Utilising Illumina sequencing for high throughput genotyping of wheat
Lead Research Organisation:
John Innes Centre
Department Name: Cell and Develop Biology
Abstract
Genetic markers are used to identify differences in the genetic make-up of individuals in large populations. In crop plants genetic markers are very important for breeding improved crops because they can be used to trace the contributions of parents to their offspring. This enable breeders to identify quickly regions of DNA that confer desirable traits and breed these regions into lines, while eliminating undesired regions. Crop breeding requires many plants to be screened for their genetic make-up over several years. The more genetic markers that are used the more precise breeding can be made, reducing the time and uncertainty in the process. Achieving improved efficiency and predictability in plant breeding is centrally important for securing future supplies of key crops such as wheat. We aim to use our expertise in wheat genomics and next-generation sequencing to develop high- throughput genotyping for wheat in collaboration with UK wheat breeders.
Publications
Luo MC
(2017)
Genome sequence of the progenitor of the wheat D genome Aegilops tauschii.
in Nature
| Description | we have analysed multiple wheat genome assemblies to identify a vast number of variety-specific sequence polymorphisms . These have been mapped to the reference genome. Capture probes across these regions have been made for selecting DNA for genotyping. These are currently being tested on multiple genetic lines for variation on group 3 chromosomes. WE have completed work using capture probes as an approach to wheat genotyping. This worked very well and heterozygous lines could be readily distinguished. However the method is very expensive, and bar-coding and pooling would be sufficient to reduce the cost. However, low-coverage long read Illumina sequencing using LITE library methods (in which 384 libraries can be made simultaneously and bar-coded) are providing to be more cost effective. Imputation methods and approaches to displaying large polymorphic datasets are now the subject of intense effort by JIC scientists |
| Exploitation Route | Once the technology has been optimised, we aim to expand the scope for use in wheat breeding programmes. We hope to implement this approach in partnership with UK breeding companies |
| Sectors | Agriculture, Food and Drink |
| Description | New marker technologies for wheat using Illumina sequencing |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping |
| Collaborator Contribution | The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data. |
| Impact | It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding |
| Start Year | 2017 |
| Description | New marker technologies for wheat using Illumina sequencing |
| Organisation | National Institute Of Agricultural Botany |
| Country | United Kingdom |
| Sector | Private |
| PI Contribution | The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping |
| Collaborator Contribution | The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data. |
| Impact | It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding |
| Start Year | 2017 |
| Description | New marker technologies for wheat using Illumina sequencing |
| Organisation | Natural History Museum |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | The overall aim of the partnership with EI is to develop a new set of sequencing technologies for high-throughput genotyping of wheat using the power of Illumina sequencing. JIC is providing ideas and concepts and wheat DNA samples for analyses and coordinates the project; UPDATE: NIAB is providing access to populations for genotyping |
| Collaborator Contribution | The EI provides sequencing and analyses and interpretation in the partnership. NIAB provide lines for testing genotyping and assistance with analysis of data. |
| Impact | It is too early for any outputs of the project. We have done extensive computational analyses of 10 sequenced and assembled wheat varieties and identified vast numbers of variety-specific polymorphisms. These have been mapped to the reference assembly. A set of 1000 polymorphic regions mapped to each Mb of group 3 chromosomes was identified and gene capture probes designed. DNA from a wide variety of testing lines has been made. In the coming months this DNA will be genotyped to test the method. Future goals are to refine the method to make it cost effective for application in pedigree breeding |
| Start Year | 2017 |
| Description | Wheat genome sequencing |
| Organisation | Earlham Institute |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We are working together to sequence and annotate multiple wheat genomes. This involves its applications to wheat improvement by engagement with international wheat improvement organisations, principally CIMMYT and the International Wheat Yield Programme. One goal goal is to provide genomics expertise for these groups to accelerate their breeding programmes. We also work directly with UK wheat breeders. |
| Collaborator Contribution | TGAC provide the lion's share of the expertise and sequencing capacity. I provide connections and strategy. |
| Impact | Too soon to tell, but has led to a joint applications to ODA and Grand Challenge Funds with international wheat breeders and researchers to support breeding |
| Start Year | 2015 |
| Description | Wheat genome sequencing |
| Organisation | University of Western Australia |
| Country | Australia |
| Sector | Academic/University |
| PI Contribution | We are working together to sequence and annotate multiple wheat genomes. This involves its applications to wheat improvement by engagement with international wheat improvement organisations, principally CIMMYT and the International Wheat Yield Programme. One goal goal is to provide genomics expertise for these groups to accelerate their breeding programmes. We also work directly with UK wheat breeders. |
| Collaborator Contribution | TGAC provide the lion's share of the expertise and sequencing capacity. I provide connections and strategy. |
| Impact | Too soon to tell, but has led to a joint applications to ODA and Grand Challenge Funds with international wheat breeders and researchers to support breeding |
| Start Year | 2015 |
