Individualized mating system estimation using genomic data

Jack Colicchio, Patrick J. Monnahan, Carolyn A. Wessinger, Keely Brown, James Russell Kern, John K. Kelly

Research output: Contribution to journalArticlepeer-review

5 Scopus citations

Abstract

The estimation of outcrossing rates in hermaphroditic species has been a major focus in the evolutionary study of reproductive strategies, and is also essential for plant breeding and conservation. Surprisingly, genomics has thus far minimally influenced outcrossing rate studies. In this article, we generalize a Bayesian inference method (BORICE) to accommodate genomic data from multiple subpopulations of a species. As an empirical demonstration, BORICE is applied to 115 maternal families of Mimulus guttatus. The analysis shows that low-level whole genome sequencing of parents and offspring is sufficient for individualized mating system estimation: 208 offspring (88.5%) were definitively called as outcrossed, 23 (9.8%) as selfed. After mating system parameters are established (each offspring as outcrossed or selfed and the inbreeding level of maternal plants), BORICE outputs posterior genotype probabilities for each SNP genomewide. Individual SNP calls are often burdened with considerable uncertainty and distilling information from closely linked sites (within genomic windows) can be a useful strategy. For the Mimulus data, principal components based on window statistics were sufficient to diagnose inversion polymorphisms and estimate their effects on spatial structure, phenotypic and fitness measures. More generally, mating system estimation with BORICE can set the stage for population and quantitative genomic analyses, particularly researchers collect phenotypic or fitness data from maternal individuals.

Original languageEnglish (US)
Pages (from-to)333-347
Number of pages15
JournalMolecular Ecology Resources
Volume20
Issue number1
DOIs
StatePublished - Jan 1 2020

Bibliographical note

Funding Information:
We thank C. Crawford, M. Warner, M. Orive, M.T. Holder, P. Stokes, A. Gaudinier, and M. Akman for input on the project and/or manuscript. We thank P. Vogler and J. Colicchio for field assistance and C. Friesen (U.S. Forest Service) for site access. This work was supported by grants from the National Institutes of Health to JKK (R01 GM073990) and the KU Botany Endowment to JC.

Funding Information:
We thank C. Crawford, M. Warner, M. Orive, M.T. Holder, P. Stokes, A. Gaudinier, and M. Akman for input on the project and/or manuscript. We thank P. Vogler and J. Colicchio for field assistance and C. Friesen (U.S. Forest Service) for site access. This work was supported by grants from the National Institutes of Health to JKK (R01 GM073990) and the KU Botany Endowment to JC.

Publisher Copyright:
© 2019 John Wiley & Sons Ltd

Keywords

  • BORICE
  • Mimulus
  • RAD-seq
  • outcrossing
  • selfing

PubMed: MeSH publication types

  • Journal Article

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