Learn how KHUFU can provide accurate genomic solutions for plant improvement.
Accurate Genomic Solutions for Plant Improvement
Future yield growth in agriculture is essential to keep up with global demand.
By 2050, the global population is expected to reach 9.8 billion, putting a great stress on food supply. New advances offer great promise for additional yield gains by making it cheaper and faster to map genetic codes of plants and test for desired DNA traits.
The Clevenger lab at the HudsonAlpha Institute for Biotechnology, a nonprofit institute dedicated to developing and applying scientific advances in agriculture through genomics, has developed a computational tool to help identify genetic factors to select for beneficial agricultural traits. Our mission is to help you create a more robust and sustainable agricultural landscape for your crops. Finding Beneficial Traits for Improving Crops Bringing Costs Down While Keeping Accuracy High Khufu’s analysis platform maps genes by using low pass whole genome sequencing that was specifically designed to be highly accurate in complex plant genomes. Current traditional high throughput genotyping technologies utilize fixed marker arrays or only sample small portions of the full genome to be cost efficient. However, Khufu’s accuracy allows the use of low coverage whole genome sequencing to access the entire genome and remain cost effective. Practically, this means that instead of checking for one or a few markers per sample, Khufu will deliver all markers of interest at once and has the following uses: s High resolution trait mapping – linking genotype to phenotype for gene identification and marker development s High throughput genotyping – genome-wide markers for genomics-assisted selection, identify contamination issues, quality assurance, and diversity analysis
With the use of Khufu and low coverage sequencing of bulks, QTL-seq is now rapid, economical, and likely to identify functional SNPs, thus game-changing for plant breeders and molecular geneticists.
Peggy Ozias-Atkins Professor and Director Institute of Plant Breeding, Genetics & Genomics University of Georgia —
Providing Complete Genomic Datasets Need complete datasets with no missing data for genomic selection or genome-wide association study (GWAS)? Khufu uses reference panel free imputation. This means markers are imputed from the data itself. Khufu does not require any up-front reference panel generation cost. s There is no need for design costs or customization. The per sample cost is only constrained by the genome size of the species s Khufu does not require a minimum sample commitment and is flexible for any project size
Taking Peak Performance to Another Level
Khufu uses low coverage, short-read sequencing data to provide genotyping results at a fraction of the normal cost.
At HudsonAlpha, we understand what is required to meet your needs with reliable and accurate results that are delivered on time. We are here to help guide your through the data so it is understandable at each step in the process and you’ll be ready to take action. Khufu provides extremely accurate single-nucleotide polymorphisms (SNP) identification using very low coverage sequence data. In order to map traits to genes, the DNA sequences of the plants being studied must be lined up against a reference genome. When focusing on complex plant genomes, It is hard for currently available software to map short DNA reads to a reference genome and accurately identify molecular markers like SNPs that correlate with an observed trait. Khufu is effective in genotyping small or large numbers of plants, regardless of the population structure or the genome complexity.
The peak occurs at the genetic location of the SNP that is correlated to the trait.
We hope that by offering other researchers the ability to use this low-cost, highly accurate computational software, we can help to advance genomic research in many different fields.
Have a target trait, and need a fully integrated mapping project?
Khufu was developed to effectively identify genes that affect traits of interest. We currently target many traits in the peanut that are important in different parts of the world. We are happy to help with a more integrated project targeting your trait of interest. This could include: s Consulting on experimental design (if needed) s Generation of chromosome level genome assemblies for both parents s 1,000 individuals sequenced and genotyped using Khufu for trait mapping s 200 individuals sequenced and genotyped for validation and fine-mapping Ready to quickly and accurately identify and analyze variants in your crop genomes? Email khufudatainfo @ hudsonalpha.org to get more information or schedule time to meet with a specialist, call toll-free at 855-511-6500 to start a conversation today or learn more at KhufuData.com
Khufu co-developer Josh Clevenger, PhD, is a Faculty Investigator at the HudsonAlpha Institute for Biotechnology. This role, coupled with his experiences working as a research scien- tist on the nut science team at Mars Wrigley, positions him perfectly to genetically improve crops by leveraging genomics technologies and computational tools.
Khufu co-developer Walid Korani, PhD, is a computational biologist at the HudsonAlpha Institute for Biotechnology. His post-doctoral research in peanut breeding and work as a bioinformatician for a bovine breeding company afforded him expert
experience in both plant and animal genomics and bioinformational analysis.
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