned breeding program. Finally, we need to implement the new design in the ICRISAT, DGR and UAS breeding programmes and test its performance.

Planned Impact

(i) The academic community. Scientifically, the project constitutes a step change by adapting genomic selection for legume and oilseed crops. Academics interested in plant and crop breeding, and quantitative geneticists, will all benefit from these developments. The impact will be delivered via publications, conference presentations and seminars, and by making data and software available.

(ii) Groundnut breeders and breeding companies. The simulations and breeding programme designs will show these organisations how to improve their products in a sustainable way. Return on investment modelling will guide investments to generate the necessary genotypes and training data. The software and scripts that we will use to impute genotypes in this project will be made available to breeders.

(iii) Plant and crop breeding organisations. The methods, particularly imputation, and the breeding programme designs and simulations are also highly relevant to vegetable and crop species breeding organisations. Therefore, the benefits to plant breeding organisations, in the developed and developing world, will be similar to those outlined for groundnut. UK farmers cultivate many diverse crop species. Active breeding programmes exist for the majority of these, most of which have UK breeding activities. With the exception of the major crops (e.g., wheat) these breeding programmes are almost exclusively based on classical breeding methods plus marker assisted selection in some cases. Adoption of genomic selection would enhance all of these breeding programmes, but the costs and risks of adoption are significant. The low-cost genotyping strategy, training population and breeding programme design, transitioning strategy, skills, computer programmes and insights developed in this grant will be applicable to breeding programmes in multiple crop and plant species where breeding resources are limited.

(iv) UK science infrastructure and capacity. The developed methods, designs and simulations will increase UK R&D capabilities. The proposed research will be embedded within training courses the PI is regularly invited to give, and the post-doctoral student working on the project will have the opportunity to be trained at a world-class institute in a cutting-edge area of research while interacting with a leading commercial partner.

(v) Policy. Genotype data are expensive, but the practical benefits of genomic selection are potentially large. Much investment will be made in genomics in the coming years, and outcomes from this project will help guide these investments.

(vi) Society. Communication will occur through Roslin's existing channels i.e. "Doors Open Day" and "Royal Highland Show".

(vii) High-school students. A 1-day programme for students, in line with UK High School curriculum's 'selective breeding' and 'global food security' modules, will be developed and taught to students. A test session will first be given to a small group of teachers and then this will be rolled out as part of the Easter Bush Science Outreach Centre's programmes available to high schools.

Publications

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Edwards SM (2019) The effects of training population design on genomic prediction accuracy in wheat. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Gorjanc G (2018) Optimal cross selection for long-term genetic gain in two-part programs with rapid recurrent genomic selection. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Hickey J (2019) The Fest Issue on Robin Thompson's contributions to statistics, genetics and animal/plant genetic improvement schemes. in Journal of animal breeding and genetics = Zeitschrift fur Tierzuchtung und Zuchtungsbiologie

 
Description A major challenge in breeding is to introduce novel alleles, for instance originating from gene-bank materials or wild accessions, into the genetic pool of elite breeding lines without losing the current performance of these elite lines for the economically relevant traits. By simulation, a novel breeding strategy has been developed and tested, that allows the incorporation of genetic material (introgression) of non-elite lines into elite breeding programs in a efficient way by using large amounts of genetic markers and genomic selection.
Exploitation Route The introgression strategy can be widely used in crop breeding to enrich the elite material with alleles that have either earlier been lost during the breeding process, or which have never been used before in breeding material. This will enable breakthrough improvements in quantitative, complex traits (i.e. yield) and the introduction of more simple traits such as disease and pest resistances. This is not only relevant to groundnut breeding, but for breeding in almost any crop species.
Sectors Agriculture, Food and Drink,Environment

 
Title AlphaMate 
Description Software for the optimisation of mating strategies in plant and animal breeding programs developed by John Hickey and Gregor Gorjanc. The software is free for download by researchers and students on the alpha genes website: http://www.alphagenes.roslin.ed.ac.uk but is licensed to companies. 
Type Of Technology Software 
Year Produced 2018 
Impact Interest from companies for a license and downloads from researchers internationally. 
URL http://www.alphagenes.roslin.ed.ac.uk/alphasuite-softwares/
 
Title AlphaPlantImpute 
Description AlphaPlantImpute is a software package designed for phasing and imputing genotype data in plant breeding populations. AlphaPlantImpute can be implemented within and across bi-parental populations to phase and impute focal individuals genotyped at low-density to high-density. 
Type Of Technology Software 
Year Produced 2018 
Impact This package was found to be extremely useful by our project partner global breeder KWS Saat SE. 
URL https://alphagenes.roslin.ed.ac.uk/wp/software/alphaplantimpute/
 
