Development of multi-parent advanced intercoss populations for fine mapping QTL in wheat

Lead Research Organisation: National Inst of Agricultural Botany
Department Name: Molecular Research

Abstract

The identification of small segments of chromosomes containing genes that control traits can improve the speed, efficiency and effectiveness of plant breeding. One method of identifying such segments is to look for correlations between DNA markers and traits. Typically, a marker is a short length of DNA with a known location on a chromosome. A strong correlation between marker and trait is an indication of a gene with an effect on the trait close to the marker. This process is typically carried out by searching for correlations among the progeny of a cross between two inbred parents. In such controlled crosses other factors affecting the genetic make-up of a population, such as migration, are eliminated. This minimises the occurrence of spurious correlations between markers and traits. This approach has two limitations. Firstly, marker-trait associations in bi-parental populations are not guaranteed to be important among the lines used by breeders. Secondly, correlations occur when marker and gene are quite a distance apart and these have little practical use. Ideally, the presence of a correlation should indicate that the marker is close to the gene. Plant breeders can then select for presence or absence of the marker, rather than selecting for the trait. This can be quicker and cheaper. Methods have been developed to overcome these limitations. One is to repeatedly cross individuals over successive generations before correlating markers and traits. These extra crosses cause thorough shuffling of genes coming from each of the parents, thereby improving the chance that marker-trait associations are only detected if the marker is very close to the gene. Such populations are called 'Advanced Intercrosses'. There is no requirement for an Advanced Intercross to have only two parents. Multiple parents can make the population more representative of the lines used by breeders. Multiparent Advanced Intercross (MAIC) populations take time to set up and more markers are required than usual. However, the cost of DNA markers is falling steadily. It is therefore important that MAIC populations are established now, to exploit cheaper marker systems as they become available. The work described in this proposal sets out to establish this resource for winter wheat. We shall set up two MAIC populations, one based on current elite lines and one based on older lines of historic importance. Within the time available, we shall also derive a set of inbred lines from the first generation of each population. These will be made available to all interested stakeholders. The use of these populations in very fine mapping is limited, but they will still allow location of genes with greater precision than possible with available alternatives. We have also identified two pre-existing highly outcrossed winter wheat populations. These have not been maintained under controlled conditions but are still likely to be of use as MAIC populations. We will generate 1000 lines from each of these populations to create a resource available immediately for very fine mapping. Although the theory behind the use of MAIC populations is understood, we need to confirm that it works in practice. For this purpose, we will use a system of cheap genetic markers called DArT (Digital Array Technology) to genotype (genetically fingerprint) samples of individuals and inbred lines. Using these data, we can check that the shuffling process occurs as expected and that the pre-existing populations can indeed be treated as if they were MAIC populations. Finally, we will use the DArT data to hunt for associations with the genes responsible for male sterility, present in the established outcrossing populations. The location of these genes in roughly known, but we shall refine it to provide a practical demonstration of the power of the MAIC. Locating this gene with greater precision will also help in the design and execution of future genetic experiments.

Technical Summary

The multiparent advanced intercross (MAIC) offers a compromise between linkage mapping and LD mapping: QTL can be located to smaller intervals than the former without the increase in false positives of the latter. Moreover, the MAIC can be used to derive material suitable for coarse mapping from early generations and for fine mapping from later generations. It also has a high probability of segregating for multiple QTL. This proposal is very timely because the MAIC takes time to construct. By establishing MAIC populations now, they will provide material in the future for fine mapping with high density genotyping. The development of high density marker sets is an area of active research. There is a risk that such research will be successful but have no application because suitable populations for fine mapping do not exist. By setting up MAIC populations now, they will be well placed to exploit high throughput methods as they become available in the fairly near future. We will establish two MAIC populations in winter wheat and derive 1000 inbred lines from each. One will have 8 founders selected from contemporary elite UK cultivars, the other 16 founders of historic importance. At least 1 founder will be common to both populations. The combination of elite and broadly based populations will establish a resource appropriate for fine mapping multiple QTL for multiple traits. We have full access to two broadly based populations of winter wheat, segregating for genetic male sterility (gms). These populations have been maintained through outcrossing. Although subject to some selection, they have been maintained in isolation and are suitable for fine mapping. From each, 1000 inbred lines will be derived for mapping studies. DArT genotyping on the founder lines, samples of the inbred lines and outcrossed individuals will be used to test the power and precision of all the populations for fine mapping. The data will also be used to fine map the gms loci.

