Using a barley Nested Association Mapping (NAM) Population to mine wild barley germplasm for crop improvement

  • Fulvia Draicchio

Student thesis: Doctoral ThesisDoctor of Philosophy


Modern cultivar barley, like other cultivated cereals, went through the so called “domestication syndrome”, by which early farmers subjected the crop to a consistent selection that led to gradual changes in its characteristics and architecture. The result is that the modern cultivar differs from the wild progenitor for several advantageous traits, such as enhanced crop yield and reduced height. However, domestication also caused fixation and narrowing of the genetic base of cultivated barley, making this crop less able to adapt to biotic and abiotic changes than its wild ancestor. This narrowed gene diversity is particularly acute in the pericentromeric heterochromatic (PCH) genomic regions because of the drastic reduction of recombination events in this area. Low gene diversity and low recombination rate in turn impinge upon subsequent breeding success to improve the cultivar. The PCH region of barley is permissive for gene expression, but any loci within it are trapped in large haplotypes by low recombination, so all this region is inaccessible to breeders who need to re-assort alleles for crop enhancement. It is estimated that ca 18% of barley genes are affected by this problem. Therefore, it has been proposed to introduce exotic genetic material from wild species into cultivar germplasm. Wild barley Hordeum vulgare ssp spontaneum is rich in allelic diversity and represents a potential source of favourable alleles for qualitative and quantitative agronomic traits. In this study, we have used the multi-parental barley Nested Association Mapping (NAM) population HEB-25,, comprising 1,420 lines, sub-divided into 25 families, each of which was generated by crossing the spring barley cultivar Barke with one of 25 different wild barley accessions. This thesis describes a two pronged strategy to exploit the genetic diversity in the HEB-25 lines, with the eventual goal of enhancing the agronomically useful biodiversity in cultivar barley. My experiments have addressed firstly Genome Wide Association Study (GWAS) of the HEB-25 population. GWAS relies on high throughput technology, which typically assays single nucleotide polymorphisms (SNPs), together with trait data obtained from experimental observation of plants. In this thesis I describe the results of a GWAS study of the HEB-25 population for yield-related traits, including the genomic regions identified, traits involved and in some cases presmptive candidate genes for future experimentation. Lastly, to improve the accuracy of the GWAS approach I describe our work on exome capture sequencing of the entire HEB-25 population. The second strategy used here involves the generation of PCH substitution lines derived by back-crossing individual HEB-25 accessions to the parental Barke cultivar parent. These derived lines contain one or more wild-derived PCH regions, together with reduced contaminating exotic genetic material in the euchromatic arms. The eventual aim is to test if substituting a Barke-derived PCH region with a corresponding wild-derived segment can lead to improved agronomic traits. Details about the generation of the PCH progenies are described, involving backcross and self-cross cycles, as well as a subsequent preliminary field trial allowing phenotypic analysis of the pericentromeric substitution lines (PCSLs). Finally, hypotheses about possible candidate genes sited in the heterochromatic substitutions and linked to the phenotypic traits observed in the HEB progenies are also discussed.
Date of Award2018
Original languageEnglish
SponsorsBiotechnology and Biological Sciences Research Council
SupervisorAndrew Flavell (Supervisor)

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