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An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion mutants

Genomics, Proteomics & Bioinformatics 2018年第6期16卷 439-450页

作者： Shangang Jia Kyla Morton Chi Zhang David Holding Department of Agronomy and Horticulture Center for Plant Science InnovationBeadle Center for BiotechnologyUniversity of Nebraska School of Biological Sciences Center for Plant Science InnovationBeadle Center for BiotechnologyUniversity of Nebraska

Despite the large number of genomic and transcriptomic resources in maize, there is still much to learn about the function of genes in developmental and biochemical processes. Some maize mutants that were generated by gamma-irradiation showed clear segregation for the kernel phenotypes in B73 ? Mo17 F2 ears. To better understand the functional genomics of kernel development,we developed a mapping and gene identi?cation pipeline, bulked segregant exome sequencing(BSEx-seq), to map mutants with kernel phenotypes including opaque endosperm and reduced kernel size. BSEx-seq generates and compares the sequence of the exon fraction from mutant and normal plant F2 DNA pools. The comparison can derive mapping peaks, identify deletions within the mapping peak, and suggest candidate genes within the deleted regions. We then used the public kernel-speci?c expression data to narrow down the list of candidate genes/mutations and identi?ed deletions ranging from several kb to more than 1 Mb. A full deletion allele of the opaque-2 gene was identi?ed in mutant 531, which occurs within a $200-kb deletion. opaque mutant 1486 has a 6248-bp deletion in the mapping interval containing two candidate genes encoding RNA-directed DNA methylation 4(RdDM4) and AMP-binding protein, respectively. This study demonstrates the ef?-ciency and cost-effectiveness of BSEx-seq for causal mutation mapping and candidate gene selection,providing a new option in mapping-by-sequencing for maize functional genomics studies.

关键词： Maize functional genomics Mapping-by-sequencing Exome-seq opaque mutant Bulked segregation analysis

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