JD Campbell, PhD
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campbell-jd-phd.bsky.social
JD Campbell, PhD
@campbell-jd-phd.bsky.social
59 followers 84 following 28 posts
Soybean geneticist and data curator for a soybean genomic, genetic and breeding database (SoyBase.org).
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campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Wattenburger
New publication about evaluation:
ieeexplore.ieee.org/document/108...
Other tools to develop pan-genome graphs
PGGB: www.nature.com/articles/s41...
A Novel Methodology for a Comprehensive Analysis of Genomic Sequence-to-Graph Alignment Tools
Genome graphs have proved to be a more compact and efficient way of representing genetic inter- and intra-individual variability. Although they overcome the traditional sequence-based genome reference...
ieeexplore.ieee.org
January 13, 2025 at 10:32 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Wattenburger
2) Completeness and Contents
- Coding regions well represented, clearer relationship to traits, better placement certainty

Mysterious missing regions are research opportunites
-Maize Knobs
- Repetition
- Non-systematic regions
January 13, 2025 at 10:32 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Wattenburger
Assessing genome graph quality using Minigraph-cactus
1) Structural stability
- Issues: Complexity, genome order and Clipping
- variability was very low
2) Completeness and contents
pubmed.ncbi.nlm.nih.gov/37165083/
Pangenome graph construction from genome alignments with Minigraph-Cactus - PubMed
Pangenome references address biases of reference genomes by storing a representative set of diverse haplotypes and their alignment, usually as a graph. Alternate alleles determined by variant callers ...
pubmed.ncbi.nlm.nih.gov
January 13, 2025 at 10:32 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Wattenburger
Genome Graph vs linear reference
- Genome Graph: Efficient representation of a population of genomes
www.nature.com/articles/s41...
Plant pangenomes for crop improvement, biodiversity and evolution - Nature Reviews Genetics
Plant pangenomes have had a transformative impact on crop enhancement, biodiversity conservation and evolutionary research. This Review delves into the application of plant pangenomes for underst...
www.nature.com
January 13, 2025 at 10:32 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Filiault
BAHAR summary: progress & expansion
Successful field trials to hybrids
Sequencing-based genotype works
- Practical Haplotype graph based genotyping & variant calling
Ambitious plans for 2025 & beyond
- Functional BAHAR-omics (long read haplotype and transcriptomics)
January 13, 2025 at 9:59 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Filiault
BAHAR lines contain ~10% diverse windows
used short read sequencing (~5x coverage)
- Most genomic windows contain diverse material but percent varies among and across chromosomes.
- Does low diverse % truly reflect resistance to introgressions?
January 13, 2025 at 9:59 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Filiault
How to genotype lines without established markers? Sequencing!
Step 1: Optimize variant calling
- Practical haplotype graph of 4 elite parents
Step 2: Identify non-elite regions by divergence
- Non-elite (diverse) regions have high SNP density
January 13, 2025 at 9:59 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Filiault
BAHAR line construction
> 2,500 varieties (1750 were tropical from USDA Plant Germplasm System; remainder from internal open pollinated germplasm)
- Selection for elite lines
- Field trials, Genotyping, GWAS, Pangenome resources
January 13, 2025 at 9:59 PM
campbell-jd-phd.bsky.social
#PAG32 | #PAG2025
Dr. Filiault
BAHAR - a mapping population
- Directly incorporate lines of interest
- Describe new alleles and their phenotypic effects
- Data to explore genetic and GxE interactions
January 13, 2025 at 9:59 PM