title: Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach.
abstract: Screening large populations for carriers of known or de novo rare single nucleotide polymorphisms (SNPs) is required both in Targeting induced local lesions in genomes (TILLING) experiments in plants and in screening of human populations. We previously suggested an approach that combines the mathematical field of compressed sensing with next-generation sequencing to allow such large-scale screening. Based on pooled measurements, this method identifies multiple carriers of heterozygous or homozygous rare alleles while using only a small fraction of resources. Its rigorous mathematical foundations allow scalable and robust detection, and provide error correction and resilience to experimental noise. Here we present a large-scale experimental demonstration of our computational approach, in which we targeted a TILLING population of 1024 Sorghum bicolor lines to detect carriers of de novo SNPs whose frequency was less than 0.1%, using only 48 pools. Subsequent validation confirmed that all detected lines were indeed carriers of the predicted mutations. This novel approach provides a highly cost-effective and robust tool for biologists and breeders to allow identification of novel alleles and subsequent functional analysis.
authors.affiliation: The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
authors.forename: Habte
authors.initials: H
authors.lastname: Nida
authors.affiliation: The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
authors.forename: Shula
authors.initials: S
authors.lastname: Blum
authors.affiliation: New York Genome Center, 101 Avenue of the Americas, New York, NY, USA.
authors.forename: Dina
authors.initials: D
authors.lastname: Zielinski
authors.affiliation: The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.|Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
authors.forename: Dhruv A
authors.initials: DA
authors.lastname: Srivastava
authors.affiliation: The Robert H. Smith Institute of Plant Sciences and Genetics in Agriculture, Robert H. Smith Faculty of Agriculture, Food and Environment, The Hebrew University of Jerusalem, Rehovot, Israel.
authors.forename: Rivka
authors.initials: R
authors.lastname: Elbaum
authors.affiliation: Plant Stress and Germplasm Development Unit, US Department of Agriculture/Agricultural Research Service, Lubbock, TX, USA.
authors.forename: Zhanguo
authors.initials: Z
authors.lastname: Xin
authors.affiliation: New York Genome Center, 101 Avenue of the Americas, New York, NY, USA.|Department of Computer Science, Fu Foundation School of Engineering, Columbia University, New York, NY, USA.|Center for Computational Biology and Bioinformatics, Columbia University, New York, NY, USA.
authors.forename: Yaniv
authors.initials: Y
authors.lastname: Erlich
authors.affiliation: Institute of Plant Sciences, Agricultural Research Organization, The Volcani Center, Bet Dagan, Israel.
authors.forename: Eyal
authors.initials: E
authors.lastname: Fridman
authors.affiliation: Department of Mathematics and Computer Science, The Open University of Israel, Raanana, Israel.
authors.forename: Noam
authors.initials: N
authors.lastname: Shental
mesh_terms: D000483:Alleles; D019295:Computational Biology / Q000379:methods; D017343:Genes, Plant; D018745:Genome, Plant; D006579:Heterozygote; D020641:Polymorphism, Single Nucleotide; D045868:Sorghum / Q000235:genetics*
keywords: Sorghum bicolor; Targeting induced local lesions in genomes; compressed sensing; de novo SNPs; large scale screening; rare alleles; technical advance