HudsonAlpha Creates Mapping Tool for Plant and Animal Breeders

Huntsville genetics hub HudsonAlpha Institute for Biotechnology has created a computational tool called Khufu to quickly and accurately identify genetic variants in complex genomes – and it’s available to plant and animal breeders, academic institutions, biofuel researchers and other agricultural groups.

“We needed to more rapidly introduce beneficial traits into cultivated crops that farmers can plant on their land,” says HudsonAlpha Institute for Biotechnology faculty investigator Josh Clevenger, PhD.

But to do it, he needed better tools.

To map desirable traits to the right genes, DNA sequences of plants must be lined up against a reference genome. Getting the mapping right is no easy task. After years of struggling to identify the right molecular markers in his research area of peanuts, Clevenger teamed up with HudsonAlpha computational biologist Walid Korani, PhD to develop a better way to analyze the data.

The result was a new computational tool, Khufu.

Khufu can be used to facilitate marker discovery, to map genes or QTL in inbred, non-inbred, non-controlled, self-pollinated, out-crossed or natural populations, to conduct genome wide association studies and to enable genomic selection (GS) based breeding programs in plant species.

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Khufu maps short DNA reads to a reference genome and accurately identifies genetic factors (single-nucleotide polymorphisms, or SNPs) to select for beneficial traits, to apply to new and rapid breeding practices to introduce these traits into existing crop lines.

Khufu uses low coverage, short-read sequencing data to provide genotyping results at a fraction of the normal cost. Using a novel approach, Khufu provides extremely accurate SNP identification based on this sequence data. Because each individual sample requires less sequence, the cost of whole genome sequencing is practical, for both small and large breeding programs.

And that’s why Clevenger wants more companies to use it.

Khufu is not a data generation service, but a data analysis service that can provide sequencing and analysis for a low cost. For a similar cost to the raw output of SNP arrays, Khufu provides full analysis of genotypes, provides marker targets for traits of interest, and saves valuable time.

“Collaborators can expect fast results, with analyses being done within days of the sequence being generated,” Clevenger explains. Khufu uses a series of algorithms that efficiently extract falsely identified SNPs, making it 99.9 percent accurate at identifying SNPs correlated to a given trait in both plant and animal populations.

Clevenger believes Khufu makes trait mapping available to a much wider group – not just geneticists, but also crop farmers, veterinary schools and animal researchers.

“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,” Clevenger says.

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