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EASTBIO: Identification and Characterisation of Genes Responsible for Cadmium Accumulation in Barley and Rice Grains


Project Description

Understanding the grain ionome is fundamentally important as the endosperm of cereal grains provide 50% of the average calories consumed globally, however some ions can be massively detrimental to human health. Cadmium (Cd) is a highly toxic heavy metal, and exposure to Cd has been shown to contribute to serious health conditions including kidney damage, several types of cancer, and osteoporosis. Plants can accumulate this heavy metal in a range of tissues, including the grain. Of critical significance in rice is the observation that any water-saving management will substantially increase grain Cd because it will promote a more aerobic soil environment. While genes contributing to variation in accumulation of Cd in various tissues in other plant species such as OsHMA3 in rice and ATPase in arabidopsis, have been identified and characterised, little work to date has been carried out in barley. The function of genes influencing the grain ionome are relatively conserved and therefore we propose to use two major crop species, barley and rice in parallel.
Aims/Objectives; To identify and functionally characterise the genes identified by a genome-wide association (GWA) study which contribute to natural variation in cadmium accumulation in barley and rice grain.

Methods/Approach; The student will expand on an unpublished dataset from barley where the grain ionome was quantified in 140 2-row spring barley cultivars1 by increasing the number of cultivars analysed to >200 to increase potential mapping resolution. This data will be combined with high resolution genotypic data (>150k exome capture derived snps) to carry out a GWA study. In parallel an equivalent analysis will be carried out using rice germplasm and exploiting data on grain cadmium already available. This will be on the Bengal and Assam Aus Panel (BAAP; 266 accessions, 2 million SNPs) grown in two water treatments in two years2 and the Rice Diversity Panel with 5 sites 3 (Norton et al. 2014). Multiple site and multiple trait GWAS will also be applied to the rice data.
The outputs from these analyses will be compared and where common targets are observed these regions will be will refined, candidate genes identified and characterised in both crops.
The student will exploit the technological strengths of each crop to facilitate this process. At JHI (The James Hutton Institute) creating and utilising CRISPR-Cas9 mutants is routine and has been successfully used to validate the function of other genes which contribute to grain composition. Initially overexpression (OX) and CRISPR-Cas9 lines of HvNramp5 (believed to influence cadmium accumulation in barley) will be developed. For rice mutants are available in many genes, and these will be utilised for the characterisation of candidate genes.
The output of this project will be the identification of genes and alleles in barley and rice that will not only deepen our understanding of cadmium accumulation in crops plants but will also be targets for breeding low cadmium rice and barley

Funding Notes

This 4 year PhD project is part of a competition funded by EASTBIO BBSRC Doctoral Training Partnership. This opportunity is only open to UK nationals (or EU students who have been resident in the UK for 3+ years immediately prior to the programme start date) due to restrictions imposed by the funding body, Application Procedure: View Website
Please send your completed EASTBIO application form, along with academic transcripts and CV to Laura Logie: . Two references should be provided by the deadline using the EASTBIO reference form. Referees should return the reference form to .

References

1. Houston K, Bayer M, Byrt C, Flis P, Gilliham M, Macaulay M, Oakey H, Qiu J, Qu Y, Russell J, Roy S, Salt D, Situmorang A, Smith P, Wege S, Waugh R. Selecting a barley HKT1;5 allele - with a grain of salt. A naturally occurring amino acid substitution in HvHKT1;5 largely determines barley grain sodium content. In prep
2. Norton GJ, Travis AJ, Douglas A, Fairley S, De Paiva Alves E, Ruang-areerate P, Naredo MEB, McNally KL, Sumon MH, Islam MR and Price AH 2018 Front. Plant Sci. 9:1223.
3. Norton GJ, Douglas A, Lahner B, Yakubova E, Guerinot ML, Pinson SRM, Tarpley L, Eizenga GC, McGrath SP, Zhao FJ, Islam MR, Islam S, Duan G, Zhu Y, Salt DE, Meharg AA and Price AH 2014 PLOS ONE 9: e89685

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