Low-pass whole-genome sequencing identifies apomictic apple genotypes in USDA germplasm

What the study did

The authors developed and applied a screening method that uses short-read whole-genome sequencing at moderately low coverage to determine whether embryos are clones of their maternal parent (apomixis) in Malus (apple) germplasm. Rather than relying on indirect readouts, this approach compares DNA sequences of mother and progeny directly using low-pass sequencing.

Why this matters

Apomixis — clonal seed production — can preserve desirable hybrid genotypes without sexual segregation. Advances in understanding apomixis genes have potential breeding applications, but practical screening methods for detecting apomictic genotypes across diverse germplasm are needed. Traditional flow cytometry seed screens have been the dominant approach but are indirect and can fail in some species or circumstances. This work evaluates a sequencing-based alternative that is relatively low-cost and rapid.

How the screen was executed

Key results

• The sequencing screen directly identified 17 previously undescribed apomictic genotypes among the sampled Malus accessions.
• Flow cytometry screens detected additional apomictic cases and helped clarify certain reproductive behaviors and noise sources in low-coverage datasets.
• The combined use of sequencing and flow cytometry improved resolution of reproductive outcomes compared with using either method alone.

Practical implications for breeders and germplasm curators

• Low-pass whole-genome sequencing can be used as a screening tool to detect apomictic genotypes across diverse collections at a lower per-sample cost than high-coverage sequencing or extensive marker genotyping.
• Sequencing provides a direct test for clonality by comparing maternal and embryo genotypes, which complements the ploidy or DNA-content–based inference of flow cytometry.

Data and tools

All demultiplexed sequencing data are available on NCBI SRA under BioProject PRJNA1379592. Scripts for sequence processing, variant calling, statistical modeling, and visualization are provided at the authors' GitHub repository: https://github.com/goeckeritz/high-throughput-sequencing-screen-for-apomixis.

Study context and contributors

The paper reports work by Charity Z. Goeckeritz, Václav Polcar, Benjamin Gutierrez, Tomáš Urfus, and Alex Harkess. Funding sources included National Science Foundation grants, USDA ARS funds to the Plant Genetic Resources Unit, and a Charles University grant. The authors note that sequencing-based screens will become more practical as technologies advance, enabling routine genetic studies of plant reproduction.