Selection for accelerated barley breeding

Lead Research Organisation: University of Dundee
Department Name: School of Life Sciences

Abstract

Continual improvement of our major crops through breeding is essential if we are to maintain our supply of food, feed and fibres. Modern crop breeding often uses a variety of molecular and statistical tools to make breeding faster and more precise. Marker assisted selection can help in breeding programmes by following the presence of molecular DNA markers that correspond to traits of interest, such as high yield or disease resistance, even when nothing is known about the exact genes controlling the trait. In livestock breeding, as opposed to crop breeding, an alternative method is sometimes used called genomic selection. In genomic selection, all of the specific DNA markers that define the genetic make-up of an animal, and not just those correlated with the trait, are used to predict its 'breeding value' i.e. how good a parent it will be for producing superior offspring with improved specific characteristics. We have produced a new model for adapting genomic selection methods to barley breeding. Our statistical model correlates all of the specific DNA markers that are present in a cultivar (indicative of the specific gene variants in that cultivar) with a range of different phenotypes we have measured including grain yield, biomass yield, straw strength etc. The model can be used to predict which cultivars are best to use to improve specific traits, and can further predict how progeny will perform for that trait by determining the complement of molecular markers that they inherit from their parents. This is a more efficient way of predicting the best cultivars to breed from as it takes into account all of their molecular markers and not just those that are obviously correlated with the trait, as is the case with traditional marker assisted selection.

This studentship will explore the use of this model for its value in barley pre-breeding, by using it to select the best barley cultivars to breed from in order to improve a couple of specific traits (e.g. digestibility, yield). The project will train the PhD student in many aspects of plant breeding including the use of both molecular and statistical analyses, the design and performance of field trials, field phenotyping, production of di-haploid populations etc. The student will be supervised by Prof Claire Halpin of the University of Dundee (based on the James Hutton Institute site) and the barley breeder at the James Hutton Institute (JHI), Dr. Bill Thomas. The student will also receive training from Prof Robbie Waugh (cereal genetics), Hazel Bull (trainee barley breeder) and Helena Oakey (biological statistician). The successful applicant will benefit from all of the expertise and resources available at both UoD and JHI. Candidates must fulfil RCUK eligibility requirements, which can be found at: http://www.bbsrc.ac.uk/web/FILES/Guidelines/studentship_eligibility.pdf

Publications

10 25 50
publication icon
Thomas WTB (2019) A Practical Guide to Barley Crossing. in Methods in molecular biology (Clifton, N.J.)

Studentship Projects

Project Reference Relationship Related To Start End Student Name
BB/M017362/1 01/10/2015 30/09/2019
1653751 Studentship BB/M017362/1 19/10/2015 30/09/2019 Ruth Hamilton
 
Description A genomic selection (GS) model (created by Dr Helena Oakey) was used to support a four year barley breeding program. The aim of the breeding program was to improve barley straw digestibility for biofuel production. In addition to the GS breeding program, techniques were used and investigated to accelerate barley breeding.

This was the first time that Oakey's model had been used to breed barley. The GS model was trained to predict straw digestibility and other secondary traits. The GS model predicted plant height and thousand grain weight (a yield measurement) well. Straw digestibility is a complex trait to measure and predict, Oakey's model predicted digestibility reasonably well (similar to other complex traits in barley).

One time saving technique used in this project was speed breeding. Speed breeding involves growing plants in glasshouses run with extended daylight (22hrs light/2hrs dark) reducing generation time. Straw digestibility was measured in barley lines grown in a speed breeding glasshouse and field trial. There was a strong correlation between digestibility from speed breeding glasshouse and field samples. This is promising as digestibility screens could be carried out more quickly/with fewer resources.
Exploitation Route Implementing Oakey's GS model to predict other traits or use different populations to train the model.

Progeny created in the barley breeding program that have been improved (beyond initial parent lines used) should be taken forward for further testing/analysis.
Sectors Agriculture, Food and Drink,Energy,Manufacturing, including Industrial Biotechology

 
Description Exploring partnerships in barley and cell wall research with australian ECRs 
Organisation Murdoch University
Country Australia 
Sector Academic/University 
PI Contribution Provided funding for eight excellent early career researchers from Australia to visit Dundee with a view to setting up strategic research partnerships for the future. Funding was provided via a successful bid to the UUKI Rutherford Fund : RF-2018-30 - Rutherford Fund Strategic Partner Grant 2018 (£ 150000; 2018 - 2019)
Collaborator Contribution ECRs visited Dundee for 1-11 months each and performed collaborative research which is leading to longer-term future interactions.
Impact Plant biologists; crop breeders; bioinformaticists; genome scientists
Start Year 2018
 
Description Exploring partnerships in barley and cell wall research with australian ECRs 
Organisation University of Adelaide
Country Australia 
Sector Academic/University 
PI Contribution Provided funding for eight excellent early career researchers from Australia to visit Dundee with a view to setting up strategic research partnerships for the future. Funding was provided via a successful bid to the UUKI Rutherford Fund : RF-2018-30 - Rutherford Fund Strategic Partner Grant 2018 (£ 150000; 2018 - 2019)
Collaborator Contribution ECRs visited Dundee for 1-11 months each and performed collaborative research which is leading to longer-term future interactions.
Impact Plant biologists; crop breeders; bioinformaticists; genome scientists
Start Year 2018
 
