SEQUENCING THE GENIC PORTION OF SEEDS OF DISCOVERY ADVANCE PRE- BREEDING GERMPLASM TO UNCOVER THE GENETIC VARIATION
Lead Research Organisation:
Earlham Institute
Department Name: UNLISTED
Abstract
Abstracts are not currently available in GtR for all funded research. This is normally because the abstract was not required at the time of proposal submission, but may be because it included sensitive information such as personal details.
Technical Summary
OBJECTIVES
? Design, build and test a genic sequence capture probe-set based on the gold standard
reference of the genic portion of wheat
? Re-sequence 20 CIMMYT elite lines used as parents in CIMMYTs global breeding
programs and 100 of the advanced pre-breeding derived lines
? Re-sequence 200 lines of the high biomass association panel generated from the world
wheat diversity panel
? Associate performance in marginal environments with genomic regions and
potentially candidate genes and SNPs
? Develop a powered by iplant/Cyverse as a community repository for phenotypic,
genotypic data and bioinformatics tools developed as part of this project
? Design, build and test a genic sequence capture probe-set based on the gold standard
reference of the genic portion of wheat
? Re-sequence 20 CIMMYT elite lines used as parents in CIMMYTs global breeding
programs and 100 of the advanced pre-breeding derived lines
? Re-sequence 200 lines of the high biomass association panel generated from the world
wheat diversity panel
? Associate performance in marginal environments with genomic regions and
potentially candidate genes and SNPs
? Develop a powered by iplant/Cyverse as a community repository for phenotypic,
genotypic data and bioinformatics tools developed as part of this project
Planned Impact
unavailable
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
Gardiner L
(2017)
Hidden variation in polyploid wheat drives local adaptation
Gardiner LJ
(2019)
Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat.
in GigaScience
Gardiner LJ
(2019)
Analysis of the recombination landscape of hexaploid bread wheat reveals genes controlling recombination and gene conversion frequency.
in Genome biology
Joynson R
(2021)
Uncovering candidate genes involved in photosynthetic capacity using unexplored genetic variation in Spring Wheat.
in Plant biotechnology journal
Lyra DH
(2021)
Gene-based mapping of trehalose biosynthetic pathway genes reveals association with source- and sink-related yield traits in a spring wheat panel.
in Food and energy security
| Description | Sequence capture is one of the main techniques employed by the crop research community for re-sequencing large complex genomes at reduced cost. In wheat, to date, many studies have implemented exon capture probe sets that are based on incomplete reference genome sequence and are largely missing promoter and intronic sequence. There is a need to update the go-to resources for cost effective analysis of hexaploid bread wheat, therefore we demonstrate; • The design and validation of a gold standard gene and promoter capture probe set for wheat, using recently developed genome resources. • A unique capture design employing an 'island strategy' to enable analysis of the large gene/promoter space of wheat (~1Gb) with only 2x160 Mb probe sets. • Enrichment of the high confidence genes promoters that were identified in the genome alongside most of the low confidence genes and promoters. • The use of the capture probe sets to analyze a diverse set of material. • Successful sample multiplexing to significantly reduce the cost per sample for gene and promoter capture. We have now used this to re-sequecned 32 ket CIMMYT lines identified as ket lines for the seeds of discovery project. We have now re-sequenced and generated SNPs for HIBAP 2 a critical panel for IWYP. We have also generated RNA-seq and Iso-Seq data for the annotation of Weedil a line that underpins much of the CIMMYT germplasm. |
| Exploitation Route | The data is availabe on Grass route and on the ERA |
| Sectors | Agriculture Food and Drink |
| Description | We are now using the genotyping data from HiBAP 2. Markerm trait association from this will support those identified in HiBAP 2 and enter the pre-breeding cycle for CIMMYT. |
| Sector | Agriculture, Food and Drink |
| 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 | Supporting data for "Integrating genomic resources to present full gene and putative promoter capture probe sets for bread wheat" |
| 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. 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. 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 | Database/Collection of data |
| Year Produced | 2019 |
| Provided To Others? | Yes |
| 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 | 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 | 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 | Agro-Biodiverstiy conference -India |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Invited speaker at "Present and Future Opportunities for Using Biodiversity for Wheat Improvement" |
| Year(s) Of Engagement Activity | 2016 |
| 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 | 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/ |