Local trees from two genomic regions showed distinct patterns: (A) revealed deep separation between indica and japonica, linked to the DST gene associated with panicle length in japonica. The (B) region segregated in both subspecies and was linked to panicle traits in both. - ThreadSky

About ThreadSky

gregorgorjanc.bsky.social • 37 days ago

Local trees from two genomic regions showed distinct patterns: (A) revealed deep separation between indica and japonica, linked to the DST gene associated with panicle length in japonica. The (B) region segregated in both subspecies and was linked to panicle traits in both.

Comments

gregorgorjanc.bsky.social•37 days ago

The ARG encoded genomic data more efficiently than the standard VCF: the tree sequence file for all chromosomes was 62 MB, compared to 228 MB for the VCF—nearly four times smaller!

gregorgorjanc.bsky.social•37 days ago

The age distributions for (A) nodes (ancestors), (B) mutations, and (C) SNP sites (i.e., first mutation at each site) were heavily right-skewed towards the present (as expected).

gregorgorjanc.bsky.social•37 days ago

(A) The standard site-based relationship matrix (SRM, VanRaden’s) and (B) the ARG-based branch relationship matrix (BRM) revealed similar population structure, with highly correlated (C) diagonal and (D) off-diagonal elements, though on different scales.

gregorgorjanc.bsky.social•37 days ago

GWAS hits with SRM (A) and BRM (B) were similar

gregorgorjanc.bsky.social•37 days ago

In cross-validation for yield prediction, the ARG-based branch relationship matrix (BRM) demonstrated higher predictive ability than the standard site-based relationship matrix (SRM) when combining both subspecies.

Posting Rules

Be respectful to others
No spam or self-promotion
Stay on topic
Follow Bluesky's terms of service

Comments

Posting Rules

Reply