Exploring genetic loci for the improvement of inflorescence traits in the polyploid cereals wheat and tef

Jones, Maximillian R. W. (2025) Exploring genetic loci for the improvement of inflorescence traits in the polyploid cereals wheat and tef. Doctoral thesis, University of East Anglia.

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Abstract

Genetic gains in both major and minor crops will be essential to meet the human population’s future agricultural demands. In this thesis we explore how different types of variation for inflorescence traits – natural and engineered, recessive and dominant, coding and cis-regulatory – can contribute to yield for two polyploid cereal crops; wheat and tef (Eragrostis tef).

We initially describe resequencing and multi-location phenotyping of an important tef germplasm collection. Through k-mer-based genome-wide association we uncovered multiple marker-trait associations for inflorescence and grain traits. This included identification of a strong link between grain size and grain colour. We proposed the tef orthologues of TRANSPARENT TESTA 2 as key regulators of these traits and detected natural variation in both homoeologs.

Next, we moved to wheat for an opportunity to study induced variation. The spikelets (grain-bearing inflorescence structures) of wheat are not created equally. The basal-most spikelets initiate first but quickly fall behind their central counterparts in development, ultimately producing smaller and fewer (or even zero) grains. Little natural variation has been identified which alters the resulting grain mass distribution across the spike. We conducted semi-spatial transcriptomics across a developmental time course of early wheat spikes and identified potential regulators of this process. We then manipulated two candidate genes via transgenic misexpression, and preliminary results suggest that one construct reduced the incidence of basal spikelets bearing no viable grain.

These results led us to conclude that reliable tissue and time-specific cis-regulomes are a powerful resource for testing developmental hypotheses and inducing novel, breeding-relevant variation. We pursued this goal by attempting to generate a genome-wide catalogue of cis-regulatory elements (CREs) relevant to early wheat spike development. Our methodology was to correlate chromatin accessibility with gene expression, integrating DNA hypomethylation as another CRE marker. This approach exhibited some capacity to detect enhancers, but not silencers.

Item Type:	Thesis (Doctoral)
Faculty \ School:	Faculty of Science > School of Biological Sciences
Depositing User:	Chris White
Date Deposited:	08 Apr 2026 08:59
Last Modified:	08 Apr 2026 08:59
URI:	https://ueaeprints.uea.ac.uk/id/eprint/102709
DOI:

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