Unlocking the genetic potential of the root system, rhizosheath mucilage and microbiome of wheat (Triticum aestivum L.)
Lead Research Organisation:
University of Cambridge
Department Name: Plant Sciences
Abstract
An increasing global population, projections of climates that will challenge sufficient crop production, and a detrimental use of fertiliser and pesticides mean that we need to increase the productivity of land currently under cultivation with minimal impact on the environment. Wheat is the second largest contributor to global crop production and is cultivated across a range of latitudes across both hemispheres. The wheat root system is a crucial determinant of plant performance, yet roots are overlooked in breeding due to the challenge of studying organs below ground. Evidence from the literature indicate that water and nutrient uptake are often suboptimal in high yielding and stressed environments. Facilitating the incorporation of root system characteristics into breeding programmes and developing crop management strategies that enhance root function could be key to increasing yield potential and stability, while minimising inputs. To fill the knowledge gap on root-rhizosphere-yield interactions the research presented here falls into three strategic areas: root system architecture (RSA), root secretions and the rhizosphere microbiome.
1) Genetic mapping of RSA in the Avalon x Cadenza Doubled Haploid (AxC) mapping population identified quantitative trait loci (QTL) for seedling seminal root angle, length and growth rate. Replicable QTLs were associated with root angle and mapped to chromosomes 3A and 4D, explaining 7% of phenotypic variation. After extensive root phenotyping, the tails displaying phenotypes at the extremes of the population distribution were taken forward for field trials. Correlations between seedling root phenotypes and the root and canopy phenotypes of mature plants grown in the field were calculated.
2) Root secretions represent a significant loss of fixed carbon from the plant, yet they are thought to confer benefits in relation to plant water status, nutrition, salinity stress, microbial interactions and the development of the rhizosheath. Enzyme-linked immunosorbent assays (ELISAs) were used to quantify the amount of high molecular weight polysaccharides in the rhizosheath of AxC tails, determine the influence of genotype on secretion and investigate potential interactions with RSA.
3) A metagenomics study of the microbial population within the rhizosheath of AxC tails uncovered differences in microbial community composition between lines of the same species. Lines grouped according to phenotype (level of secretion, RSA, yield) showed that the microbiome of high-yielding lines differed from that of low-yielding lines. The level of secreted polysaccharides was associated with differences in the microbiome.
Overall, this research presents a novel, multi-faceted study of the root system, from seedling to mature plant in the field, as a holistic approach to crop improvement is more robust than the unlikely discovery of a "silver bullet".
1) Genetic mapping of RSA in the Avalon x Cadenza Doubled Haploid (AxC) mapping population identified quantitative trait loci (QTL) for seedling seminal root angle, length and growth rate. Replicable QTLs were associated with root angle and mapped to chromosomes 3A and 4D, explaining 7% of phenotypic variation. After extensive root phenotyping, the tails displaying phenotypes at the extremes of the population distribution were taken forward for field trials. Correlations between seedling root phenotypes and the root and canopy phenotypes of mature plants grown in the field were calculated.
2) Root secretions represent a significant loss of fixed carbon from the plant, yet they are thought to confer benefits in relation to plant water status, nutrition, salinity stress, microbial interactions and the development of the rhizosheath. Enzyme-linked immunosorbent assays (ELISAs) were used to quantify the amount of high molecular weight polysaccharides in the rhizosheath of AxC tails, determine the influence of genotype on secretion and investigate potential interactions with RSA.
3) A metagenomics study of the microbial population within the rhizosheath of AxC tails uncovered differences in microbial community composition between lines of the same species. Lines grouped according to phenotype (level of secretion, RSA, yield) showed that the microbiome of high-yielding lines differed from that of low-yielding lines. The level of secreted polysaccharides was associated with differences in the microbiome.
Overall, this research presents a novel, multi-faceted study of the root system, from seedling to mature plant in the field, as a holistic approach to crop improvement is more robust than the unlikely discovery of a "silver bullet".
