15-IWYP Using Next Generation Genetic Approaches to Exploit Phenotypic Variation in Photosynthetic Efficiency to Increase Wheat Yield
Lead Research Organisation:
University of Liverpool
Department Name: Institute of Integrative Biology
Abstract
Not required
Technical Summary
Phenotyping photosynthetic characters from diverse lines of wheat will be combined with next generation genetic approaches to enable the identification of markers and genes associated with each trait. Such knowledge will enable combinations of these traits to be rapidly incorporated into elite wheat lines to increase yields based on improved photosynthetic efficiency. Moreover, identifying the genes and mutations responsible for the traits will provide an understanding of the biology underpinning the trait and the ability to use precision genome engineering tools in the future. The project will identify wheat material, develop markers and build bioinformatics tools. All of this will be made available to the international community via CIMMYT and iPlant. The project builds upon high throughput methods and knowledge developed by the wheat yield consortium and utilises exome capture technology to discover the relevant genetic information in a cost effective manner. The project combines the diverse expertise in photosynthesis, genetics, wheat physiology and breeding from Lancaster, Liverpool, ANU and CIMMYT and leverages off related existing research.
Planned Impact
Not required
Organisations
Publications
Akhunova Alina
(2019)
Supporting data for "Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat"
in GigaScience Database
Correia PMP
(2021)
Photoprotection and optimization of sucrose usage contribute to faster recovery of photosynthesis after water deficit at high temperatures in wheat.
in Physiologia plantarum
Gardiner LJ
(2019)
Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency.
in Genome biology
Gardiner LJ
(2019)
Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat.
in GigaScience
Gardiner LJ
(2018)
Hidden variation in polyploid wheat drives local adaptation.
in Genome research
Joynson R
(2021)
Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat.
in Plant biotechnology journal
Molero G
(2023)
Exotic alleles contribute to heat tolerance in wheat under field conditions.
in Communications biology
Molero G
(2019)
Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential.
in Plant biotechnology journal
Pixley K
(2018)
CIMMYT's Seeds of Discovery Initiative: Harnessing Biodiversity for Food Security and Sustainable Development
in Indian Journal of Plant Genetic Resources
Singh S
(2018)
Harnessing genetic potential of wheat germplasm banks through impact-oriented-prebreeding for future food and nutritional security.
in Scientific reports
Walkowiak S
(2020)
Multiple wheat genomes reveal global variation in modern breeding.
in Nature
| Description | Earlham institute • Sample collection from and genotyping of >700 CIMMYT wheat lines and 104 Watkins landrace collection members using SNP arrays/genetic capture strategies. • Bisulphite sequencing and epigenetic variation analysis carried out on 104 Watkins landrace collection members. • Population structure and relatedness analysis of CIMMYT wheat lines to aid selection of a "phenotypic tails panel" for fine phenotyping/bulk segregation analysis in years 2/3. • Successful GWA study associating CIMMYT line derived SNPs to yield and photosynthetic efficiency related traits. CIMMYT • Phenotypic measurements of proxy photosynthetic traits and leaf material for genetic analyses were collected from diverse sets of spring wheat lines in the representative high yield growing environment of Cd. Obregon, México. • "Phenotypic Tails" Panels have been assembled, comprising most promising lines in terms of proxy photosynthetic traits plus contrasts, for detailed phenotyping and genotyping in Years 2 and 3. Lancaster • Initial growth and screen of the Watkins diversity panel and Paragon control • Optimisation of fine phenotyping methods |
| Exploitation Route | We are promoting the work at International conferences and to industry |
| Sectors | Agriculture, Food and Drink,Manufacturing, including Industrial Biotechology |
| Description | The genotyping and resequencinging are being used by other project funded through IWYP |
| First Year Of Impact | 2020 |
| Sector | Agriculture, Food and Drink |
| Description | Exploiting night-time traits to improve wheat yield and water use efficiency in the warming climate of North-western Mexico |
| Amount | £541,034 (GBP) |
| Funding ID | BB/S012834/1 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 05/2019 |
| End | 05/2022 |
| Description | SEQUENCING THE GENIC PORTION OF SEEDS OF DISCOVERY ADVANCE PRE- BREEDING GERMPLASM TO UNCOVER THE GENETIC VARIATION |
| Amount | £330,000 (GBP) |
| Funding ID | BBS/OS/NW/000017 |
| Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
| Sector | Public |
| Country | United Kingdom |
| Start | 10/2016 |
