Genetic Analysis of Ethiopian and Eritrean Barley Landraces

Student thesis: Doctoral ThesisDoctor of Philosophy

Abstract

Food security is one of the challenges of the 21st century, particularly considering the increasing population and limited capacity to produce enough food for all. On top of this, malnutrition is affecting many people worldwide. Barley is one of the top staple crops for countries like Ethiopia on which more than 4 million households depend both for food and income. Crop productivity is limited by biotic factors like diseases, insect pests and weeds and abiotic factors that include bioclimatic, radiation and soil factors. Ethiopia is considered as one of the Vavilovian centres of diversity for several species including barley where most of its accessions housed in gene banks remain largely uncharacterised. Utilisation of the available natural variation within the gene pool is of paramount importance to alleviate these challenges through modern plant breeding approaches like marker assisted selection. Genome-Wide Association Study (GWAS) is a powerful tool to map genetic loci that control traits of interest, and its power depends on the germplasm, analysis model, marker density, extent of LD and quality of genetic and phenotypic data. In this study, I identified both known and novel sources of genetic variation for important traits such as heading date, plant height, grain traits and yield as well as for grain ionome and environmental variables. The photoperiod responsive gene Ppd-H1 and the row-type gene Vrs1 appear to play a central role and have pleiotropic effect on heading dates, plant height, grain traits and yield of the EEBC germplasm. Number of other novel QTLs were also identified which await follow-up investigations to characterise and validate their causality. Identification of the novel gene HvZIFL1 for grain Zn accumulation through GWAS in the Ethiopian and Eritrean Barley Collection (EEBC) panel and validation of polymorphic markers for marker assisted selection were significant findings of this study. In global perspectives, the haplotype carrying the favourable HvZIFL1 allele in the barley legacy (WHEALBI) collection was composed of 60% of germplasm from the East African origin indicating the importance of these gene pool as source of unique alleles for important adaptive traits including nutrient accumulation for which several QTLs were highlighted. Higher correlation was observed between grain ions such as Zn, Cu, Mg, P and Mn which may suggest similar mechanism underlying their homeostasis and hence a wholistic approach is required in future studies involving grain Ionome. Extending the application of GWAS to environmental variables (EnvGWAS) proved effective to detect QTLs involved in adaptation of the germplasm to their local growing environments. Among several QTLs associated with bioclimatic variables related with temperature were those detected on 2H harbouring the photoperiod responsive Ppd-H1, and the flowering time (FT) genes which were also associated with heading dates in the polytunnel and field trials at Dundee. Several bioclimatic, edaphic, solar radiation and topographic factors were associated with number of QTLs distributed across all chromosomes which need further validation. Taken together, EnvGWAS can be an alternative approach for GWAS to map QTLs for environmental adaptation as high throughput and spatially predicted environmental data become increasingly available.
Date of Award2023
Original languageEnglish
SupervisorRobbie Waugh (Supervisor), Claire Halpin (Supervisor) & Joanne Russell (Supervisor)

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