Publications
Studentship Projects
| Project Reference | Relationship | Related To | Start | End | Student Name |
|---|---|---|---|---|---|
| BB/M011194/1 | 01/10/2015 | 31/03/2024 | |||
| 1804473 | Studentship | BB/M011194/1 | 01/10/2016 | 31/12/2020 | Emily Marr |
| Description | This research project has taken a genetically and phenotypically characterised set of lines in an important crop species, and tested performance at multiple developmental stages in the glasshouse and in the field, looking at roots, shoots, and grain yield. In addition to this, the project has characterised the degree and molecular composition of secretion of polysaccharides from the roots of the same lines and dissected the bacterial and fungal populations occurring in the rhizosheath of the lines. The use of the Avalon x Cadenza (AxC) doubled haploid population for all these studies enabled direct comparison of the same lines for a range of agronomically important plant characters. In a series of glasshouse trials in seedlings of a wheat mapping population, I identified regions of the genome that regulate root system architecture. More specifically, I have identified regions of the genome that regulate the angle at which roots grow in the soil. This has significance in relation to water and nutrient uptake as root angle is a proxy for rooting depth. Nutrient losses can be reduced and water capture increased by developing crop cultivars capable of exploring deeper soil strata. The regions of the genome, termed quantitative trait loci (QTLs), were named QRa.niab.4D-1 and QRa.niab.3A-1. They were mapped to the long arm of chromosome 4D and the long arm of chromosome 3A respectively, and each contributed a proportion of phenotypic variance (PVE) of around 7%. Thanks to field trials corroborating the glasshouse trials, it was found that in general, the narrower the seedling seminal root angle, the greater the rate of green canopy gain early in the season, and the greater the maximum canopy greenness, the greater the number of roots per tiller observed at maturity and the wider the crown root angle. Studies on the composition of rhizosheath (soil adhering to the roots) mucilage have not previously been conducted on such a large scale. Here, individuals of a wheat mapping population were evaluated for the concentration of xylan, heteroxylan, arabinogalactan protein, extensin and xyloglucan in their rhizosheath at the seedling stage. There was significant genotypic variation among the wheat lines for rhizosheath size, root length, shoot length and the concentration of polysaccharides in the rhizosheath. There were significant positive correlations between levels of AGP and heteroxylan, and between xylan, extensin and homogalacturonan, indicating that these polysaccharides may be linked in a polysaccharide matrix in proportional concentrations. Rhizosheath size per unit root length displayed a significant positive correlation with heteroxylan and AGP. The correlation indicates that rhizosheath formation may be enhanced by the secretion of these polysaccharides. Selecting for cultivars that have heteroxylan- and AGP-rich mucilage could promote rhizosheath formation and resilience to abiotic stress. Microorganisms exert a significant effect on diverse aspects of plant health, growth and development, including nutrient acquisition. This study found that bacterial and fungal communities in the rhizosheath of lines from the wheat mapping population did not vary in terms of alpha diversity but did vary in species composition. This indicates that specific plant genotypes exhibit differential selection of the microbial inhabitants of the rhizosheath. Bacterial and fungal communities were dominated by a small number of phyla, each of which was dominated by a small number of classes. There were differences in microbial beta diversity between lines known to contrast for the level of AGP, extensin, homogalacturonan, heteroxylan and xyloglucan in the rhizosheath. The fungal beta diversity of higher-yielding wheat lines differed significantly from lower-yielding lines. This was not the case for bacterial beta diversity. Higher yields could arise from enhanced nutrient acquisition thanks to a more beneficial population of fungi. |