| End | 10/2019 |
| Title | promoter exon capture platform |
| Description | Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. Previous studies have implemented cDNA/exon or gene-based probe sets where promoter and intron sequence is largely missing alongside newly characterized genes from the recent improved reference sequences. Results We present and validate two gold standard capture probe sets for hexaploid bread wheat, a gene and a putative promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. We demonstrate that the capture probe sets effectively enrich the high confidence genes and putative promoter regions that were identified in the genome alongside a large proportion of the low confidence genes and associated promoters. Finally, we demonstrate successful sample multiplexing that allows generation of adequate sequence coverage for SNP calling while significantly reducing cost per sample for gene and putative promoter capture. Conclusions We show that a capture design employing an 'island strategy' can enable analysis of the large gene/putative promoter space of wheat with only 2x160 Mb probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. |
| Type Of Material | Technology assay or reagent |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Currently being used by DFW, CIMMYT and US CAPS projects |
| Title | Genotyping of 150 CIMMYT wheat lines (paper DOI |
| Description | 35K affymetrix array data for the High Biomass Association Panel of 150 spring wheat lines from CIMMYT. A paper explaining the panel and the use we made of these snps is available here: http://dx.doi.org/10.1111/pbi.13052 |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Facilitated the identification of multiple marker trait associations which have now been incorporated into CIMMYT spring wheat marker assisted selection program. |
| Title | Watkins core collection re-sequencing data |
| Description | Re-sequence data for the Watkins collection |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | International collabration |
| URL | https://grassroots.tools/data/under_license/toronto/ |
| Title | promoter exon capture data |
| Description | The data contain the design space for the promoter and exon used in our capture |
| Type Of Material | Database/Collection of data |
| Year Produced | 2018 |
| Provided To Others? | Yes |
| Impact | Whole genome shotgun re-sequencing of wheat is expensive because of its large, repetitive genome. Moreover, sequence data can fail to map uniquely to the reference genome making it difficult to unambiguously assign variation. Re-sequencing using target capture enables sequencing of large numbers of individuals at high coverage to reliably identify variants associated with important agronomic traits. We present two gold standard capture probe sets for hexaploid bread wheat, a gene and a promoter capture, which are designed using recently developed genome sequence and annotation resources. The captures can be combined or used independently. The capture probe sets effectively enrich the high confidence genes and promoters that were identified in the genome alongside a large proportion of the low confidence genes and promoters. We use a capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat with only 2x160 Mb NimbelGen probe sets. Furthermore, these assays extend the regions of the wheat genome that are amenable to analyses beyond its exome, providing tools for detailed characterization of these regulatory regions in large populations. Here, we release the targeted sequence of the capture probe sets on the wheat RefSeqv1, the design space that was used to tile our capture probes across and finally the positions of the probes themselves across this design space for both the gene and promoter capture probe sets. |
| URL | https://opendata.earlham.ac.uk/wheat/under_license/toronto/Gardiner_2018-07-04_Wheat-gene-promoter-c... |
| Description | BASF |
| Organisation | BASF |
| Country | Germany |
| Sector | Private |
| PI Contribution | We are using the the promoter capture platform developed in (https://doi.org/10.1093/gigascience/giz018) to sequence wheat cultivars |
| Collaborator Contribution | Paying for sequencing and capture |
| Impact | Funded ICASE studentship "Using open data and machine learning approaches to decode the regulatory regions of wheat" |
| Start Year | 2020 |
| Description | CIMMYT seeds of discovery |
| Organisation | Australian National University (ANU) |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | Collaboration to provide Advance genetic approaches |
| Collaborator Contribution | Access to wheat material and phenotyping data |
| Impact | None yet |
| Start Year | 2016 |
| Description | CIMMYT seeds of discovery |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | Collaboration to provide Advance genetic approaches |
| Collaborator Contribution | Access to wheat material and phenotyping data |
| Impact | None yet |
| Start Year | 2016 |
