Highly efficient de novo mutant identification in a Sorghum bicolor TILLING population using the ComSeq approach

Habte Nida, Shula Blum, Dina Zielinski, Dhruv A. Srivastava, Rivka Elbaum, Zhanguo Xin, Yaniv Erlich, Eyal Fridman, Noam Shental

Research output: Contribution to journalArticlepeer-review

17 Scopus citations

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.

Original languageAmerican English
Pages (from-to)349-359
Number of pages11
JournalPlant Journal
Volume86
Issue number4
DOIs
StatePublished - 1 May 2016

Bibliographical note

Publisher Copyright:
© 2016 The Authors The Plant Journal © 2016 John Wiley & Sons Ltd.

Keywords

  • Sorghum bicolor
  • Targeting induced local lesions in genomes
  • compressed sensing
  • de novo SNPs
  • large scale screening
  • rare alleles
  • technical advance

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