Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach

TY - JOUR

T1 - Identification of factors required for meristem function in Arabidopsis using a novel next generation sequencing fast forward genetics approach

AU - Mokry, M.

AU - Nijman, I.J.

AU - van Dijken, A.

AU - Benjamins, R.

AU - Heidstra, R.

AU - Scheres, B.

AU - Cuppen, E.

N1 - Reporting year: 2011 Metis note: 3114748;

PY - 2011

Y1 - 2011

N2 - BACKGROUND: Phenotype-driven forward genetic experiments are powerful approaches for linking phenotypes to genomic elements but they still involve a laborious positional cloning process. Although sequencing of complete genomes now becomes available, discriminating causal mutations from the enormous amounts of background variation remains a major challenge. METHOD: To improve this, we developed a universal two-step approach, named 'fast forward genetics', which combines traditional bulk segregant techniques with targeted genomic enrichment and next-generation sequencing technology RESULTS: As a proof of principle we successfully applied this approach to two Arabidopsis mutants and identified a novel factor required for stem cell activity. CONCLUSION: We demonstrated that the 'fast forward genetics' procedure efficiently identifies a small number of testable candidate mutations. As the approach is independent of genome size, it can be applied to any model system of interest. Furthermore, we show that experiments can be multiplexed and easily scaled for the identification of multiple individual mutants in a single sequencing run.

AB - BACKGROUND: Phenotype-driven forward genetic experiments are powerful approaches for linking phenotypes to genomic elements but they still involve a laborious positional cloning process. Although sequencing of complete genomes now becomes available, discriminating causal mutations from the enormous amounts of background variation remains a major challenge. METHOD: To improve this, we developed a universal two-step approach, named 'fast forward genetics', which combines traditional bulk segregant techniques with targeted genomic enrichment and next-generation sequencing technology RESULTS: As a proof of principle we successfully applied this approach to two Arabidopsis mutants and identified a novel factor required for stem cell activity. CONCLUSION: We demonstrated that the 'fast forward genetics' procedure efficiently identifies a small number of testable candidate mutations. As the approach is independent of genome size, it can be applied to any model system of interest. Furthermore, we show that experiments can be multiplexed and easily scaled for the identification of multiple individual mutants in a single sequencing run.

U2 - 10.1186/1471-2164-12-256

DO - 10.1186/1471-2164-12-256

M3 - Article

SN - 1471-2164

VL - 12

SP - 256

JO - BMC Genomics

JF - BMC Genomics

ER -