Molecular Improvement of Disease Resistance in Barley (MIDRIB)

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Centre for Research

Abstract

This project develops an approach, genomic selection, to increase the rate at which varieties of Spring barley are developed. This is a very important crop in national agriculture, particularly for the malting, brewing and distilling industries. It is important that the rate with which improved varieties are created is increased so that more effort can be placed by breeders on improving disease resistance while maintaining or increasing grain yield and grain quality, which remain of greatest importance to growers and end users.Genomic selection represents a way of predicting traits purely from genetic markers rather than by direct measurement. These predictions require that a set of plants is first measured for the target traits so that the effect of each marker can be estimated. However, after that, selection can occur for several generations purely on markers.Direct measurement of many traits can take much longer than a single growing season: seed must first be bulked up over several generations to provide a sufficient quantity for yield trials. In contrast, marker data can be collected within the generation time of any crop and is therefore much faster than conventional selection.Other approaches to plant breeding using genetic molecular markers have been in use for many years. In these, a very small numbers of markers with strong evidence of an affect on a trait are first identified. These are then tracked through the breeding programme. Genomic selection differs in that all available markers are used to predict traits: the more markers the better. The inclusion of all markers gives more accurate prediction of overall trait values even though the precise involvement of each marker is known with less certainty.Our study has four themes. Firstly, throughout the life of the project, we shall develop new statistical methods to establish relationships between very high numbers of genetic markers and traits. The methods we develop will be more focussed on the problems of plant breeding: most methods to date have been targeted at animal breeding. Secondly, we shall test methods which are available now using historical data available from to an existing Spring barley scheme. Results will be used immediately to make selections within this scheme. We expect to register new varieties from these selections within the five year life of the project.Next, we shall use results from the analysis of the historical data together with any early methodological developments we make to create crosses specifically to exploit genomic selection. These crosses may not necessarily be the typical crosses between two parents which are commonly used by breeders but may involve more complicated crossing schemes involving, for example four parents. Within the life of the project, we shall test whether this approach gives a greater response to selection that achieved by more conventional breeding, but there will be insufficient time to resister a new variety.Finally, we shall integrate results and methods from the first three phases to completely redesign the breeding programme to get the greatest advantage out of genomic selection.In short, we plan to develop a new approach to Spring barley breeding .Genomic selection could result in a fundamental change to the way crops are bred and enable targets for increased food production and environmental sustainability to be met. Compared to other temperate crops, Spring barley has a short generation time which make it well suited to develop and test these ideas, which may also be applicable to other crops.

Publications

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Bentley AR (2014) Applying association mapping and genomic selection to the dissection of key traits in elite European wheat. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Jones H (2013) Evaluation of the use of high-density SNP genotyping to implement UPOV Model 2 for DUS testing in barley. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Jones H (2015) Implications of using genomic prediction within a high-density SNP dataset to predict DUS traits in barley. in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik

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Scutari M (2013) Improving the efficiency of genomic selection. in Statistical applications in genetics and molecular biology

 
Description The findings of the project have been used to produce the first barley variety submitted to the National Recommended List that has been selected using only genetic information, as opposed to classic evaluation of a set of phenotypes. Investigations into which trials are most useful in this approach to selection have prompted changes in Limagrain's planning procedures for new trials. Using only genetic information for selection has changed Limagrain's standard procedures in designing new breeding programmes
Exploitation Route See above. Results are being used by our industrial partner Limagrain, and through publication the wider crop breeding industry.
Sectors Agriculture, Food and Drink

 
Description We have developed a protocol for selecting new barley varieties favorable traits, such as yield and disease resistance, using genetic information available from a commercial selection program. This protocol has the potential to reduce the number of field trials required by the programme and has the advantage to both speed it up and reduce its operational costs. The protocol is based on statistical models that predict such traits in future generations using historical records from the selection program. We have explored the limits of current statistical methods for this task, which relate to how different new barley plants are compared to those in the selection programme's records. Two common situations in which such limits are tested are exporting barley varieties to new countries and trying to implement predictions far into the future for optimising the speed of selection. We have developed a protocol to estimate when the statistical models produce reliable predictions in such circumstances. The project has curated a comprehensive set of treated/untreated trial data for hundreds of barley varieties. We have thoroughly investigated which conditions make field trials problematic for use in the statistical models above, in terms of the countries the trials are performed in and differing weather patterns in different years. Limagrain have now incorporated the routine use of genomic selection in their commercial breeding programme.
First Year Of Impact 2014
Sector Agriculture, Food and Drink
Impact Types Economic

 
Title DiPR: Differentially Penalized Regression 
Description A simple method of independently weighting two or more sets of variables in ridge regression, while using standard ridge regression software. Useful in genomic prediction models with separate classes of genetic markers, and for incorporating different sets of predictors eg plant metabolites and genetic markers. 
Type Of Material Data analysis technique 
Year Produced 2015 
Provided To Others? Yes  
Impact Is being tested in various genomic selection projects. 
URL http://bmcgenet.biomedcentral.com/articles/10.1186/s12863-015-0169-0
 
Description Collaboration with Portugal 
Organisation National Institute of Agrarian and Veterinary Research
Country Portugal 
Sector Public 
PI Contribution I advise the Portuguese FASTBREED project: Implementation of a bread and durum wheat breeding program based on genomic selection using genomic selection. This is a project to introduce genomic selection into the state wheat breeding programmes. In 2016, at the kick off meetings, I gave two seminars; one to the breeders and one to molecular biologists and bioinformaticians to explain how genomic selection works. I also proposed a crossing and testing programme with their own breeding material to introduce genomic selection. This is now being put in place.
Collaborator Contribution Portuguese breeders and geneticists are running the breeding programme and carrying out all genotyping, analytical and other activities.
Impact None so far.
Start Year 2016
 
Description Camb. Plant Sci epidemiology groups 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Professional Practitioners
Results and Impact A seminar to the two epidemiology groups in the University of Cambridge Plant Sciences Department. To introduce to the methods and approaches of trait mapping and genomic selection in crops, highlighting some overlaps with epidemiological methodology.
Year(s) Of Engagement Activity 2016
 
Description JHI offsite meeting 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Regional
Primary Audience Professional Practitioners
Results and Impact Gave talk to James Hutton Institute scientific staff at their annual off-site workshop in Dunkeld on genomic selection and how it can be implemented in small breeding programmes.
Year(s) Of Engagement Activity 2016
 
Description Landmark artucle on GS 
Form Of Engagement Activity A magazine, newsletter or online publication
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact I wrote an article on genomic selection "Genomic selection and the quantitative geneticists' revenge" for the NIAB members quarterly journal: LandMark Bulletin. This described the potential of genomic selection in plant breeding in lay terms.
Year(s) Of Engagement Activity 2016
 
Description QMPB 
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 NIAB run a two week intensive course in Quantitative Methods for Plant Breeding, covering relevant aspects of statistics, quantitative genuetics and population genetics. There are 25 participants every year. To date, no-one has said they would not recommend the course to others. The course has also been put on in Australia, France, India (once at ICRISAT and once at the Punjab Agricultural University) and Malaysia. We update it every year to disseminate developments and methods resulting from out own research work in MAGIC, genomic selection, association mapping and plant breeding strategy. It has resulted in a global set of new contacts, some of which have resulted in successful collaborations.
Year(s) Of Engagement Activity 2008,2009,2010,2011,2012
URL http://www.niab.com/pages/id/360/quantitative_methods_in_plant_breeding