Publications

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Cockram J (2018) Genetic Mapping Populations for Conducting High-Resolution Trait Mapping in Plants. in Advances in biochemical engineering/biotechnology

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Ladejobi O (2016) Maximizing the potential of multi-parental crop populations. in Applied & translational genomics

 
Description MAGIC populations created.
Marker-assisted method of bulk inbreeding developed
Simple method for analysis taking into account familial relationships tested successfully
QTL for resistance to fusarium, yellow rust, brown rust and septoria have been identified and are being followed up in funded work.
Initial marker and trait data available for download
SNP map published and disseminated
Location of introgression from T diccocoides identified and targeted for follow-up. Markers released to breeders to tag this region.
Seed and data supplied to several interested parties - academic and commercial - on request.
Exploitation Route Direct use of selection in breeding and pre-breeding programmes. Grant applications for follow-up studies

Self funded work on phenotyping and genotyping has completed its third year. Fourth year trials have been sown in collaboration with UK breeders - funded by BBSRC link project.

BBSRC BBR project to phenotype and genotype the 16 founder population has been funded and has started.

Grant applications with international collaborators.

Release/publication of marker trait associations

Currently 5 PhD students are working on the MAGIC wheat population. Novel explanations of durable disease resistance are emerging from this work.

Projects are being developed to rapidly create near isogenic lines within MAGIC, In particular to characterize the dicoccoides introgression carried by Robigus.

The SNP genetic map has been supplied to many wheat breeders and is likely to be used extensively in marker assisted selection programmes,
Sectors Agriculture, Food and Drink

URL http://www.niab.com/magic
 
Description The adoption of the MAGIC approach to mapping in crops continues. Follow up studies of QTL for disease resistance are under way. Collaborative phenotyping and genotyping projects with UK breeders have started. Seed has been supplied to commercial and academic organisations nationally and internationally. The genetic map of SNP markers is the best available globally. It is freely available to download and was supplied to a number of commercial breeders prior to publication. An introgression from T dicoccoides, carried by the founder line Robigus has been unambiguously located. Genetic stocks (near isogenic lines) are being created to characterise its phenotypic effects more accurately. Markers are available for breeders for marker assisted selection. Additional uses and advantages of MAGIC continue to be found. Matching patterns of gene expression and allelic imbalance between founders, their F1s, MAGIC RILs and QTL in heterozygous inbred families (HIFs) is emerging as a way of refining QTL intervals further, to the order of twenty or so genes. MAGIC is a globally recognised and widely adopted method of trait mapping with extended use into other areas of genetics and breeding
First Year Of Impact 2011
Sector Agriculture, Food and Drink,Education
Impact Types Cultural,Economic

 
Description BBSRC BBR; MAGIC CARPET
Amount £513,840 (GBP)
Funding ID BB/M011666/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 11/2015 
End 10/2018
 
Description BBSRC DTP PhD Studentship
Amount £15,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2014 
End 06/2017
 
Description BBSRC DTP PhD Studentship
Amount £15,000 (GBP)
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 07/2014 
End 06/2017
 
Description BBSRC Responsive Mode grant: Wheat PanGenome
Amount £1,493,352 (GBP)
Funding ID BB/P010741/1, BB/P010768/1, BB/P010733/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2017 
End 03/2020
 
