Send to

Choose Destination
Plant Methods. 2019 May 18;15:47. doi: 10.1186/s13007-019-0433-9. eCollection 2019.

A high-throughput amplicon-based method for estimating outcrossing rates.

Author information

1Institute for Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, House 26, 14476 Potsdam-Golm, Germany.
2Present Address: Molecular Genetics and Physiology of Plants, Faculty of Biology and Biotechnology, Ruhr University Bochum, Universitätsstraße 150, Building ND North, 44801 Bochum, Germany.
3Present Address: Department of Plant Biology, Swedish University of Agricultural, Sciences and Linnean Center for Plant Biology, Uppsala, Sweden.



The outcrossing rate is a key determinant of the population-genetic structure of species and their long-term evolutionary trajectories. However, determining the outcrossing rate using current methods based on PCR-genotyping individual offspring of focal plants for multiple polymorphic markers is laborious and time-consuming.


We have developed an amplicon-based, high-throughput enabled method for estimating the outcrossing rate and have applied this to an example of scented versus non-scented Capsella (Shepherd's Purse) genotypes. Our results show that the method is able to robustly capture differences in outcrossing rates. They also highlight potential biases in the estimates resulting from differential haplotype sharing of the focal plants with the pollen-donor population at individual amplicons.


This novel method for estimating outcrossing rates will allow determining this key population-genetic parameter with high-throughput across many genotypes in a population, enabling studies into the genetic determinants of successful pollinator attraction and outcrossing.


Amplicon sequencing; Capsella; Mixed mating; Outcrossing; Outcrossing rate

Conflict of interest statement

Competing interestsThe authors declare that they have no competing interests.

Supplemental Content

Full text links

Icon for BioMed Central Icon for PubMed Central
Loading ...
Support Center