Title AlphaSimR 
Description AlphaSimR is a next generation software package in the line of our successful earlier package AlphaSim. The new package is accessible in a user-friendly way via an interface in the public domain environment R. The package is used for stochastic simulations of breeding programs to the level of DNA sequence for every individual. Contained is a wide range of functions for modeling common tasks in a breeding program, such as selection and crossing. These functions allow for constructing simulations of highly complex plant and animal breeding programs via scripting in the R software environment. Such simulations can be used to evaluate overall breeding program performance and conduct research into breeding program design, such as implementation of genomic selection. Included is the 'Markovian Coalescent Simulator' ('MaCS') for fast simulation of biallelic sequences according to a population demographic history [Chen et al. (2009)]. 
Type Of Technology Software 
Year Produced 2018 
Impact This package has rapidly expanded our possibilities to apply breeding simulation in research projects, both in academic research projects and for the breeding industry (most notably Driscolles and Bayer). Several graduate students used the package for their internship projects. 
URL https://alphagenes.roslin.ed.ac.uk/wp/software/alphasimr/
 
Description AlphaGenes Twitter channel 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The AlphaGenes updates the scientific community and a broader audience about news around our research group, scientific output and engagement activities
Year(s) Of Engagement Activity 2012,2013,2014,2015,2016,2017,2018,2019,2020
URL https://twitter.com/Alpha_Genes
 
Description AlphaGenes website 
Form Of Engagement Activity Engagement focused website, blog or social media channel
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact The AlphaGenes website informs the scientific community about the groups research activities, outputs, courses and available software tools.
Year(s) Of Engagement Activity 2017,2018,2019,2020
URL https://alphagenes.roslin.ed.ac.uk
 
Description Big Data in Agriculture, Part of the DuPont Pioneer Plant Sciences Symposia Series, at Roslin Institute, 14-15 May 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other audiences
Results and Impact Symposium held at the Roslin institute, organised by members of my group, sponsored by third parties from the breeding industry
Year(s) Of Engagement Activity 2018
 
Description Co-organized workshop "Simulation of Genetic and Genomic Systems" at Plant and Animal Genome xxviii conference 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact This workshop was held for the first time in the worlds most important Ag-Genomics meeting. It made academic and industry scientists aware of the power of simulation as a important emerging research discipline in this area.
Year(s) Of Engagement Activity 2020
URL https://www.intlpag.org/2020/
 
Description Course on The Next Generation Breeding (Iowa State University) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We organised a course on The Next Generation Breeding at The Iowa State University in Ames in May 2018 to present and teach about our research, principles of the developed methods and application of our software with real data. The course was very well received with plenty of discussions involving both academia, research and industry participants. It also initiated a series of offline research and application discussions.
Year(s) Of Engagement Activity 2018
 
Description Course on The Next Generation Breeding (KWS group) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact We organised an internal course on The Next Generation Breeding at The KWS group in Germany in Einbeck in March 2019 to present and teach about our research, principles of the developed methods and application of our software with real data. The course was very well received with plenty of discussions involving both academia, research and industry participants. It also initiated a series of offline research and application discussions.
Year(s) Of Engagement Activity 2019
 
Description Course on The Next Generation Breeding (University of Zagreb) 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact We organised a course on The Next Generation Breeding at The University Of Zagreb (Croatia) in July 2018 to present and teach about our research, principles of the developed methods and application of our software with real data. The course was very well received with plenty of discussions involving both academia, research and industry participants. It also initiated a series of offline research and application discussions.
Year(s) Of Engagement Activity 2018
 
Description Excellence in Breeding: Breeding Scheme Optimization Tools Training 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Breeders and Quantitative Geneticists play an important role in the seed sector as designers of manufacturing pipelines. In this workshop, the students learned to work with our breeding simulation platform AlphaSimR. The students reported back they had become aware of the power of the simulation of breeding programs, as well as the possibilities to make breeding programs more effective by using less conventional breeding schemes.
Year(s) Of Engagement Activity 2020
URL https://excellenceinbreeding.org/module2
 
Description Invited talk at Plant Quantitative Genetics meeting "Genomic and temporal analysis of genetic variance" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Genomic and temporal analysis of genetic variance, UK Plant Quantitative Genetics meeting, 2019-11-07, Birmingham, UK.
Year(s) Of Engagement Activity 2019
 