| Description | IWYP |
| Organisation | Australian National University (ANU) |
| Department | Division of Plant Sciences |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | My group lead this work, we are involved in the genotyping and bioinformatics |
| Collaborator Contribution | The three other groups are involved in generating the field phenotyping and plant physiology measurements. |
| Impact | none yet |
| Start Year | 2016 |
| Description | IWYP |
| Organisation | International Centre for Maize and Wheat Improvement (CIMMYT) |
| Country | Mexico |
| Sector | Charity/Non Profit |
| PI Contribution | My group lead this work, we are involved in the genotyping and bioinformatics |
| Collaborator Contribution | The three other groups are involved in generating the field phenotyping and plant physiology measurements. |
| Impact | none yet |
| Start Year | 2016 |
| Description | IWYP |
| Organisation | Lancaster University |
| Department | Lancaster Environment Centre |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | My group lead this work, we are involved in the genotyping and bioinformatics |
| Collaborator Contribution | The three other groups are involved in generating the field phenotyping and plant physiology measurements. |
| Impact | none yet |
| Start Year | 2016 |
| Description | KWS |
| Organisation | KWS UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Generated double haploid population for the IWYP project and provide material for INTREPID and the BBSRC/EAGER work |
| Collaborator Contribution | Know of the techniques and approaches we are using, early access to the data we generate |
| Impact | Double haploid seed population |
| Start Year | 2017 |
| Description | KWS methylation collabration |
| Organisation | KWS UK |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | We are generating genome wide methylation data and genotype data for key KWS lines |
| Collaborator Contribution | Identified lines to use |
| Impact | Not yet |
| Start Year | 2019 |
| Description | RAGT |
| Organisation | RAGT Seeds |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | Identify key material for our EAGER project and Design future wheat. Support for collaboration with IBM. |
| Collaborator Contribution | Discussion of methods and analysis of material relevant to RAGT. |
| Impact | none yet |
| Start Year | 2018 |
| Description | 10 plus wheat genome project 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 | The meeting was to provide a consortium update on the 10 plus wheat genome project |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.10wheatgenomes.com |
| Description | Hosting a PhD student from CIMMYT (Mexico) for training |
| 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 | The Hall lab group hosted a Phd student supervised by Dr Matthew Reynolds (CIMMYT) and Dr John Faulkes (University of Nottingham) for training in crop genetics. Over a period of 3 days we introduced her to concepts surrounding phenotype - genotype association analysis culminating in the successful application of GWAS to her data. This lead to a very well recieved poster presentation at the Plant and Animal Genomes conference in 2019: https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/33006 Strategies for achieving genetic gains in yield potential must combine enhanced above-ground dry matter as well partitioning to the grain (harvest index). The present study aligned with NIFA-IWYP (International Wheat Yield Partnership) project N-IWYP700* aimed to identify grain partitioning traits that help maximize grain yield in high biomass backgrounds. A High Biomass Association Panel (HiBAP) comprised of 150 spring wheat elite genotypes was phenotyped in 2015-16 and 2016-17 at CIMMYT experimental station Norman E. Borlaug located in NW Mexico. Physiological traits measured included biomass, plant length (height, spike, awns, peduncle, internode 2 & 3), organ DM partitioning (spike, leaf lamina, true stem and leaf sheath) and fruiting efficiency (# of grain set per unit spike dry weight) at anthesis (GS65) + 7 days and at harvest, biomass, grain yield, yield components and harvest index was measured. BLUEs (Best Linear Unbiased Estimators) from the cross-year analysis and molecular markers generated using the 35K Wheat Breeders Axiom array were used to carry out a genome-wide association study (GWAS). Novel marker-trait associations for the grain partitioning traits were identified mainly in chromosomes 5B and 6A; resulting in 13 at anthesis (e.g. LamPI, spike length) and 9 at harvest (e.g. HI, FE_GSP). More detailed results will be presented and their potential application in breeding programs in marker-assisted selection discussed. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://pag.confex.com/pag/xxvii/meetingapp.cgi/Paper/33006 |
| Description | Monogram Grain Conference 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Professional Practitioners |
