New pre-print: “Leveraging ancestral recombination graphs for quantitative genetic analysis of rice yield in indica and japonica subspecies” by Ines Rebollo, Jana Obsteter, Daniel Tolhurst, Juan Rosas, and me www.biorxiv.org/content/10.1... - ThreadSky

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gregorgorjanc.bsky.social • 37 days ago

New pre-print: “Leveraging ancestral recombination graphs for quantitative genetic analysis of rice yield in indica and japonica subspecies” by Ines Rebollo, Jana Obsteter, Daniel Tolhurst, Juan Rosas, and me https://www.biorxiv.org/content/10.1101/2025.01.14.633033v1

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gregorgorjanc.bsky.social•37 days ago

This is from the MSc internship of Ines!

gregorgorjanc.bsky.social•37 days ago

We evaluated the application of an Ancestral Recombination Graph (ARG), encoded as a tree sequence, to characterise a breeding population, and for genomic prediction and genome-wide association studies.

gregorgorjanc.bsky.social•37 days ago

The ARG:

* Captured key biological signals
* Encoded genomic data more efficiently than conventional formats
* Resulted in the highest predictive ability when combining both subspecies (though not by much)

gregorgorjanc.bsky.social•37 days ago

Taken together, the results demonstrated the potential of ARGs for the quantitative genetic analysis of diverse populations.

gregorgorjanc.bsky.social•37 days ago

This builds upon the work of tskit community - there is an advanced manuscript in the pipeline on how to build relationship/relatedness matrix from tree sequence encoding of an ARG!

gregorgorjanc.bsky.social•37 days ago

After building the ARG, we demonstrated it captures biological signals using genealogical nearest neighbors (GNN) - it clearly distinguished indica and japonica rice subspecies and effectively represented population structure.

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