FIND-IT: Ultrafast mining of genome diversity

Novel crop improvement methodologies, including the exploitation of natural genetic variation, are urgently required to feed our rapidly growing human population in the context of global climate change. Here we describe a ‘Fast Identification of Nucleotide variants by DigITal PCR’ (FIND-IT) method for the rapid identification of pre-targeted genetic variants or rare alleles in large genomic populations. Libraries of 500,000 individuals can be screened and desired variants isolated within two weeks. FIND-IT is widely applicable for mining valuable diversity in any genomic population, including elite breeding and wild germplasm collections. The method provides single nucleotide resolution that has been validated by identifying and isolating knockout lines, non-synonymous codon changes and variants of miRNA and transcription factor binding sites in the agronomically important crop barley. In contrast to existing methods, FIND-IT does not require transformation, cloning or enzymatic steps, and is exempt from GMO regulations. Thus, FIND-IT can be applied immediately to elite crop cultivars and can be tailored to minimize or eliminate time-consuming backcrossing requirements. ### Competing Interest Statement S.K., T.W., H.C.T, M.R., M.C., A.S., O.O. and B.S. are listed as inventors in a patent application WO2018/001884, and S.K., T.W., M.R., J.O and B.S. are listed as inventors in patent application PCT/EP2020/078321, both relating to the methodology and filed by the Carlsberg A/S. Furthermore, S.K., S.B, O.O., H.T., T.W. and J.H. are listed as inventors in a patent application WO2019129736A1, and C.D., P.R.P., S.K., O.O., T.W., M.C., H.T. and M.R. are listed as inventors in a patent application WO2019129739A1, both relating to traits and filed by the Carlsberg A/S. All authors are previous or current Carlsberg A/S employees. B.L.M. is a Distinguished Professor at the Carlsberg Research Laboratory and serves as a consultant for the laboratory. G.B.F. is a Senior Scientific Consultant and Distinguished Professor of Raw Materials at the Carlsberg Research Laboratory. The methodology presented in the manuscript is applied commercially by Traitomic, a business unit at Carlsberg A/S.