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Past Presentations
16x More Variants for Blueberry Breeding with Long-Reads
Kendall Lee, PhD
In this PRISM 2026 presentation, Kendall Lee, PhD, Co-Founder of Veil Genomics, shows how HiFi long-read sequencing and long-read low-pass (LRLP) genotyping can connect blueberry genome assembly, pangenome mapping, and trait discovery.
Why Southern Highbush and Rabbiteye blueberries are challenging polyploid breeding systems.
How HiFi data, Omni-C, and CiFi supported reference genome and scaffolding work.
What peanut and blueberry examples showed about long-read low-pass coverage, read retention, and variant detection.
How LRLP identified 16x more variants overall than SRLP in the blueberry experiment and 59 vs 22 potential QTL regions.
How allele combinations translated to flowering and fruiting dates with real-world grower implications.
Long-read sequencing is no longer limited to well-funded model organism programs. This presentation covers how LRLP sequencing unlocks genomics across the full tree of life — from microbes to complex polyploid crops and animals — and how pangenomes are replacing linear references to better represent structural variation.
How LRLP sequencing makes long-read accessible and deployable at population scale
Why pangenomes outperform linear references for structural variant representation
Long-read low-pass applications in plant and animal breeding programs
Improved genotyping accuracy using pangenome-based imputation scaffolds
Beyond the Reference: How Long Read Low Pass and Pangenomes are Shaping the Future of Genomics Across the Tree of Life
Alex Harkess, PhD
A Cost-Effective Pangenome-Based Platform for Genotype Imputation, QTL Mapping, and Selection Support in Plant and Animal Genomics
Josh Clevenger, PhD
Standard genotyping approaches leave researchers choosing between affordability and data quality. This presentation introduces a pangenome-based platform that closes that gap — enabling high-resolution imputation, QTL detection, and genomic selection at population scale without the cost of full WGS.
How pangenome graphs unlock structural variation that linear references miss
Cost-effective genotyping for breeding programs using long-read low-pass sequencing
QTL mapping and selection support across plant and animal species
Real-world case studies demonstrating imputation accuracy improvements
Blueberry Pangenomics and CiFi Assembly for Complex Polyploid Genomes
Kendall Lee, PhD
Polyploid crop genomes are among the most challenging in plant genomics. This PAG presentation walks through how long-read low-pass sequencing and CiFi-adapted scaffolding are solving two persistent problems: scalable genotyping in polyploids and assembly recovery when standard Hi-C approaches fail.
Long-read low-pass sequencing for cost-effective genotyping in polyploid crops
Pangenome reference construction using KhufuPAN and reference-based scaffolding
CiFi as a rescue strategy for difficult genome assemblies
QTL identification for phenological traits using the QTLVar pipeline
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