| Description | Acidophil visit to the JIC |
| Form Of Engagement Activity | Participation in an open day or visit at my research institution |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Prof Bevan contributed to a site visit by Acidophil and discussions about collaborative research opportunities. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Agritech discussions with the purpose of forming an AgriTech centre |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Industry/Business |
| Results and Impact | Prof Bevan contributed to discussions with Agritech at Rothamsted with the aim to form an AgriTech centre. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Collaboration with Bayer Crop Sciences |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | JIC and Bayer discussed joint research project aimed at implementing DA1 technology to control seed size in oilseed rape. |
| Year(s) Of Engagement Activity | 2016 |
| Description | Engagement with companies and breeders on new marker technologies |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Two distinct objectives were addressed in these activities. First, we discussed and established a collaboration with Population Genetic Technologies Ltd, owners of IP related to primer technologies to be used. We obtained a licence to use several of the patents, and established a business connection that could be used to commercialise any product generated from the project In a second set of engagement activities, initial discussions with wheat breeders occurred in order to understand the costs, scale and precision of the their genotyping work |
| Year(s) Of Engagement Activity | 2016 |
| Description | Engagement with not for profit organisations: NFU Crop Board |
| Form Of Engagement Activity | A talk or presentation |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Third sector organisations |
| Results and Impact | Prof Bevan contributed to the meeting with the NFU Crop Board providing update on advances in crop improvement and crop protection. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Evaluation of JIC as a strategic partner |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | Regional |
| Primary Audience | Industry/Business |
| Results and Impact | Prof Bevan participated in a meeting with industry to evaluate the JIC as a strategic partner. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Newspaper commentaries about wheat genome sequencing progress |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Mike Bevan provided newspaper commentaries about wheat genome sequencing progress. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://online.wsj.com/article/SB10001424127887324205404578147823815273136.html |
| Description | Press article entitled: 'Wheat genome sequence analysis.' |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Media (as a channel to the public) |
| Results and Impact | Mike Bevan wrote a press article entitled: 'Wheat genome sequence analysis.' |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.sciencedaily.com/releases/2012/11/121128143545.htm |
| Description | Press article for BBC entitled: 'Wheat genome's key parts unlocked in new study.' |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Public/other audiences |
| Results and Impact | Mike Bevan wrote a press article for the BBC entitled: 'Wheat genome's key parts unlocked in new study.' |
| Year(s) Of Engagement Activity | 2012 |
| Description | Press article in Farmers Weekly |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Mike Bevan wrote a press article in Farmers Weekly entitled:'Wheat genome breakthrough offers food security boost'. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.fwi.co.uk/articles/29/11/2012/136475/wheat-genome-breakthrough-offers-food-security-boost... |
| Description | Press article in National Association of Wheat Growers |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Industry/Business |
| Results and Impact | Mike Bevan wrote a press article in National Association of Wheat Growers entitled: 'Scientists announce stride towards wheat genome sequence'. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.wheatworld.org/news-events/2012/11/scientists-announce-strides-toward-wheat-genome-sequen... |
| Description | Press conference with George Freeman MP and and Sir Lesek Borysiewicz with local and national TV and radio covering the event |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Prof Bevan contributed to a press conference with George Freeman MP and and Sir Lesek Borysiewicz. Local and National TV and radio covered the event. The impacts involve creating a network or researchers and industrialists to address the Govt's agri-tech strategy, and contributing to the formation of that strategy. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Press release in National Science Foundation entitled: 'International team generates major breakthrough in deciphering bread wheat's genetic code'. |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Mike Bevan participated in a press release in National Science Foundation entitled: 'International team generates major breakthrough in deciphering bread wheat's genetic code'. |
| Year(s) Of Engagement Activity | 2012 |
| URL | http://www.nsf.gov/news/news_summ.jsp?cntn_id=126008 |
| Description | San Diego Plant and Animal Genome Meeting |
| 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 | During this meeting Prof Bevan discussed wheat genomics with Chinese colleagues. |
| Year(s) Of Engagement Activity | 2016 |
| Description | TV interview with BBC Look East |
| Form Of Engagement Activity | A press release, press conference or response to a media enquiry/interview |
| Part Of Official Scheme? | No |
| Geographic Reach | National |
| Primary Audience | Policymakers/politicians |
| Results and Impact | Mike Bevan participated in a television interview with BBC Look East. |
| Year(s) Of Engagement Activity | 2013 |
| Description | Wheat genomics planning in New York |
| Form Of Engagement Activity | A formal working group, expert panel or dialogue |
| Part Of Official Scheme? | No |
| Geographic Reach | International |
| Primary Audience | Professional Practitioners |
| Results and Impact | Prof Bevan attended a wheat genomics planning meeting in New York. |
| Year(s) Of Engagement Activity | 2015 |