Local haplotyping software development and integrated bioinformatics analysis uncovering impacts of domestication on legume genomes

Jacob Marsh

Research output: ThesisDoctoral Thesis

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Abstract

This thesis includes a broad range of advancements relevant to crop genetics improvement. Comparative and multi’omic analysis was used to characterize the historical evolution of a major pod shatter locus, PDH1, between legume species, which revealed conservation, specificity and potential sources of transcriptional regulation within the Phaseoloid clade. The major soy protein QTL, cqProt-003, was explored using many of the core methods developed for crosshap, to analyse haplotype diversity and global distribution. Finally, a novel research tool, ‘crosshap’, is presented, which has been developed to capture and represent local patterns of linkage disequilibrium and the relationships between variant loci.
Original languageEnglish
QualificationDoctor of Philosophy
Awarding Institution
  • The University of Western Australia
Supervisors/Advisors
  • Ranathunge, Kosala, Supervisor
  • Bayer, Philipp, Supervisor
  • Edwards, Dave, Supervisor
  • Batley, Jacqueline, Supervisor
Thesis sponsors
Award date1 May 2023
DOIs
Publication statusUnpublished - 2022

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