Description BBSRC-LINK: MAGIC YIELD
Amount £299,595 (GBP)
Funding ID BB/M008908/1 
Organisation Biotechnology and Biological Sciences Research Council (BBSRC) 
Sector Public
Country United Kingdom
Start 04/2015 
End 03/2018
 
Description MAX-CROP EU PhD Studentship
Amount £60,000 (GBP)
Organisation Marie Sklodowska-Curie Actions 
Sector Academic/University
Country Global
Start 10/2014 
End 09/2018
 
Description Monsanto Beachell-Borlaug International Scholarship-2015
Amount £54,000 (GBP)
Organisation Monsanto 
Sector Private
Country United States
Start 10/2015 
End 09/2018
 
Description SCPRID
Amount £72,000 (GBP)
Organisation Bill and Melinda Gates Foundation 
Sector Charity/Non Profit
Country United States
Start 02/2015 
End 01/2019
 
Title MAGIC seed 
Description Seed of over 1,000 MAGIC wheat lines is available on request for use in either collaborative or independent research projects 
Type Of Material Biological samples 
Year Produced 2015 
Provided To Others? Yes  
Impact Collaboration with new partners in Ireland (teagasc) and France (Arvalis). Research programme (independent) initiated at Reading University. Seed passed to breeders fo use in their research and breeding. Colaborative research with breeders 
URL http://www.niab.com/pages/id/402/NIAB_MAGIC_population_resources
 
Title MAGIC map 
Description The MAGIC SNP Genetic map. More markers mapped with more precision than previously released by anyone 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Downloaded by breeders and researchers. 
URL http://www.niab.com/uploads/files/MAGIC_pedigree_tables.xlsx
 
Title MAGIC population raw data 
Description MAGIC wheat population. Raw data available for download 
Type Of Material Database/Collection of data 
Year Produced 2015 
Provided To Others? Yes  
Impact Data downloaded. Requests for more information 
URL http://www.niab.com/pages/id/402/NIAB_MAGIC_population_resources
 
Description Collaboration with CCDM, Curtin University, Australia 
Organisation Curtin University
Country Australia 
Sector Academic/University 
PI Contribution Undertake work providing supporting data for grant proposals. Arrange for Eurasmus EU visiting student placements to help undertake research Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript. Arrange NIAB 'Visiting Fellow' status for lead Australian collaborator.
Collaborator Contribution Undertake work providing supporting data for grant proposals. Undertake joint proposals to national/international funding agencies. Undertake joint PhD proposal applications. Undertake joint scientific manuscript.
Impact Joint grant proposal to french levy board 'FSOV' submitted and funded. Joint grant proposal to EU call 'ERA-CAPs' submitted. BBSRC DTP Targeted Studentship PhD studentship application (outcome pending).
Start Year 2013
 
Title GeneDrop 
Description Runs gene dropping simulations for any supplied pedigree structure and genotype data in Windows 
Type Of Technology Software 
Year Produced 2012 
Open Source License? Yes  
Impact Used in simulations to compare crossing schemes for MAGIC and other multi-founder mapping populations; published in Ladejobi, O., Elderfield, J., Gardner, K.A., Gaynor, R.C., Hickey, J., Hibberd, J.M., Mackay, I.J. and Bentley, A.R., 2016. Maximizing the potential of multi-parental crop populations. Applied & Translational Genomics, 11, pp.9-17. 
URL http://www.niab.com/pages/id/326/Resources
 
Title Selection of diverse subsets of lines 
Description An R script which uses genetic algorithms to select a subset of lines from a larger collection. The algorithm searches for the subset with either the greatest genetic diversity or which captures the greatest number of alleles. This is a replacement for similar functions previously available in the package PowerMarker. 
Type Of Technology Software 
Year Produced 2016 
Open Source License? Yes  
Impact The method was used to compare strategies for diversity capture in different multi-founder mapping population designs and is described in: Ladejobi, O., Elderfield, J., Gardner, K.A., Gaynor, R.C., Hickey, J., Hibberd, J.M., Mackay, I.J. and Bentley, A.R., 2016. Maximizing the potential of multi-parental crop populations. Applied & Translational Genomics, 11, pp.9-17. The software is a replacement for similar functions previously available in the package PowerMarker, which is no longer supported. 
URL http://www.niab.com/pages/id/326/Resources
 
