Researchers from Hudson Alpha Institute for Biotechnology created a computational tool, called Khufu, which can quickly and accurately identify plant variants and pinpoint desirable genes.

Khufu would allow farmers to grow crops with beneficial traits. Khufu identifies genetic factors that farmers could select to give a crop beneficial traits through breeding.Source: HudsonAlpha Institute for BiotechnologySource: HudsonAlpha Institute for Biotechnology

To map gene traits, the DNA sequences of plants are studied and the findings are lined up against a given reference genome to detect the desired trait. This is hard for software to do. Current software cannot identify molecular markers that correlate with the observed trait.

Khufu uses low coverage, short read sequencing data to cheaply provide genotyping. The result is accurate identification with low coverage sequence data. Individual traits require less sequencing so the whole genome sequencing is practical, even for small breeding programs. The availability of genome-wide markers increases the power and precision of trait mapping, integration and delivering tools to a wider array of breeders and geneticists.

Khufu provides fast results, with completion happening within days of the sequence being generated. It provides a full analysis of genotypes and provides marker targets for traits of interest and saves time. Khufu creates algorithms that extract identified traits with 99.9% accuracy.

While the tool was originally developed for peanut populations, the team found that it could work across a variety of species and populations.

A paper on the new tool was published in bioRxiV.