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ARS Home » Midwest Area » St. Paul, Minnesota » Cereal Disease Lab » Research » Publications at this Location » Publication #330223
Title: A population of deletion mutants and an integrated mapping and Exome-seq pipeline for gene discovery in maize

Author
item JIA, SHANGANG - University Of Nebraska
item LI, AIXIA - University Of Nebraska
item AVOLES-KIANIAN, PENNY - University Of Minnesota
item Kianian, Shahryar
item ZHANG, CHI - University Of Nebraska
item HOLDING, DAVID - University Of Nebraska

Submitted to: G3, Genes/Genomes/Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 5/25/2016
Publication Date: 6/25/2016
Citation: Jia, S., Li, A., Avoles-Kianian, P., Kianian, S., Zhang, C., Holding, D. 2016. A population of deletion mutants and an integrated mapping and Exome-seq pipeline for gene discovery in maize. G3, Genes/Genomes/Genetics. doi: 10.1534/g3.116.030528.

Interpretive Summary: The methods we developed using '-irradiation in generating mutants was applied to maize. The utility of this approach was tested by uitilizing a combination of genomics approaches to identify the underlying molecular basis of seed development in maize. Possible genes underlying mutations such as opaque and sugary kernel were identified. This study demonstrates the utility of gamma irradiation for forward and reverse genetics in large non-dense genomes such as maize since deletions often affect single genes. Furthermore, it illustrates how this classical mutagenesis method becomes more applicable for functional genomics when combined with state-of-the-art genomics tools. The two major findings of this work are: 1) '-irradiation can be broadly applied to many plant species to generate functional mutations for important traits and 2) this method in combination with modern sequencing methods provides an efficient and rapid procedure for analysis of genes underlying those traits.

Technical Abstract: To better understand maize endosperm filling and maturation, we developed a novel functional genomics platform that combined Bulked Segregant RNA and Exome sequencing (BSREx-seq) to map causative mutations and identify candidate genes within mapping intervals. Using gamma-irradiation of B73 maize to generate mutants with opaque endosperm and reduced kernel fill phenotypes, we created a population of 1788 B73 lines including 47 Mo17×B73 F2s showing stable segregating and viable kernel phenotypes. As proof-of-concept, we present detailed characterization of line 937; an opaque mutant harboring a 6203-bp in-frame deletion covering six exons within the Opaque-1 gene. In addition, we describe mutant line 146 which contains a 4.8 Kb intra-gene deletion within the Sugary-1 gene and line 916 in which an 8.6 Kb deletion knocks out a Cyclin A2 gene. The developed algorithm improves the identification of causative deletions and its corresponding gaps within mapping peaks. Therefore, this study demonstrates the utility of gamma irradiation for forward and reverse genetics in large non-dense genomes such as maize since deletions often affect single genes. Furthermore, we show how this classical mutagenesis method becomes more applicable for functional genomics when combined with state-of-the-art genomics tools.