Deletion mutagenesis and identification of causative mutations in Maize

Shangang Jia, Aixia Li, Chi Zhang, David Holding

Research output: Chapter in Book/Report/Conference proceedingChapter

Abstract

We describe a method for gamma-irradiation of mature maize seeds to generate mutants with opaque endosperm and reduced kernel fill phenotypes. We also describe methods for mapping mutants and identifying causal gene mutations. Using this method, a population of 1788M2 families and 47 Mo17 × F2s showing stable, segregating, and viable kernel phenotypes was developed. For molecular characterization of the mutants, we utilized a novel functional genomics platform that combines separate Bulked Segregant RNA and exome sequencing data sets (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. We also describe the use of exome capture sequencing of F2 mutant and normal pools to perform mapping and candidate gene identification without the need for separate RNA-seq (BSEx-seq). To exemplify the utility of the deletion mutants for functional genomics and provide proof-of-concept for the bioinformatics platform, we summarize the identification of the causative deletion in two mutants. Mutant 937, which was characterized by BSREx-seq, harbors a 6203-bp in-frame deletion covering six exons within the Opaque-1 gene on chromosome 4. Preliminary investigation of opaque mutant 1486 with BSEx-seq shows a tight mapping interval and associated deletion on chromosome 10.

Original languageEnglish (US)
Title of host publicationMethods in Molecular Biology
PublisherHumana Press Inc.
Pages97-108
Number of pages12
DOIs
StatePublished - Jan 1 2018

Publication series

NameMethods in Molecular Biology
Volume1676
ISSN (Print)1064-3745

Fingerprint

Exome
Mutagenesis
Zea mays
RNA Sequence Analysis
Genomics
Mutation
Phenotype
Chromosomes, Human, Pair 10
Endosperm
Chromosomes, Human, Pair 4
Chromosome Mapping
Genetic Association Studies
Computational Biology
Genes
Exons
Seeds
RNA
Population
Datasets

Keywords

  • BSR-seq
  • Causative mutation
  • Exome-seq
  • Maize functional genomics
  • Opaque

ASJC Scopus subject areas

  • Molecular Biology
  • Genetics

Cite this

Jia, S., Li, A., Zhang, C., & Holding, D. (2018). Deletion mutagenesis and identification of causative mutations in Maize. In Methods in Molecular Biology (pp. 97-108). (Methods in Molecular Biology; Vol. 1676). Humana Press Inc.. https://doi.org/10.1007/978-1-4939-7315-6_5

Deletion mutagenesis and identification of causative mutations in Maize. / Jia, Shangang; Li, Aixia; Zhang, Chi; Holding, David.

Methods in Molecular Biology. Humana Press Inc., 2018. p. 97-108 (Methods in Molecular Biology; Vol. 1676).

Research output: Chapter in Book/Report/Conference proceedingChapter

Jia, S, Li, A, Zhang, C & Holding, D 2018, Deletion mutagenesis and identification of causative mutations in Maize. in Methods in Molecular Biology. Methods in Molecular Biology, vol. 1676, Humana Press Inc., pp. 97-108. https://doi.org/10.1007/978-1-4939-7315-6_5
Jia S, Li A, Zhang C, Holding D. Deletion mutagenesis and identification of causative mutations in Maize. In Methods in Molecular Biology. Humana Press Inc. 2018. p. 97-108. (Methods in Molecular Biology). https://doi.org/10.1007/978-1-4939-7315-6_5
Jia, Shangang ; Li, Aixia ; Zhang, Chi ; Holding, David. / Deletion mutagenesis and identification of causative mutations in Maize. Methods in Molecular Biology. Humana Press Inc., 2018. pp. 97-108 (Methods in Molecular Biology).
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