Natural Genetic Variation in Phenotypic, Reproductive and Gene Expression Responses to Whole Genome Duplication in Arabidopsis thaliana.

  • Sarah Chordekar

Student thesis: Doctoral ThesisPhD

Abstract

Polyploidy is a key evolutionary process that has helped shape the genomes of several extant eukaryotes, especially flowering plants. Polyploids display significant phenotypic, transcriptomic and reproductive differences relative to their diploids. Oftentimes, this is attributed to large scale genomic reorganisation over evolutionary timescales in ancient polyploids (paleopolyploids), or genetic novelty in polyploids originating from interspecies hybridization (allopolyploids). However, the effects of genome doubling per se in polyploids are yet to be clearly understood. Newly formed polyploids that are formed by the somatic doubling of chromosomes (neoautopolyploids) are a good model to study such effects.
Differences between diploids and neoautopolyploids are frequently linked to changes in nucleotype (cell volume, surface area and ratios of components) brought about by the increase in bulk DNA amounts within the nucleus. While true, is unlikely that nucleotype exclusively explains the responses to increased ploidy. The influence that the genetic background of the plant (genotype) has on the determination of ploidy responses has gained little attention.
We used Arabidopsis thaliana as a model to address this gap. Neoautopolyploid A. thaliana lines of multiple genotypes were generated synthetically using colchicine. The lines were analysed for various phenotypic traits, transcriptomic changes and reproductive differences relative to diploids. We found that in addition to common nucleotype-related responses, the genotype significantly contributed to the responses to increased ploidy. Genotype-related ploidy effects led to a variation in how phenotypic traits responded to increased ploidy; variation in the number and functions of genes that were differentially expressed between genotypes in response to increased ploidy; and variation in the genetic regions of the chromosome that contributed to seed abortion responses in interploidy hybridization. We also observed that colchicine treatment per se influenced ploidy responses, highlighting the need to use appropriate controls when comparing synthetic polyploids to diploids.
Our findings demonstrate that genotype is a key component in determining ploidy responses that is capable of impacting all aspects of plant function – molecular, phenotypic and reproductive.
Date of Award24 Jun 2020
Original languageEnglish
Awarding Institution
  • University of Bath
SupervisorPaula Kover (Supervisor) & Leslie Turner (Supervisor)

Keywords

  • Polyploidy
  • Whole Genome Duplication
  • Arabidopsis thaliana
  • Colchicine
  • RNASeq
  • MAGIC lines
  • Phenotying
  • Tetraploid
  • Octoploid
  • Neopolyploid
  • Autopolyploid
  • Genotype Effects

Cite this

Natural Genetic Variation in Phenotypic, Reproductive and Gene Expression Responses to Whole Genome Duplication in Arabidopsis thaliana.
Chordekar, S. (Author). 24 Jun 2020

Student thesis: Doctoral ThesisPhD