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

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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.