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

Shangang Jia,Kyla Morton,Chi Zhang,David Holding

doi:10.1016/j.gpb.2018.02.003

Shangang Jia, Kyla Morton + Show 2 more

Open Access

https://doi.org/10.1016/j.gpb.2018.02.003

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Abstract

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 identification 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-specific expression data to narrow down the list of candidate genes/mutations and identified deletions ranging from several kb to more than 1 Mb. A full deletion allele of the Opaque-2 gene was identified 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 efficiency 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.

Highlights

Maize (Zea mays) has been used extensively as a model organism for genetics and developmental studies
We focused on opaque endosperm and reduced kernel size phenotypes which, along with other mutant classes, were numbered according to a common scheme (Table 1)
We found that positive single nucleotide polymorphisms (SNPs)/indels intensively appeared on chromosome 1, and the highest linkage peak was identified with a summit at the genomic coordinate 46.05 Mb as shown in the circle b of Figure 3B, indicating a linkage disequilibrium with causative mutation

Summary

Introduction

Maize (Zea mays) has been used extensively as a model organism for genetics and developmental studies. Seed mutants of maize are especially attractive for crop researchers because the ordered rows of kernels, held in place on the ears, allows easy identification of genetically-segregating kernel phenotypes. The well-characterized opaque-2 (o2) mutant possesses increased levels of essential amino acids lysine and tryptophan [1], and the identified gene encodes the endosperm-specific basic leucine zipper domain (bZIP) transcription factor O2. Many other genes causing opaque phenotypes in maize mutants [4] have been identified, such as opaque1 [5], floury1 [6], floury2 [7], defective endosperm B30 [8], and floury4 [9]. It is likely that characterization of new opaque mutants would lead to the identification of more genes involved in endosperm maturation

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