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A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens.

Juan Viruel1, María Conejero1, Oriane Hidalgo1,2

  • 1Royal Botanic Gardens, Kew, Richmond, United Kingdom.

Frontiers in Plant Science
|August 10, 2019
PubMed
Summary

High-throughput sequencing (HTS) effectively determines plant ploidy from herbarium samples, overcoming limitations of flow cytometry for historical specimens. This method reveals polyploidization events in ancient plant collections.

Keywords:
Dioscoreacrop wild relativesflow cytometryphylogenomicspolyploidysequence capturewhole genome duplicationyams

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Area of Science:

  • Plant evolutionary biology
  • Genomics
  • Bioinformatics

Background:

  • Whole genome duplication (WGD) is frequent in plants, but ploidy status is unknown for most species.
  • Traditional ploidy determination methods like flow cytometry often require fresh tissue.
  • Dried plant specimens, including herbarium vouchers, offer a valuable historical resource but pose challenges for ploidy analysis.

Purpose of the Study:

  • To evaluate the efficacy of flow cytometry for determining ploidy levels in dried plant samples, including historical herbarium specimens.
  • To develop and optimize a high-throughput sequencing (HTS)-based method for estimating ploidy using allelic frequencies from nuclear genes in dried tissues.
  • To assess the potential of HTS for uncovering ploidy diversity and polyploidization events in historical plant collections.

Main Methods:

  • Comparison of flow cytometry and HTS-based methods for ploidy determination using yam (Dioscorea) tissues of varying age, drying method, and quality.
  • Analysis of allelic frequencies from nuclear genes using a target-capture HTS method.
  • Validation of HTS ploidy estimates against known ploidy levels in dried samples and comparison with flow cytometry results from herbarium specimens.

Main Results:

  • Flow cytometry showed a low success rate (5.9%) for determining ploidy from herbarium specimens older than fifteen years.
  • The optimized HTS method successfully estimated ploidy for 91.7% of 85 analyzed herbarium samples across the Dioscorea phylogeny.
  • HTS analysis revealed ploidy diversity and allowed the determination of polyploidization events from samples dating back up to two centuries.

Conclusions:

  • High-throughput sequencing offers a robust method for assessing plant ploidy from historical herbarium collections, significantly outperforming flow cytometry for aged samples.
  • This HTS approach enables the study of ploidy variation and evolutionary dynamics, including crop domestication, using historical botanical records.
  • The findings highlight the potential of leveraging historical collections for genomic studies of plant evolution and diversification.