An Exome-seq Based Tool for Mapping and Selection of Candidate Genes in Maize Deletion Mutants
Tài liệu tham khảo
Mertz, 1964, Mutant gene that changes protein composition and increases lysine content of maize endosperm, Science, 145, 279, 10.1126/science.145.3629.279
Yang, 2016, Divergent transactivation of maize storage protein zein genes by the transcription factors Opaque2 and OHPs, Genetics, 204, 581, 10.1534/genetics.116.192385
Zhang, 2016, Maize endosperm-specific transcription factors O2 and PBF network the regulation of protein and starch synthesis, Proc Natl Acad Sci U S A, 113, 10842, 10.1073/pnas.1613721113
Hunter, 2002, Maize opaque endosperm mutations create extensive changes in patterns of gene expression, Plant Cell, 14, 2591, 10.1105/tpc.003905
Wang, 2012, Opaque1 encodes a myosin XI motor protein that is required for endoplasmic reticulum motility and protein body formation in maize endosperm, Plant Cell, 24, 3447, 10.1105/tpc.112.101360
Holding, 2007, The maize floury1 gene encodes a novel endoplasmic reticulum protein involved in zein protein body formation, Plant Cell, 19, 2569, 10.1105/tpc.107.053538
Coleman, 1997, Expression of a mutant α-zein creates the floury2 phenotype in transgenic maize, Proc Natl Acad Sci U S A, 94, 7094, 10.1073/pnas.94.13.7094
Kim, 2004, A defective signal peptide in a 19-kD α-zein protein causes the unfolded protein response and an opaque endosperm phenotype in the maize De*-B30 mutant, Plant Physiol, 134, 380, 10.1104/pp.103.031310
Wang, 2014, Identification and characterization of maize floury4 as a novel semidominant opaque mutant that disrupts protein body assembly, Plant Physiol, 165, 582, 10.1104/pp.114.238030
Nannas, 2015, Genetic and genomic toolbox of Zea mays, Genetics, 199, 655, 10.1534/genetics.114.165183
Sato, 2006, Mutant selection from progeny of gamma-ray-irradiated rice by DNA heteroduplex cleavage using Brassica petiole extract, Breed Sci, 56, 179, 10.1270/jsbbs.56.179
Yuan, 2014, Deletion mutagenesis identifies a haploinsufficient role for gamma-zein in opaque2 endosperm modification, Plant Physiol, 164, 119, 10.1104/pp.113.230961
Jia, 2016, A population of deletion mutants and an integrated mapping and exome-seq pipeline for gene discovery in maize, G3 (Bethesda), 6, 2385, 10.1534/g3.116.030528
Mizuno, 2013, Genomic inversion caused by gamma irradiation contributes to downregulation of a WBC11 homolog in bloomless sorghum, Theor Appl Genet, 126, 1513, 10.1007/s00122-013-2069-x
Belfield, 2012, Genome-wide analysis of mutations in mutant lineages selected following fast-neutron irradiation mutagenesis of Arabidopsis thaliana, Genome Res, 22, 1306, 10.1101/gr.131474.111
Jia, 2017, A mapping-by-sequencing tool for searching causative genes in mutants, IEEE Int Conf Electro Inf Technol, 380
Galili, 1998, The endoplasmic reticulum of plant cells and its role in protein maturation and biogenesis of oil bodies, Plant Mol Biol, 38, 1, 10.1023/A:1006011919671
Layer, 2014, LUMPY: a probabilistic framework for structural variant discovery, Genome Biol, 15, R84, 10.1186/gb-2014-15-6-r84
Ye, 2009, Pindel: a pattern growth approach to detect break points of large deletions and medium sized insertions from paired-end short reads, Bioinformatics, 25, 2865, 10.1093/bioinformatics/btp394
Zhang, 2012, An improved approach for accurate and efficient calling of structural variations with low-coverage sequence data, BMC Bioinformatics, 13, S6, 10.1186/1471-2105-13-S6-S6
Rausch, 2012, DELLY: structural variant discovery by integrated paired-end and split-read analysis, Bioinformatics, 28, i333, 10.1093/bioinformatics/bts378
Zhang, 2016, Sprites: detection of deletions from sequencing data by re-aligning split reads, Bioinformatics, 32, 1788, 10.1093/bioinformatics/btw053
Safavi-Hemami, 2016, Rapid expansion of the protein disulfide isomerase gene family facilitates the folding of venom peptides, Proc Natl Acad Sci U S A, 113, 3227, 10.1073/pnas.1525790113
Houston, 2005, Phylogenetic analyses identify 10 classes of the protein disulfide isomerase family in plants, including single-domain protein disulfide isomerase-related proteins, Plant Physiol, 137, 762, 10.1104/pp.104.056507
Iwasaki, 2009, Molecular cloning and characterization of soybean protein disulfide isomerase family proteins with nonclassic active center motifs, FEBS J, 276, 4130, 10.1111/j.1742-4658.2009.07123.x
Li, 1996, Expression of protein disulfide isomerase is elevated in the endosperm of the maize floury-2 mutant, Plant Mol Biol, 30, 873, 10.1007/BF00020800
Kim, 2006, The maize Mucronate mutation is a deletion in the 16-kDa γ-zein gene that induces the unfolded protein response, Plant J, 48, 440, 10.1111/j.1365-313X.2006.02884.x
Bolger, 2014, Trimmomatic: a flexible trimmer for Illumina sequence data, Bioinformatics, 30, 2114, 10.1093/bioinformatics/btu170
Langmead, 2012, Fast gapped-read alignment with Bowtie 2, Nat Methods, 9, 357, 10.1038/nmeth.1923
Li, 2011, A statistical framework for SNP calling, mutation discovery, association mapping and population genetical parameter estimation from sequencing data, Bioinformatics, 27, 2987, 10.1093/bioinformatics/btr509
Koboldt, 2012, VarScan 2: somatic mutation and copy number alteration discovery in cancer by exome sequencing, Genome Res, 22, 568, 10.1101/gr.129684.111
Krzywinski, 2009, Circos: an information aesthetic for comparative genomics, Genome Res, 19, 1639, 10.1101/gr.092759.109
Chiang, 2015, SpeedSeq: ultra-fast personal genome analysis and interpretation, Nat Methods, 12, 966, 10.1038/nmeth.3505
Davidson, 2011, Utility of RNA sequencing for analysis of maize reproductive transcriptomes, Plant Genome, 4, 191, 10.3835/plantgenome2011.05.0015
Wallace, 1990, New methods for extraction and quantitation of zeins reveal a high content of γ-zein in modified opaque-2 maize, Plant Physiol, 92, 191, 10.1104/pp.92.1.191
