TY - JOUR
T1 - An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants
AU - Jia, Shangang
AU - Morton, Kyla
AU - Zhang, Chi
AU - Holding, David
N1 - Funding Information:
The authors thank Patrick Schnable and his group for designing the maize Zeanome array. The authors thank Penny Avoles-Kianian and Shahryar Kianian for the initial mutagenesis performed and described previously [13]. The authors thank Aixia Li, Ying Ren, Kan Liu, Qian Du, and Weilong Yang for helpful discussions during this project. This work was supported by the Agriculture and Food Research Initiative competitive grant (Grant No. 2013-02278 ) of the United States Department of Agriculture , National Institute of Food and Agriculture (USDA-NIFA), as well as Center for Plant Science Innovation Program of Excellence and Department of Agronomy and Horticulture , University of Nebraska-Lincoln , United States.
Funding Information:
The authors thank Patrick Schnable and his group for designing the maize Zeanome array. The authors thank Penny Avoles-Kianian and Shahryar Kianian for the initial mutagenesis performed and described previously [13]. The authors thank Aixia Li, Ying Ren, Kan Liu, Qian Du, and Weilong Yang for helpful discussions during this project. This work was supported by the Agriculture and Food Research Initiative competitive grant (Grant No. 2013-02278) of the United States Department of Agriculture, National Institute of Food and Agriculture (USDA-NIFA), as well as Center for Plant Science Innovation Program of Excellence and Department of Agronomy and Horticulture, University of Nebraska-Lincoln, United States.
Publisher Copyright:
© 2019 The Authors
PY - 2018/12
Y1 - 2018/12
N2 - 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.
AB - 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.
KW - Bulked segregation analysis
KW - Exome-seq
KW - Maize functional genomics
KW - Mapping-by-sequencing
KW - Opaque mutant
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U2 - 10.1016/j.gpb.2018.02.003
DO - 10.1016/j.gpb.2018.02.003
M3 - Article
C2 - 30743052
AN - SCOPUS:85061594722
VL - 16
SP - 439
EP - 450
JO - Genomics Proteomics Bioinformatics
JF - Genomics Proteomics Bioinformatics
SN - 1672-0229
IS - 6
ER -