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

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.

(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.