Harnessing cis-regulatory variation to improve polyploid wheat


Wheat is a major cereal crop providing 20% of global calorie and protein intake for humans. To keep pace with population growth, crop yields need to increase, but the current rates of yield improvement are insufficient to achieve this goal. It is therefore critical and urgent to identify ways of increasing yields, for example, by improving spike architecture.

Our lab recently cloned two closely related SVP MADS-box transcription factors which affect spike architecture, floral organ morphology, and grain weight in wheat. Naturally occurring alleles in these genes contain non-coding variation which leads to their misexpression and phenotypic consequences on spike, flowers, and grains. We do not, however, know the mechanism by which these non-coding variants affect cis-regulation and ultimately gene expression of these SVP transcription factors.

The aim of this PhD will be to investigate the mechanisms by which variation in the promoter and introns of SVP genes affects their regulation and ultimately impacts spike and grain development. We hypothesise that conserved domains in the promoter and introns of SVP genes, along with histone modifications, provide tight regulation of these transcription factors.

To address this, the student will determine the effect of conserved promoter and intron motifs on SVP transcriptional profiles using CRISPR-Cas9 editing. The student will investigate how manipulation of these different motifs impacts on molecular and morphological phenotypes by characterising plants with different gene edited alleles.

The student will also explore the dynamics of chromatin modifications in SVP genes across spike development and other tissues using available germplasm. The project provides complementary approaches that allow room for the student to take ownership of the project and expand into their areas of interest. The student will receive mentoring and outstanding training in modern crop genetics, developmental biology, molecular biology, data analysis, and bioinformatics, alongside essential core scientific skills.


Backhaus AE, Lister A, Tomkins M, Adamski NM, Simmonds J, Macaulay I, Morris RJ, Haerty W, Uauy C. 2022. High expression of the MADS-box gene VRT2 increases the number of rudimentary basal spikelets in wheat. Plant Physiology 189:1536–1552 (Uauy corresponding, Backhaus current PhD student, collaboration across NRP with Earlham).

Chen Y, Liu Y, Zhang J, Torrance A, Watanabe N, Adamski NM, Uauy C. 2022. The Triticum ispahanicum elongated glume locus P2 maps to chromosome 6A and is associated with the ectopic expression of SVP-A1. Theoretical and Applied Genetics 135:2313-2331 (Uauy corresponding, Chen current PhD student, Torrance UEA undergrad student).

Adamski NM, Simmonds J, Brinton JF, Backhaus AE, Chen Y, Smedley M, Hayta S, Florio T, Crane P, Scott P, Pieri A, Hall O, Barclay EJ, Clayton M, Doonan JH, Nibau C, Uauy C. 2021. Ectopic expression of Triticum polonicum VRT-A2 underlies elongated glumes and grains in hexaploid wheat in a dosage-dependent manner. The Plant Cell 33: 2296–2319 (Uauy corresponding, Adamski and Brinton ex PhD students; Backhaus, Chen current PhD students).