| Exploitation Route | Crop management practices such as tillage and crop rotation have a crucial impact on agricultural output but are often neglected when studying the rhizosphere microbiome (Zhou et al., 2020). My data suggest that the choice of variety, too, could be an important management tool to optimise rhizosphere dynamics for different farming systems. This is particularly true for our understanding of the establishment of the rhizosphere microbial communities at the seedling stage. A recent paper demonstrates that early rhizosphere communities are defined by the detritusphere: the soil surrounding the decaying root from the previous crop (Zhou et al., 2020). Future work could examine microbial succession in the field at specific developmental stages in the panel of AxC tails, taking samples of bulk soil, rhizosheath soil and roots. The same samples could be tested for polysaccharides in order to test the hypothesis that the change in root secretion during plant development drives a change in microbial communities. The trial would also test the hypothesis that the microbial community at the seedling stage helps to determine crop performance at later stages, including grain yield. Other measurements at multiple developmental stages could include leaf canopy cover and root crown phenotypes. In order to test the effect of specific polysaccharides on microbial diversity in a controlled setting without confounding environmental factors, further work should include a metagenomics analysis of soil samples supplemented with purified solutions of polysaccharide at concentrations equivalent those found in the rhizosheath. With added labour, scaling up to the entire AxC population would allow QTL analysis on these traits. Further investigation of heteroxylan, AGP, homogalacturonan and xyloglucan could utilise a candidate gene approach using exome capture data. To take the root angle QTLs forward, the development of NILs by backcrossing to reduce the introgression size and eliminate other introgressions could be undertaken. The development of sub-NILs could further allow fine-mapping. There is still uncertainty over the location of mucilage secretion and whether different polysaccharides are secreted from different root zones. Further work could use the probing of nitrocellulose sheets with antibodies on which roots of a growing plant had been placed. |
| Sectors | Agriculture, Food and Drink,Education,Environment |
| Description | (i) NIAB (National Institute of Agricultural Botany) holds open days with breeders and farmers. I have presented my work there and raised awareness and understanding about the importance of roots for contributing to yield. (ii) I have talked about my work at the University of Cambridge Science Festival to educate the public about crop root systems, sustainability and agriculture. |
| First Year Of Impact | 2018 |
| Sector | Agriculture, Food and Drink,Education |
| Impact Types | Cultural,Societal |
| Description | GARNet travel award |
| Amount | £200 (GBP) |
| Organisation | GARNet |
| Sector | Learned Society |
| Country | United Kingdom |
| Start | 04/2019 |
| End | 04/2019 |
| Description | IPPN Root Phenotyping working group travel prize |
| Amount | € 500 (EUR) |
| Organisation | International Plant Phenotyping Network (IPPN) |
| Sector | Charity/Non Profit |
| Country | Germany |
| Start | 07/2018 |
| End | 07/2018 |
| Description | Travel Award for ISRR10 Conference |
| Amount | £800 (GBP) |
| Organisation | University of Cambridge |
| Department | Christ's College |
| Sector | Academic/University |
| Country | United Kingdom |
| Start | 07/2018 |
| End | 07/2018 |
| Description | Assays of genetic variation in root exudate composition |
| Organisation | University of Leeds |
| Country | United Kingdom |
| Sector | Academic/University |
| PI Contribution | We have analysed a panel of wheat varieties that vary in root exudate composition. The ELISA assay techniques were learned during a visit to Paul Knox's lab at Leeds U. |
| Collaborator Contribution | Paul Knox contributed know-how and a gift of antibodies to several carbohydrate epitopes for Emily's research. |
| Impact | Experimental results are in thesis, which has been submitted and is under revision. A paper describing results is in preparation. |
| Start Year | 2019 |
| Description | Rhizosphere metagenomics of diverse wheat germplasm |
| Organisation | Natural History Museum |
| Country | United Kingdom |
| Sector | Public |
| PI Contribution | We worked together with the team from NHM. We planted field trials, sampled shoot, root and soil , and ship the samples on dry ice to NHM for analysis. |
| Collaborator Contribution | Samples were analysed, and data are to be shared for joint publication and use. |
| Impact | work is still ongoing. Genetics, bioinformatics, agronomy, physiology |
| Start Year | 2019 |