Uploaded July 2026 | Updated September 2026, 2 hours ago
Long-read low-pass genotyping found 16x more variants than short-read low-pass in this blueberry experiment. 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.
*Key takeaways*
- 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.
*Featured speakers*
- Kendall Lee, PhD, Co-Founder, Veil Genomics
*Chapters*
00:00 Introduction and talk overview
00:53 Blueberry breeding context
01:36 Why blueberry genomes get complicated
03:40 Traits of interest: flowering, fruit set, and fruit weight
05:57 Building a Southern Highbush reference genome
07:35 Reference-based scaffolding and the blueberry pangraph
09:21 Rabbiteye assembly and CiFi
11:14 Using HiFi data for genotyping
12:44 Peanut detour: long-read low-pass in silico
14:31 Wet-lab pipeline and read retention
15:10 Coverage versus depth
16:28 Variant detection and SV impact
17:29 Tomato spotted wilt virus resistance example
18:33 Back to blueberry LRLP
19:28 LRLP versus SRLP variant discovery
20:04 Fruit-weight region missed by SRLP
21:03 Flowering and fruit-set marker examples
21:50 What marker timing can mean for growers
22:56 Veil Genomics services and analytics
25:01 Acknowledgments
*Resources*
- Plant and animal genomics with PacBio HiFi systems: pacb.com/plant-animal-sciences
- HiFi sequencing technology: pacb.com/technology/hifi-sequencing
- Revio system for accurate long-read sequencing at scale: pacb.com/revio
- Sequencing 101: long-read sequencing: pacb.com/blog/long-read-sequencing
If you run low-pass genotyping, which constraint is harder in your system: sample prep, coverage, or marker interpretation? *Comment below.*
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: pacb.com/legal-and-trademarks
For Research Use Only. Not for use in diagnostic procedures.
#PacBio #HiFiSequencing #PlantGenomics
Long-read low-pass genotyping found 16x more variants than short-read low-pass in this blueberry experiment. 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.
*Key takeaways*
- 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.
*Featured speakers*
- Kendall Lee, PhD, Co-Founder, Veil Genomics
*Chapters*
00:00 Introduction and talk overview
00:53 Blueberry breeding context
01:36 Why blueberry genomes get complicated
03:40 Traits of interest: flowering, fruit set, and fruit weight
05:57 Building a Southern Highbush reference genome
07:35 Reference-based scaffolding and the blueberry pangraph
09:21 Rabbiteye assembly and CiFi
11:14 Using HiFi data for genotyping
12:44 Peanut detour: long-read low-pass in silico
14:31 Wet-lab pipeline and read retention
15:10 Coverage versus depth
16:28 Variant detection and SV impact
17:29 Tomato spotted wilt virus resistance example
18:33 Back to blueberry LRLP
19:28 LRLP versus SRLP variant discovery
20:04 Fruit-weight region missed by SRLP
21:03 Flowering and fruit-set marker examples
21:50 What marker timing can mean for growers
22:56 Veil Genomics services and analytics
25:01 Acknowledgments
*Resources*
- Plant and animal genomics with PacBio HiFi systems: pacb.com/plant-animal-sciences
- HiFi sequencing technology: pacb.com/technology/hifi-sequencing
- Revio system for accurate long-read sequencing at scale: pacb.com/revio
- Sequencing 101: long-read sequencing: pacb.com/blog/long-read-sequencing
If you run low-pass genotyping, which constraint is harder in your system: sample prep, coverage, or marker interpretation? *Comment below.*
*Subscribe for more PacBio genomics content:*
youtube.com/@PacificBiosciences?sub_confirmation=1
Learn more about PacBio at pacb.com
Legal & Trademarks: pacb.com/legal-and-trademarks
For Research Use Only. Not for use in diagnostic procedures.
#PacBio #HiFiSequencing #PlantGenomics