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 Eucarpia keith 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Kieth Gardner's talk at the Biometrics setion of Eucarpia, Wageningen, 2015. Discsussion of the merits of MAGIC populations in general and their use in mapping markers in particular.
Year(s) Of Engagement Activity 2015
 
Description MAGIC-type population workshop, NIAB, 2013 
Form Of Engagement Activity A formal working group, expert panel or dialogue
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact the scientific contacts made led to submission of a subsequent successful BBSRC BBR grant application, and to the formulation of other grant applications (to submit Feb 2015)

The scientific contacts made led to submission of a subsequent successful BBSRC BBR grant application
Year(s) Of Engagement Activity 2013
URL http://mus.well.ox.ac.uk/19genomes/MAGIC-WORKSHOP/
 
Description Oral presentation at EMBRAPA-Trigo, Passo Fundo, Brazil 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact talks sparked questions and discussion afterwards

led to the formulation of a research proposal, to be submitted to the appropriate upcoming UK-Brazil call
Year(s) Of Engagement Activity 2013
 
Description Oral presentation for Cambridge University Biological Sciences undergraduate students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach Local
Primary Audience Undergraduate students
Results and Impact talk sparked questions and discussions afterwards

Cambridge university undergradueates schedulaed to visit again next year
Year(s) Of Engagement Activity 2014
 
Description Oral presentation to Indian crop science deligation, NIAB 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Other academic audiences (collaborators, peers etc.)
Results and Impact sparked questions and discussion afterwards

helped cement ties between participants of UK-India bi-lateral funding grants.
Year(s) Of Engagement Activity 2014
 
Description Oral presentation to MAX-CROP EU PhD students 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact talk sparked questions and discussions afterwards

Students and supervisors made aware of association mapping resources available at NIAB
Year(s) Of Engagement Activity 2014
 
Description Poster presentation at NIAB Open Day, 2014 
Form Of Engagement Activity Participation in an open day or visit at my research institution
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Public/other audiences
Results and Impact Poster sparked questions and discussions afterwards

N/A
Year(s) Of Engagement Activity 2014
 
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
 
Description Turkey Wheat Workshop 
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 Participation in one week workshop over multiple sites in Turkey to discuss UK - Turkish collaboration over wheat research, representing the NIAB Genetics and Breeding group on behalf of Dr Alison Bentley, the Director of Genetics and Breeding. Aside from questions and discussions at the time, it resulted in an agreement to sent some of our most resistant yellow rust lines to Turkey for screening, a novel approach to participatory plant breeding incorporating genomic selection and a collaborative grant application to the GCRF.
Year(s) Of Engagement Activity 2016
 
Description monogram 2015 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach National
Primary Audience Professional Practitioners
Results and Impact Keith Gardner presented the MAGIC SNP map at the annual Monogram meeting
Year(s) Of Engagement Activity 2015
 
Description multi-founder mapping populations in plants and animals 
Form Of Engagement Activity Participation in an activity, workshop or similar
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Postgraduate students
Results and Impact Workshop to discuss methods for creation and exploitation of MAGIC and MAGIC-like populations. A review paper will be written and submitted.

no actual impacts realised to date
Year(s) Of Engagement Activity 2013
 
Description poster presentation at the HeDWIC meeting, Germany, 2014 
Form Of Engagement Activity A talk or presentation
Part Of Official Scheme? No
Geographic Reach International
Primary Audience Professional Practitioners
Results and Impact Poster at the HeDWIC meeting: Cockram et al. The ICARDA Wheat MAGIC Resource. HeDWIC meeting, Frankfurt, Germany, 2-3rd December 2014
Year(s) Of Engagement Activity 2014