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Forward genetics by sequencing EMS variation induced inbred lines

Author: Addo-Quaye, C.
Author: Buescher, E.
Author: Best, N.
Author: Chaikam, Vijay
Author: Baxter, I.
Author: Dilkes, B.P.
Year: 2017
Descriptors: Maize
Descriptors: Inbred lines
Descriptors: Genetics
Abstract: In order to leverage novel sequencing techniques for cloning genes in eukaryotic organisms with complex genomes, the false positive rate of variant discovery must be controlled for by experimental design and informatics. We sequenced five lines from three pedigrees of EMS mutagenized Sorghum bicolor, including a pedigree segregating a recessive dwarf mutant. Comparing the sequences of the lines, we were able to identify and eliminate error prone positions. One genomic region contained EMS mutant alleles in dwarfs that were homozygous reference sequence in wild-type siblings and heterozygous in segregating families. This region contained a single non-synonymous change that cosegregated with dwarfism in a validation population and caused a premature stop codon in the sorghum ortholog encoding the gibberellic acid biosynthetic enzyme ent-kaurene oxidase. Application of exogenous gibberellic acid rescued the mutant phenotype. Our method for mapping did not require outcrossing and introduced no segregation variance. This enables work when line crossing is complicated by life history, permitting gene discovery outside of genetic models. This inverts the historical approach of first using recombination to define a locus and then sequencing genes. Our formally identical approach first sequences all the genes and then seeks co-segregation with the trait. Mutagenized lines lacking obvious phenotypic alterations are available for an extension of this approach: mapping with a known marker set in a line that is phenotypically identical to starting material for EMS mutant generation.
Language: English
Publisher: Genetics Society of America
Copyright: CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose.
Type: Article
Place: Bethesda, MD
Pages: 413-425
Journal issue: 2
Journal: G3: Genes, Genomes, Genetics
Journal volume: 7
DOI: 10.1534/g3.116.029660

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  • Maize
    Maize breeding, phytopathology, entomology, physiology, quality, and biotech

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