USA
November 26, 2025
Thanksgiving is almost here, and we’re filled with gratitude for the food on our tables and the science that helps make this possible. From the corn in a casserole to the apples in a pie, today’s agriculture depends on research that keeps crops productive, livestock healthy, and food systems sustainable.
At PacBio, we’re proud to see genomics playing an increasingly vital role in that story. As we get ready to connect with the global plant and animal genomics community at the Plant and Animal Genome (PAG) Conference in January, we’re reflecting on how accurate, long-read sequencing is helping strengthen the foundations of sustainable agriculture around the world.
Genomics for sustainable agriculture
Feeding a global population means embracing innovation and using tools like genomics to make agriculture more productive, adaptive, and environmentally sound. With high-quality genomic data, researchers can identify valuable traits, improve breeding programs, protect against pests and diseases, and guide genome engineering efforts that enhance resilience and sustainability.
HiFi sequencing combines exceptional accuracy with long reads to produce reference-quality halplotype-resolved pangenomes for nearly any species. The insights revealed in these HiFi genomes enable three key areas of agricultural innovation:
- Breeding: Haplotype-resolved pangenomes give breeders a detailed map of genetic diversity, accelerating the discovery of traits like yield, flavor, and disease resistance.
- Pest and disease research: HiFi sequencing supports whole-genome, RNA, targeted, and metagenomic sequencing that helps detect, understand, and respond to emerging threats.
- Germplasm recharacteriztion: With precise and efficient genome-wide genotyping, HiFi sequencing supports agricultural researchers in selecting for valuable traits and improving breeding programs aimed at sustainability and food security.
Together, these applications help create a food system that’s more efficient, secure, and resilient, benefitting both people and the planet.
HiFi on every table
This Thanksgiving, many of the foods we enjoy are shaped by advances in agrigenomics. From potatoes to pecans, HiFi sequencing has helped scientists better understand, protect, and improve the plants that make up our meals.
These examples showcase how high-quality genomic data informs agricultural research and how innovations in sequencing translate to the crops that end up on our tables.
Haplotype-resolved breeding with HiFi sequencing
Modern breeding depends on having access to the full picture of genetic diversity. Traditional reference genomes capture only a single version of a species, leaving much of the natural variation unseen. Yet, breeders need to understand how genetic differences across populations shape traits like yield, resilience, and health.
This is where pangenomes come in. By combining multiple high-quality assemblies, pangenomes reveal the complete range of genetic diversity within a species. They uncover structural variants, novel genes, and haplotypes that single reference genomes often miss, offering a deeper understanding of the traits that drive agricultural success.
HiFi sequencing provides the accuracy, long reads, and phasing power needed to build these detailed genomic resources. Its ability to resolve complex and repetitive regions ensures that every genome contributes to a true, comprehensive view of diversity. With this level of insight, breeders can make more informed decisions, preserve genetic diversity, and accelerate improvement across crops and livestock.
Protecting crop and livestock health through HiFi sequencing
Pests and diseases remain one of the greatest risks to global food security. Understanding these threats at the genomic level helps researchers track pathogens, identify resistance genes, and design strategies to strengthen biosecurity.
HiFi sequencing supports this work through a range of applications: whole genome sequencing for invasive species monitoring, RNA sequencing to characterize plant-host adaptations, targeted sequencing for understanding fungicide resistance, and metagenomics for microbial community profiling.
These capabilities help researchers anticipate and respond to emerging threats, protecting the health of both crops and livestock while supporting sustainable production systems.
Population-scale low-coverage sequencing for a sustainable future
To meet mounting agricultural pressures from climate change, emerging diseases, and resource constraints, breeders need a clear understanding of the genetic diversity that underpins resilient, productive crops and livestock.
Population-scale low-coverage sequencing offers a powerful way to explore that diversity. By sequencing many individuals at lower depth, researchers can uncover patterns of genetic variation that shape traits such as yield, nutrition, and stress tolerance. HiFi sequencing strengthens this approach by providing the accuracy and long reads needed to capture large structural variants and variation in complex regions of the genome that other methods often miss or overlook.
For example, in the study by Lee et al. (2025), low-pass sequencing in a peanut breeding population allowed researchers to examine how genetic variation across many samples correlates with phenotypic traits. Their work demonstrates how HiFi-enhanced low-coverage approaches can support large-scale genome-to-phenome investigations in agriculture.
By combining the efficiency of low-coverage sequencing with the accuracy of HiFi data, researchers can uncover the full range of genetic diversity that drives key traits, helping breeders make informed choices and advance more resilient and sustainable agriculture.
The genomics behind every harvest
From breeding programs to population-scale genotyping that capture genetic diversity, genomics is helping shape a more secure and resilient food future. HiFi sequencing is at the heart of that progress, powering the discoveries that make agriculture stronger from root to table.
To learn more about how PacBio HiFi sequencing supports agrigenomics, explore our agrigenomics webpage and download the agrigenomics brochure.
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