Modelling and applying the innovative two-part genomic selection strategy in inbred and hybrid barley breeding

Supervisors: John Hickey, Hazel Bull

Project description:

Barley is a crucial crop for food security: it is the fourth most important grain crop globally, and the ever-expanding world population will put continual and increasing demands for genetic gain on barley breeding programmes.

Genomic selection has been revolutionary for animal breeding and its potential in plant breeding is increasingly realised. Classic barley breeding techniques require phenotypic and genetic information on each generation of selection candidates. Genomic selection, however, only requires phenotyping of an initial ‘training set’ of genotyped plants which are then used to calculate the breeding values  of genotyped selection candidates. Genotyping is cheaper and faster than phenotyping, so more data can be collected at shorter generation intervals.  In this way, genomic selection increases the rate of genetic gain achieved by a breeding program, which allows crop breeders to meet the challenges of significant increasing yield, and to tailor their crops more rapidly to changes in climatic and input conditions.

Our group has developed a two-part strategy to implement genomic selection in inbred crops, such as barley (Gaynor et al., 2017, Crop Science; Hickey et al., 2017, Nature Genetics). This strategy further reduces the generation interval by dividing the breeding programme into two distinct parts: a) population improvement, inspired by animal breeding methodologies; and b) product development, inspired by plant breeding techniques. Our simulations indicate that the two-part strategy produces ~2.4 times the genetic gain of conventional breeding, but also ~1.3 times that of other genomic selection strategies.

The full adoption of the two-part strategy in inbred barley lines requires fundamental changes in breeding program structure. Such changes are often unpalatable due to start-up costs, requirements for different skill sets within the breeding program, and potential risks. Therefore, this studentship will use simulations, accompanied by carefully chosen analysis of routine barley field trial data at the James Hutton Institute (JHI), to further develop and test the two-part strategy.

Hybrid barley, made by crossing two barley varieties, can produce significant gains in both yield and resilience to abiotic and biotic stress. The challenge for breeders is overcoming barley’s self-pollination and the associated costs. This studentship will expand the two-part strategy to a scenario involving hybrid barley by developing quantitative genetic theory underpinning hybrid performance.  We will simulate a breeding program based on the JHI traditional program. From this baseline, we will develop and test practicable implementation based on the two-part strategy.

This studentship offers excellent opportunities for training in quantitative genetics, crop breeding, and bioinformatics. At the JHI the student will learn practical crop breeding and contribute to select field trial design. The student will establish a solid foundation in field and bioinformatic aspects of crop breeding, which will be crucial to developing genomic selection transition strategies.


Gaynor, R., Gorjanc, G., Bentley, A., Ober, E., Howell, P., Jackson, R., Mackay, I., and Hickey, J. 2017. A two-part strategy for using genomic selection to develop inbred lines. Crop Science 57, 5

Hickey, J.M., Chiurugwi, T., Mackay, I., and Powell, W. 2017. Genomic prediction unifies animal and plant breeding programs to form platforms for biological discovery. Nature Genetics 49