| Results and Impact | Poster presentation of GWAS of 150 spring wheat lines associating agronomic, yield and biomass related traits to SNP markers for use in the CIMMYT (Mexico) pre-preeding marker trait assisted breeding program. This work is now published here: https://onlinelibrary.wiley.com/doi/full/10.1111/pbi.13052 and was carried out as part of the International Wheat Yield Partnership to provide essential marker trait associations to wheat breeders at CIMMT for tracking high biomass and radiation use efficiency, both which are thought to be a current bottleneck in genetic gains in their populations. The poster was well received and gained a lot of attention during the poster session. A link made during this yielded an on going collaboration with scientists at Rothamsted Research (Mathew Paul). |
| Year(s) Of Engagement Activity | 2018 |
| URL | http://www.monogram.ac.uk/MgNW2018.php |
| Description | Oral Presentation The Rank Prize meeting |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | The meeting was run as an invitational meeting run by the "The Rank Prize Fund" and was named "The shape of wheat to come". The meeting was attended by 30 early career scientists and around 20 more seasoned scientists with the aim of introduction of early career scientists to long established members of the wheat community (including breeding companies). A participant was invited from the most influential groups studying wheat mainly from the UK and France. Each participant was required to A brief description below: The Trustees' Advisory Committee on Nutrition is arranging a series of symposia on topics that are of current interest. In 2018 we intend to organise a mini-symposium on The Shape of Wheat to Come which will be held at The Wordsworth Hotel, Grasmere, Cumbria, England, from 19th to 22nd March 2018. The aim of the meeting is to provide a forum in which leading scientists and young research workers can meet and interact, in order to stimulate discussion and to advance the development of the subject. Attendance is by invitation only and will be limited to about 30 participants. The main speakers will have about 40 minutes for their talk and related discussion and the young scientists will be allocated 20 minutes to give an account of their work. The value of these symposia lies in their small, fully interactive nature, not only during the presentations and discussion, but at other times over meals, in the hotel bar and during recreational periods. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Plant and Animal genomes conference 2019 |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Attendance to plant and animal genomes conference 2019- including 2 x poster presentations. One poster contained work carried out and reported in a recent publication ( 10.1111/pbi.13052). This poster recieved a lot of attention and we were approached multiple times by scientists working in wheat barley and rice along with making contact with a member of the breeding community (KWS) who was interested in the marker trait associations (MTAs) we had discovered and presented in the poster. The second poster featured collaborative work we have carried out with Dr John Faulkes from the University of Nottingham, which also gain wide interest as it denotes the first identifiaction of markers relating to various stem and spike partitioning indices. These presentations also have lead to further discussions with scientists from NIAB about the use of a capture probe set we have designed as part of Designing Future Wheat ISP and our International Wheat Yield partnership grant. |
| Year(s) Of Engagement Activity | 2019 |
| URL | https://www.intlpag.org/2019/ |
| Description | Talk and discussion with Elsoms seeds |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | The talk was to breeders and crop scientist work at Elsoms seed, The aim was to raise awareness of the work that Design future wheat and my group were doing. This lead to a letter of support for our BBSRC grant and a line of communication with their wheat and brassica breeders. |
| Year(s) Of Engagement Activity | 2018 |
| Description | Training course delivery: BecA-ILRI Hub |
| 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 | Myself and Laura Jayne Gardiner were approached to deliver a 1 week training session at the BecA-ILRI Hub, Nairobi, Kenya. The course was a 3 month training program ran by the Alliance for Accelerated Crop Improvement in Africa. Our contribution to the program was training in the background of NGS technologies and their use in crop development along with teaching applied bioinformatics fundamentals to the group of students. The students on the course were from >15 countries in Africa and returned to their host institutes with a fantastic base knowledge of bioinformatics which they will apply for crop/livestock improvement throughout Africa. |
| Year(s) Of Engagement Activity | 2018 |
| URL | https://acaciaafrica.org/bioinformatics-community-practice/members-and-management/ |