Characterising the genes responsible for segregation distortion in wheat
Lead Research Organisation:
University of Bristol
Department Name: Biological Sciences
Abstract
Food security relies on the development of new varieties, with increased yield and/or increased resistance to biotic and abiotic stress. However, commercial breeding is a numbers game, the more progeny generated, the greater the chance the breeder has of generating that rare future elite variety. Like the breeders of all commercial species, the efforts of wheat breeders are confounded by a phenomenon referred to as segregation distortion (SD). SD commonly occurs in mapping populations and is thought to occur due to the favourable transmission or selection of specific alleles during either meiosis or the subsequent selection of seed/seedlings via, for instance, their growth characteristics. Unfortunately, SD interferes with the breeding process as certain regions of the genome are either over or under-represented in the progeny. The under or over representation of specific alleles means that more progeny than expected are required to be generated, resulting in wasted resources. Interestingly, SD also interferes with the construction of genetic maps and as a consequence markers showing distortion are often removed from the mapping process. As such understanding, the genes that underpin SD is a neglected area but one that is of critical importance in the breeding process.
In this four-year project, you will work with the cereal functional genomics group at Bristol to characterise and clone regions of the wheat genome involved in SD. The Bristol group leads the world in wheat molecular marker technology and as such you will utilise the latest techniques such as high-throughput genotyping, next-generation sequencing and various bioinformatical procedures to characterise genomic regions identified in a number of wheat mapping populations. In addition, during your project, you will have ample opportunity to interact with, and possibly influence the activities of, a range of international wheat breeders.
In this four-year project, you will work with the cereal functional genomics group at Bristol to characterise and clone regions of the wheat genome involved in SD. The Bristol group leads the world in wheat molecular marker technology and as such you will utilise the latest techniques such as high-throughput genotyping, next-generation sequencing and various bioinformatical procedures to characterise genomic regions identified in a number of wheat mapping populations. In addition, during your project, you will have ample opportunity to interact with, and possibly influence the activities of, a range of international wheat breeders.
People |
ORCID iD |
Keith Edwards (Primary Supervisor) | |
Alexander Coulton (Student) |
Publications
Tock AJ
(2021)
Crossover-active regions of the wheat genome are distinguished by DMC1, the chromosome axis, H3K27me3, and signatures of adaptation.
in Genome research
Przewieslik-Allen AM
(2021)
The role of gene flow and chromosomal instability in shaping the bread wheat genome.
in Nature plants
Przewieslik-Allen AM
(2018)
Developing a High-Throughput SNP-Based Marker System to Facilitate the Introgression of Traits From Aegilops Species Into Bread Wheat (Triticum aestivum).
in Frontiers in plant science
Coulton A
(2020)
Examining the Effects of Temperature on Recombination in Wheat.
in Frontiers in plant science
Coulton A
(2020)
Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods.
in PloS one
Coulton A
(2020)
AutoCloner: automatic homologue-specific primer design for full-gene cloning in polyploids.
in BMC bioinformatics
Burridge AJ
(2017)
High-Density SNP Genotyping Array for Hexaploid Wheat and Its Relatives.
in Methods in molecular biology (Clifton, N.J.)
Allen AM
(2017)
Characterization of a Wheat Breeders' Array suitable for high-throughput SNP genotyping of global accessions of hexaploid bread wheat (Triticum aestivum).
in Plant biotechnology journal
Studentship Projects
Project Reference | Relationship | Related To | Start | End | Student Name |
---|---|---|---|---|---|
BB/M009122/1 | 01/10/2015 | 31/03/2024 | |||
1933018 | Studentship | BB/M009122/1 | 01/10/2017 | 30/09/2021 | Alexander Coulton |
Description | One of the main achievements of the award is the publication of our paper "Segregation distortion: Utilizing simulated genotyping data to evaluate statistical methods". This paper addresses widespread misconceptions in the scientific community regarding the identification of genetic markers that show a skewed inheritance pattern, otherwise known as segregation distortion. Segregation distortion can be problematic for crop breeders, who wish to generate varieties with novel genetic compositions that are better suited to meeting the various aims of modern agriculture, such as increased yields or improved resistance to biotic or abiotic stresses. Distorted segregation in the genome could skew most lines in a population of crops away from the desired genotype, requiring breeders to create larger numbers of lines to compensate. It would be useful if we could attribute regions of segregation distortion to causative loci in the genome, as this would allow breeders to plan for the occurrence ahead of time. We used simulations of meiosis, the process that generates egg and sperm cells, as well as empirical data from a population of wheat plants, to identify the ideal statistical test for detecting segregation distortion. We show that many of the markers supposedly exhibiting segregation distortion in the literature are actually simply distorted by chance, rather than a genuine selection pressure operating during development. We also examined the effect of segregation distortion on the genetic mapping process, showing that only extreme distortion effects genetic mapping. |
Exploitation Route | These findings should inform future studies on best practices in both the identification and the use of genetic markers exhibiting segregation distortion, unlocking information on regions of the genome that were previously hidden to researchers. |
Sectors | Agriculture, Food and Drink |
Description | Problems caused by introgessions |
Geographic Reach | Multiple continents/international |
Policy Influence Type | Influenced training of practitioners or researchers |
Impact | Wheat breeding companies were made aware about the effect that introgressions have on recombination and why this may lead to difficulties in the future, this has caused some companies to re-examine their breeding strategies |
Description | BBSRC Flexible Talent Mobility Award (FTMA) |
Amount | £25,000 (GGP) |
Organisation | Biotechnology and Biological Sciences Research Council (BBSRC) |
Sector | Public |
Country | United Kingdom |
Start | 08/2019 |
End | 12/2019 |
Title | Introgression plotter added to Cerealsdb |
Description | Software to allow users to screen wheat germplasm for potential introgressions from wheat relative |
Type Of Material | Data analysis technique |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | At the request of the wheat breeding companies we have made this tool available via Cerealsdb so that breeders can check on the presence of possible introgressed regions in the bread wheat genome |
Title | QTL database |
Description | Upload of QTL database to Cerealsdb |
Type Of Material | Data analysis technique |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Breeders and academics are now able to download/examine various QTL-based datasets |
Title | Upgrade to cerealsdb (cerealsdb3) |
Description | We have carried out a significant upgrade of cerealsdb to include new analytical tools and a much larger data set |
Type Of Material | Database/Collection of data |
Year Produced | 2019 |
Provided To Others? | Yes |
Impact | Increased level of data downloads and use of tools to detect introgressions in wheat |
URL | http://www.cerealsdb.uk.net/cerealgenomics/CerealsDB/indexNEW.php |
Description | Collaboartion with Syngenta to exchnage knowledge on trasformation and double haploid production |
Organisation | Syngenta International AG |
Department | Syngenta Ltd (Bracknell) |
Country | United Kingdom |
Sector | Private |
PI Contribution | exchange of personal to improve our technology in double haploid production |
Collaborator Contribution | Spent time at Syngenta providing input into transformation technolgy |
Impact | Better transformation and double haploid technology available to Bristol |
Start Year | 2019 |
Description | Keynote presentation at 2019 Monogram |
Form Of Engagement Activity | A talk or presentation |
Part Of Official Scheme? | No |
Geographic Reach | International |
Primary Audience | Professional Practitioners |
Results and Impact | Keynote, plenary lecture at Monogram 2019 |
Year(s) Of Engagement Activity | 2019 |