Skip to main content
bioRxiv
  • Home
  • About
  • Submit
  • ALERTS / RSS
Advanced Search
New Results

Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations

Enrique J. Schwarzkopf, Juan C. Motamayor, Omar E. Cornejo
doi: https://doi.org/10.1101/482299
Enrique J. Schwarzkopf
1School of Biological Sciences, Washington State University, Pullman, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Juan C. Motamayor
2Universal Genetic Solutions, LLC
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
Omar E. Cornejo
1School of Biological Sciences, Washington State University, Pullman, WA, USA
  • Find this author on Google Scholar
  • Find this author on PubMed
  • Search for this author on this site
  • For correspondence: ocornejo@gmail.com
  • Abstract
  • Full Text
  • Info/History
  • Metrics
  • Preview PDF
Loading

Abstract

Our study investigates the possible drivers of recombination hotspots in Theobroma cacao using ten genetically differentiated populations. By comparing recombination patterns between multiple populations, we obtain a novel view of recombination at the population-divergence timescale. For each population, a fine-scale recombination map was generated using the coalescent with a standard method based on linkage disequilibrium (LD). These maps revealed higher recombination rates in a domesticated population and a population that has undergone a recent bottleneck. We inferred hotspots of recombination for each population and find that the genomic locations of hotspots correlate with genetic differentiation between populations (FST). We used randomization approaches to generate appropriate null models to understand the association between hotspots of recombination and both DNA sequence motifs and genomic features. We found that hotspot regions contained fewer known retroelement sequences than expected and were overrepresented near transcription start and termination sites. Our findings indicate that recombination hotspots are evolving in a way that is consistent with genetic differentiation but are also preferentially driven to near coding regions. We illustrate that, consistent with predictions in plant domestication, the recombination rate of the domesticated population is orders of magnitude higher than that of other populations. More importantly, we find two fixed mutations in the domesticated population’s FIGL1 protein. FIGL1 has been shown to increase recombination rates in Arabidopsis by several orders of magnitude, suggesting a possible mechanism for the observed increased recombination rate in the domesticated population.

Footnotes

  • Exploration of FIGL1 and FLIP orthologs as possible mechanisms for observed increased recombination in the domesticated variety of cacao was added.

Copyright 
The copyright holder for this preprint is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under a CC-BY-NC-ND 4.0 International license.
Back to top
PreviousNext
Posted January 10, 2020.
Download PDF
Email

Thank you for your interest in spreading the word about bioRxiv.

NOTE: Your email address is requested solely to identify you as the sender of this article.

Enter multiple addresses on separate lines or separate them with commas.
Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
(Your Name) has forwarded a page to you from bioRxiv
(Your Name) thought you would like to see this page from the bioRxiv website.
CAPTCHA
This question is for testing whether or not you are a human visitor and to prevent automated spam submissions.
Share
Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
Enrique J. Schwarzkopf, Juan C. Motamayor, Omar E. Cornejo
bioRxiv 482299; doi: https://doi.org/10.1101/482299
Digg logo Reddit logo Twitter logo Facebook logo Google logo LinkedIn logo Mendeley logo
Citation Tools
Genetic differentiation and intrinsic genomic features explain variation in recombination hotspots among cocoa tree populations
Enrique J. Schwarzkopf, Juan C. Motamayor, Omar E. Cornejo
bioRxiv 482299; doi: https://doi.org/10.1101/482299

Citation Manager Formats

  • BibTeX
  • Bookends
  • EasyBib
  • EndNote (tagged)
  • EndNote 8 (xml)
  • Medlars
  • Mendeley
  • Papers
  • RefWorks Tagged
  • Ref Manager
  • RIS
  • Zotero
  • Tweet Widget
  • Facebook Like
  • Google Plus One

Subject Area

  • Genomics
Subject Areas
All Articles
  • Animal Behavior and Cognition (3574)
  • Biochemistry (7517)
  • Bioengineering (5479)
  • Bioinformatics (20675)
  • Biophysics (10257)
  • Cancer Biology (7931)
  • Cell Biology (11583)
  • Clinical Trials (138)
  • Developmental Biology (6563)
  • Ecology (10135)
  • Epidemiology (2065)
  • Evolutionary Biology (13537)
  • Genetics (9498)
  • Genomics (12788)
  • Immunology (7871)
  • Microbiology (19451)
  • Molecular Biology (7614)
  • Neuroscience (41873)
  • Paleontology (306)
  • Pathology (1252)
  • Pharmacology and Toxicology (2179)
  • Physiology (3249)
  • Plant Biology (7007)
  • Scientific Communication and Education (1291)
  • Synthetic Biology (1942)
  • Systems Biology (5406)
  • Zoology (1107)