Uploaded January 2026 | Updated September 2026, 1 day ago
Identify breeding markers that short-read sequencing misses. In this presentation from the Plant and Animal Genome (PAG) Conference, learn how long-read low-pass (LRLP) sequencing and CiFi-adapted scaffolding are solving two major challenges in polyploid crop genomics.
Blueberry breeders need markers for flowering time, fruiting time, and fruit weight—but the autotetraploid genome makes variant detection difficult. Kendall Lee, PhD built a six-genome pangenome for southern highbush blueberry using KhufuPAN, then compared LRLP to short-read genotyping. The results: 32% more variants detected, including structural variants critical for QTL discovery. For the hexaploid rabbiteye genome, where standard Omni-C scaffolding failed, CiFi-adapted long-read Hi-C achieved chromosome-scale assembly with just 4x coverage.
*What you'll learn*
- Apply long-read low-pass sequencing for cost-effective genotyping in polyploid crops
- Build a pangenome reference using KhufuPAN and reference-based scaffolding
- Use CiFi to rescue difficult genome assemblies where standard Hi-C fails
- Identify QTLs for phenological traits using the QTLVar pipeline
*Featured speakers*
- Kendall Lee, PhD, USDA-NIFA Postdoctoral Fellow and Veil Genomics Co-Founder
*Chapters*
00:00 Introduction
00:56 Why blueberries matter
01:53 Blueberry types and growing regions
03:03 Key breeding traits
04:36 Building genomic resources
05:11 Suziblue reference genome assembly
06:37 Pangenome construction with KhufuPAN
07:30 Long-read low-pass sequencing
08:52 LRLP vs short-read variant detection
10:46 Introduction to CiFi
11:47 CiFi-adapted Omni-C for rabbiteye
14:28 Key takeaways
*Resources*
- Long-read low-pass for plant breeding: pacb.com/blog/publication-spotlight-advancing-plant-breeding-with-long-read-low-pass-sequencing
- Agrigenomics solutions: pacb.com/plant-animal-sciences/agrigenomics
- CiFi method introduction: pacb.com/press_releases/pacbio-and-uc-davis-researchers-introduce-cifi-a-new-long-read-3c-method-that-enables-chromosome-scale-assemblies-from-a-single-smrt-cell
What polyploid species would you like to see tackled with these methods? *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
#Blueberry #Pangenomics #HiFiSequencing
Identify breeding markers that short-read sequencing misses. In this presentation from the Plant and Animal Genome (PAG) Conference, learn how long-read low-pass (LRLP) sequencing and CiFi-adapted scaffolding are solving two major challenges in polyploid crop genomics.
Blueberry breeders need markers for flowering time, fruiting time, and fruit weight—but the autotetraploid genome makes variant detection difficult. Kendall Lee, PhD built a six-genome pangenome for southern highbush blueberry using KhufuPAN, then compared LRLP to short-read genotyping. The results: 32% more variants detected, including structural variants critical for QTL discovery. For the hexaploid rabbiteye genome, where standard Omni-C scaffolding failed, CiFi-adapted long-read Hi-C achieved chromosome-scale assembly with just 4x coverage.
*What you'll learn*
- Apply long-read low-pass sequencing for cost-effective genotyping in polyploid crops
- Build a pangenome reference using KhufuPAN and reference-based scaffolding
- Use CiFi to rescue difficult genome assemblies where standard Hi-C fails
- Identify QTLs for phenological traits using the QTLVar pipeline
*Featured speakers*
- Kendall Lee, PhD, USDA-NIFA Postdoctoral Fellow and Veil Genomics Co-Founder
*Chapters*
00:00 Introduction
00:56 Why blueberries matter
01:53 Blueberry types and growing regions
03:03 Key breeding traits
04:36 Building genomic resources
05:11 Suziblue reference genome assembly
06:37 Pangenome construction with KhufuPAN
07:30 Long-read low-pass sequencing
08:52 LRLP vs short-read variant detection
10:46 Introduction to CiFi
11:47 CiFi-adapted Omni-C for rabbiteye
14:28 Key takeaways
*Resources*
- Long-read low-pass for plant breeding: pacb.com/blog/publication-spotlight-advancing-plant-breeding-with-long-read-low-pass-sequencing
- Agrigenomics solutions: pacb.com/plant-animal-sciences/agrigenomics
- CiFi method introduction: pacb.com/press_releases/pacbio-and-uc-davis-researchers-introduce-cifi-a-new-long-read-3c-method-that-enables-chromosome-scale-assemblies-from-a-single-smrt-cell
What polyploid species would you like to see tackled with these methods? *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
#Blueberry #Pangenomics #HiFiSequencing