Description Exploring partnerships in barley and cell wall research with australian ECRs 
Organisation University of Melbourne
Country Australia 
Sector Academic/University 
PI Contribution Provided funding for eight excellent early career researchers from Australia to visit Dundee with a view to setting up strategic research partnerships for the future. Funding was provided via a successful bid to the UUKI Rutherford Fund : RF-2018-30 - Rutherford Fund Strategic Partner Grant 2018 (£ 150000; 2018 - 2019)
Collaborator Contribution ECRs visited Dundee for 1-11 months each and performed collaborative research which is leading to longer-term future interactions.
Impact Plant biologists; crop breeders; bioinformaticists; genome scientists
Start Year 2018
 
Description Exploring partnerships in barley and cell wall research with australian ECRs 
Organisation University of Queensland
Country Australia 
Sector Academic/University 
PI Contribution Provided funding for eight excellent early career researchers from Australia to visit Dundee with a view to setting up strategic research partnerships for the future. Funding was provided via a successful bid to the UUKI Rutherford Fund : RF-2018-30 - Rutherford Fund Strategic Partner Grant 2018 (£ 150000; 2018 - 2019)
Collaborator Contribution ECRs visited Dundee for 1-11 months each and performed collaborative research which is leading to longer-term future interactions.
Impact Plant biologists; crop breeders; bioinformaticists; genome scientists
Start Year 2018
 
Description University of Dundee-University of Queensland barley Speed breeding project 
Organisation University of Queensland
Department Queensland Alliance for Agriculture and Food Innovation
Country Australia 
Sector Academic/University 
PI Contribution Two month placement at the University of Queensland to learn the Speed breeding technique/evaluate barley straw saccharification in an Australian barley panel Collaboration with Lee Hickey's lab group based at the University of Queensland. Lee Hickey is part of QAAFI (The Queensland Alliance for Agriculture and Food Innovation) and a lead researcher in Speed breeding growth systems
Collaborator Contribution This collaboration was to learn about the Speed breeding growth system which rapidly decreases plant generation time. The Hickey lab based at the University of Queensland have taken forward this method which was originally developed by NASA. Ruth worked with Lee Hickey's lab for a short placement. An Australian barley panel was grown in Speed breeding conditions, samples were taken for straw saccharification (sugar release) analysis. This will give us an insight into the saccharification range present in the Australian barley, straw sugar release is an indicator of potential biofuel yield from the barley straw. Samples were also taken of the barley panel from field grown material, this will allow a comparison of Speed breeding grown and field grown barley for straw saccharification. Many traits in plants can be scored in Speed breeding systems, it is currently unknown if straw saccharification can be screened for using the Speed Breeding system. If this is the case this will be advantageous for future breeding projects aimed at improving straw saccharification/similar traits, as plants can be taken through rapid generation advance by using Speed breeding growth systems.
Impact This partnership has led to further research of Speed breeding growth systems at the James Hutton Institute. A range of Speed breeding experiments will be carried out based at the James Hutton Institute that will show the potential that Speed breeding can have to plant science research in Scotland.
Start Year 2017
 
Description Arable Scotland 2019 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Industry/Business
Results and Impact Engaged with attendees (mainly farmers) discussing second generation biofuels and surveying farmers to ask about straw use/potential uses and markets for cereal straw.
Year(s) Of Engagement Activity 2019
URL https://www.arablescotland.org.uk/
 
Description Plant Power Day- Botanical gardens Dundee 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Plant power day is a joint event between the University of Dundee and the James Hutton Institute held annually at the Botanical gardens in Dundee. The event was attended by +1000 visitors in the past few years. A range of activities are organised for visiting families, including face painting, science workshops and birds of prey.

We ran the Crop wild relative activity and the crop origins game, where members of the public need to guess where in the world crops major crops originated from.
Year(s) Of Engagement Activity 2015,2016,2017,2018,2019
 
Description Street Food event- University of Dundee-Dundee Science Festival 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact Two games were taken to the Street Food event, an +18 event run within the Dundee Science Festival. The event aimed to link food production, particularly with local businesses to science research at the University of Dundee. Local businesses at the event included a brewing company and an ice cream company. Talks were also given about research/facilities at the University of Dundee.

I ran the Crop Wild Relative game, where members of the public need to guess which picture matches the modern crop variety.
Year(s) Of Engagement Activity 2017,2018
URL https://www.dundee.ac.uk/festival-future/programme/2018/18-10-18-street-food-.php
 
Description Women in Science- Family Fun event at Mills Observatory 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Public/other audiences
Results and Impact As part of the Women in Science festival, a Family fun day event was run at Mills Observatory. Multiple research groups from the University of Dundee attended.

A DNA extraction activity was organised, where children assisted in extracting DNA from raspberries.
Year(s) Of Engagement Activity 2017,2019
URL https://www.facebook.com/events/2177285275625203/