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Genetics of alternative splicing evolution during sunflower domestication.

Chris C R Smith1, Silas Tittes2, J Paul Mendieta2

  • 1Department of Ecology and Evolutionary Biology, University of Colorado Boulder, Boulder, CO 80309-0334; chriscs@colorado.edu.

Proceedings of the National Academy of Sciences of the United States of America
|June 13, 2018
PubMed
Summary

Alternative splicing rapidly evolved during sunflower domestication, driven by selection on regulatory genes. This process generated new protein forms, contributing to adaptation and population divergence in sunflowers.

Keywords:
RNA-seqalternative splicingdomesticationquantitative trait loci

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Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Genetics

Background:

  • Alternative splicing generates protein diversity from limited genes.
  • Shorter-term evolution of splicing and its role in evolutionary transitions are understudied.

Purpose of the Study:

  • To investigate splice differentiation and regulation during sunflower domestication.
  • To understand the origins and impact of alternative splicing in recent evolutionary events.

Main Methods:

  • Transcriptome analysis of wild and domesticated sunflowers.
  • Quantitative trait loci (QTL) mapping for differential splicing.
  • Genotyping across diverse sunflower populations.

Main Results:

  • Significant splicing divergence, primarily intron retention, observed between wild and domesticated sunflowers.
  • Divergent splicing enriched for seed development functions, indicating artificial selection.
  • Primarily trans-acting variation, often involving spliceosome proteins, underlies splicing differences.
  • Most domesticate splicing patterns originated from standing variation in wild sunflowers, with some introgressed from other species.

Conclusions:

  • Sunflower domestication involved selection on pleiotropic regulatory alleles affecting splicing.
  • Rapid evolution of isoform abundances contributes to adaptation and population divergence.
  • Alternative splicing plays a significant role in recent evolutionary transitions.