Agrigenomics

Drive innovation in agriculture like never before by harnessing the full power of genomics

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Agrigenomics solutions

Whether your focus is crop or livestock breeding, genetic engineering, or pest and disease mitigation, HiFi sequencing delivers genomic data of unparalleled quality and detail to meet the demands of your most ambitious research programs.

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Genomic breeding

Use HiFi sequencing to breed better by quickly assembling phased reference-quality genomes for the imputation of the most desirable complex traits.

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Genetic engineering of plants and animals

Create high-quality reference genomes, validate constructs, confirm edits, and evaluate off-target effects quickly and reliably with HiFi reads.

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Pest and disease research

Dig into genomes and transcriptomes of the highest quality and specificity. Uncover hard-to-find novel genes responsible for traits like immunity, metabolic detoxification, and pesticide resistance.

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Tackle global challenges to feed a growing population

As the challenges of a growing global population and a changing climate mount, cutting-edge agricultural biotechnology is needed to drive scientific advances to sustainably feed our world.

At PacBio, we provide state-of-the-art genome sequencing solutions that enable you to uncover and harness agrigenomic insights from data of unparalleled quality and detail.

Use these biological insights to enhance marker development, facilitate the production of more nutritious foods, safe-guard crop and livestock health, and increase agricultural yields for the world of tomorrow, today.

Common questions about genomics in agriculture

A pangenome is a collection of genomes from a population of species that represents the genetic diversity of the population. Pangenomes typically are 20-30 genomes depending on the biodiversity of the population. Pangenomes obtained through HiFi sequencing can be resolved into haplotype databases for enhanced trait imputation for desirable phenotypes for breeding.

Whole genome sequencing, transcriptome sequencing, epigenomics, metagenomics, and the targeted sequencing of plants, animals, fungi, bacteria, and complex populations can all be leveraged for your agricultural research in different areas. This includes breeding, pest management, and genome engineering.

Genome engineering, or gene editing, is a process where scientists can change the genetic information of agriculturally important species with biomolecular tools such as CRISPR-Cas9. HiFi sequencing can help you validate where edits are made on a genome-wide or targeted basis. It can also help you design more efficient workflows with extremely accurate genomic information.

HiFi sequencing enables agriscientists to generate haplotype-resolved, high-quality genomes that span most variant types. Complex traits, such as drought resistance and pest resistance, can be explained by a combination of genes, structural variants, copy number variants, and more. Agriscientists can harness this genetic information to inform marker development.

Agrigenomics in action

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Soybean pangenome captures genetic diversity

Learn how HiFi reads were used to identify key structural variants for functional studies and breeding of one of the world’s most important sources of protein.

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Whole genome sequencing best practices

See recommended workflows for procuring reference-quality genomes, de novo.

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HiFi sequencing for a better view into the bovine genome

Evaluate how HiFi sequencing was used to assemble a bovine pangenome with hundreds of structural variants important to phenotype — all while achieving coverage, quality, accuracy, and completeness metrics that cannot be matched.

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Explore

Did you know we have a comprehensive library of articles, reports, papers, and videos related to plant + animal genomics?

Explore resources

“…high-quality [HiFi] genomes enabled the identification of numerous complex variations that cannot be detected by simply mapping short reads to a single genome…”

—Yucheng Liu et al., Cell 2020
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Agrigenomics for crop and livestock breeding

Unlock whole-new capabilities for your plant or animal breeding programs with long, high-quality, genomic reads made possible only with HiFi sequencing.

• Build reference-quality, haplotype-resolved pangenomes for breeding.
• Impute desirable traits to SNPs, structural variants, and complex genotypes.
• Capture genomic variants on a genome-wide scale for outbreds, inbreds, and populations.

Agrigenomics for genome engineering

Obtain the detailed sequence information you need for your most sophisticated gene editing programs using highly accurate HiFi sequencing data.

• Speed up design workflows with accurate reference genomes.
• Find splice variants within the transcriptome.
• Validate edited sites.
• Capture on and off-target effects.
• Determine structural rearrangements across chromosomes.

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Agrigenomics for pest and disease research

Find genomic clues hidden in the highly variable genetics of organisms such as insects, weeds, and fungi harming agricultural yield to tackle pests on the molecular level.

• Capture pest genomic diversity in incredible detail.
• Generate complete genome assemblies from just 5 ng of DNA input.
• Build annotations to better understand gene functions for targeting.

AGRIGENOMICS BLOG SERIES

Dive in to our latest blog series to learn more about biodiversity to advance breeding, how genomics can protect crops and livestock, and what improved accuracy means for gene editing workflows.

Crop and livestock breeding     Pest and disease research     Genome engineering

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PacBio vs Oxford Nanopore*

Long-read sequencing performance
PacBio HiFi sequencing Oxford Nanopore
Coverage required to meet quality targets
19x diploid 56x diploid
CPU hours required 600 2200
Peak memory usage required 200GB 750GB

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*Alexander S. Leonard, Danang Crysnanto, Zih-Hua Fang, Michael P Heaton, Brian L. Vander Ley, Carolina Herrera, Heinrich Bollwein, Derek M. Bickhart, Kristen L. Kuhn, Timothy PL. Smith, Benjamin D. Rosen, Hubert Pausch. Structural Variant-based Pangenome Construction has Low Sensitivity to Variability of Haplotype-resolved Bovine Assemblies. [Preprint] bioRxiv 2021.11.02.466900; doi: https://doi.org/10.1101/2021.11.02.466900

Agrigenomics applications

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Whole genome sequencing

Quickly and affordably create contiguous, complete, and correct de novo assemblies of even the most complex genomes.

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Structural variant calling

Acquire high-sensitivity variant calls with low false discovery rates to gain actionable insights across populations.

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Targeted sequencing

Combine long-read sequencing with targeted sequence capture for a comprehensive view of specific genomic regions of interest, regardless of size.

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RNA sequencing

Leverage the isoform sequence (Iso-Seq) method to obtain full-length cDNA sequences — from 5’ to the poly-A tail — to confidently characterize the full transcriptome.

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Sequel II Systems

Sequel II systems can generate longer reads with greater accuracy and throughput, at a significantly lower cost.

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Talk with an expert

If you have a question, need to check the status of an order, or are interested in purchasing an instrument, we're here to help.