JD Campbell, PhD

🖥️ & 🧬
#Genomics
#CropResearch
#PlantResearch

Soybean Symposium

2026 NDSU #Soybean Symposium - Communication in Science
On March 5, 2026 in Fargo, ND
www.ndsu.edu/agriculture/...
The symposium bridges multiple disciplines: soybean agronomy, #breeding, foster collaboration, & develop new networks for cutting edge soybean #research.
#PlantScience

Symposium // Missouri Soybean Center // University of Missouri US Soybean Symposium, Missouri Soybean Center

2026 Missouri #Soybean Symposium
This free in-person symposium is open to researchers, students, industry, farmers, and other stakeholders interested in soybean.
This symposium will be held at University of Missouri, Columbia, MO.
soybeancenter.missouri.edu/symposium/
#PlantScience

USDA-ARS Computational Plant Biology Fellowship
- Use computational biology & ML to gather information about gene function in the legume family
- Identify correspondences among agronomically important genes across legume family.
www.zintellect.com/Opportunity/...
🧬 🖥️
🧪
🌾
#plantsciencejobs

The theme of the 2026 #Soybean Breeders Workshop 🌱🧬is: Abiotic Stress.

Topics include:
- abiotic stress resistance breeding methods
- physiology of stress tolerance
- developments in high-throughput phenotyping technology
- and more

Registration opens soon.
#plantscience
#plantbreeding

May 2025 SoyBase Update:
Newest tool from SoyBase: Allele Search
- Search for alleles within a gene and flanking region
- Search for alleles within a region of a chromosome
Link to tool: www.soybase.org/tools/allele...
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Link to update:
eocampaign1.com/web-version?...

Discover the fast-growing field of plant single-cell biology, interact with pioneers and experts in various aspects of single-cell biology, estimate its future impact on your research, and develop your collaborative network.
www.grc.org/single-cell-...
#plantscience
@plantpostdocs.bsky.social

SoyBase.org April 2025 Update Soy2025 abstract deadline is approaching and the Soybean Career Awards nominations are open.

April 2025 SoyBase Update:
- Soy2025 Abstract submission deadline approaching
- Soybean Career Award nomination open
- Survey to tell the SoyBase team how we are doing
eocampaign1.com/web-version?...

2025 NAPB Annual Meeting, taking place May 19–23 at the breathtaking Outrigger Kona Resort and Spa on Hawai‘i Island.
www.napbannualmeeting.org
Student opportunities to present research, connect with mentors, and explore career paths
#PlantBreeding
#PlantScience 🧪

Advancements in genomic research reveal alternative transcription initiation sites in thousands of soybean genes In 2010, Jianxin Ma, a professor of agronomy, and his collaborators built the first reference genome for soybeans on the widely studied Williams 82 variety. Thousands of scientists and plant breeders ...

The database I curate was highlighted in a Purdue University new post.

“The database serves as an important resource for both basic and applied research. By making our data available there, we catalyze further research." said Professor Ma
ag.purdue.edu/news/2024/11...

There is still time to register for the Soybean Breeders' Workshop! The theme this year is Pathology & Breeding Innovations. There are 10 days submit a poster abstract.

Plus, there are a few spots left in the Effective Visualization Techniques workshop!
www.soybase.org/community/sb...

Great presentation from @johannconfais.bsky.social at #PAG2025 #PAG32 on the first result obtained with panREPET tool a non reference centric approach

If you are at #PAG32 and want to learn more about how long read sequencing is enabling plant and soil microbiome research, come by our session this evening in Pacific H-I at 6:20.

Hey #PAG32, don’t miss the Compositae session this morning at 10:30am! @reidselby.bsky.social will be presenting new work on capitulum development and lettuce genomics 🥬🌻

How long does it take to commercialize a GMO tomato? At #PAG32 Cathie Martin shares the journey of the purple tomato.

Amazing talk from Cathie Martin at #PAG32 today on how crops can be fortified through biotechnology to improve diets and address the global challenge of escalating chronic disease.

#PAG2025 | #PAG32 continues! Todays highlights are the Bioinformatics session (starting now in Pacific A) and the Galaxy Workshop (starting at 4pm in T&C D)!

Fantastic turnout and standing room only at the #PacBio workshop at #PAG32!

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...

#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...

#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

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 ...

#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/

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...

#PAG32 | #PAG2025
Dr. Wattenburger
Genome Graph vs linear reference
- Genome Graph: Efficient representation of a population of genomes
www.nature.com/articles/s41...

#PAG32 | #PAG2025
Dr. Cassandra J. Wattenburger presents about
"Evaluating Genome Graph Quality for Zea mays with Minigraph-Cactus" in the Application of Genetics and Genomics for Large-scale Breeding Programs workshop

#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)

#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?

#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

#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

#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

#PAG32 | #PAG2025
Dr. Filiault speaking about "Evaluating and Incorporating Diverse Maize Genomes through the Bayer Haplotype Resource (BAHAR)"

Diverse Germplasm:
Broad source of potential new variation
Select for local important traits
Open pollated populations

Low-pass sequencing: leveraging entire genomes for trait selection WATCH ON DEMAND | This webcast took place on: Wednesday 26 April 2023

#PAG32 | #PAG2025
Dr. Lee
What will this LRLP get us?
- Selection Accuracy
- Large Inserion Capture
nature.com/articles/d44...
Publication has been submitted to bio-archive and should be availble soon.