Description Invited talk at the Symposium in Statistics on "Modelling Genomic and Spatial Effects in Breeding" 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Modelling Genomic and Spatial Effects in Breeding, NTNU Trondheim Symposium in Statistics 2019, 2019-09-28, Trondheim, Norway.
Year(s) Of Engagement Activity 2019
 
Description Modern plant and animal applied genomics driven by genotype and sequence data, Universitat Politècnica de Valencia, 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Visiting teaching activity with advanced course in plant and animal breeding.
Year(s) Of Engagement Activity 2018
 
Description Modern plant and animal applied genomics driven by genotype and sequence data, University of Zagreb, Croatia, 17-19 July 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Workshop organised and given by me and two other members of my group.
Year(s) Of Engagement Activity 2018
 
Description Newton Fund workshop UK-Mexico on Genetic Improvement of Populations 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Newton Fund workshop UK-Mexico on Genetic Improvement of Populations took place in February 2018 at the Centro Nacional de Recursos Genéticos (Jalisco, Mexico). Participants (undergraduate and postgraduate students, group leaders and professionals) from UK and Mexico exchanged research results and showed applications of genetic improvement in different agricultural populations, including livestock, fish, crops, grasses and trees. I have contributed with a lecture on "Statistical methods for genetic evaluation of populations" and two talks titled "Economics of genotyping for genomic selection" and "Optimising selection, maintenance of genetic diversity and logistic constraints". The local organisers have increased interest in the presented topics.
Year(s) Of Engagement Activity 2018
 
Description Public engagement at the Royal Highland Show 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact All members of the research group engaged the visitors of the RHS, to show the importance of their research towards the enhancement of the agricultural sector in direct or indirect ways.
Year(s) Of Engagement Activity 2019
URL https://www.royalhighlandshow.org
 
Description Researcher Links workshop at CNRG, INIFAP, Tepatitlán and Guadalajara, Mexico, 3-7 February 2018 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Workshop organised and given by me and the members of my group
Year(s) Of Engagement Activity 2018
 
Description Roslin symposium in honour of Professor Robin Thompson 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact In June 2018 The University of Edinburgh has conferred the degree of Doctor Honoris Causa to Robin Thompson for contributions to statistics, quantitative genetics, and animal and plant breeding. To celebrate this occasion we organised a symposium at The Roslin Institute in his honour. More than 100 delegates came from Argentina, Australia, Finland, Netherlands, New Zealand, Mexico, Spain, Sweden, UK, and USA. Speakers' talks covered animal breeding, statistics in breeding, plant breeding and human genetics, which showed the breadth of impact of the work of Professor Robin Thompson.
Year(s) Of Engagement Activity 2018
 
Description Short course: The Search for Selection, Roslin Institute, University of Edinburgh 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Description
Biologists are obsessed (indeed, seduced) by the search for signatures of selection in organismal features of interest, ranging from specific traits to genome-wide signatures. A vast number of approaches have been suggested in this search for selection, including genomic-based signatures of recent or ongoing selection, tests based on either excessive amounts or nonrandom patterns of divergence (in both fossil sequences and functional genomics data) and the more classical Lande-Arnold fitness estimates (direct association of phenotypic values with fitness estimates) and their modern extensions (such as aster models). Given the breadth of such searches, a large amount of machinery has been developed, but is rarely presented in a unified fashion. This course presents an integrated overview of all these approaches, highlighting common themes and divergent assumptions.

The goal of this course is to expose investigators from all branches of biology to this rich menagerie of tests, applicable for population geneticists, genome biologists, evolutionary ecologists, paleontologists, functional morphologists, and just about any biologist who ponders on how to formally demonstrate that a feature (or features) of interest might have been shaped by selection.

Intended Audience.
The intended audience is advanced graduate students, postdocs, and faculty with an interest in searching for targets of selection, be they particular genomic sequences or specific traits. Given the breadth of this topic, the material is of interest to students from functional genomics, population and evolutionary genetics, ecology, paleobiology, functional morphology, and statistics (as well as other fields). Background required: some basic introduction to population and/or quantitative genetics.
Year(s) Of Engagement Activity 2018
URL https://wheat.pw.usda.gov/GG3/node/695
 
Description Training: Next generation plant breeding programs 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Industry/Business
Results and Impact Workshop to teach professionals in the crop breeding sector to use modern bioinformatics tools to process molecular data and simulate breeding programs in order to make these more efficient. The audience was very pleased with their acquired insights and skills, and considered the training extremely useful.
Year(s) Of Engagement Activity 2019
URL https://alphagenes.roslin.ed.ac.uk/wp/teaching-2/kwsgermany/