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Protocols

MaizeGDB specifications

Information


Unique identifier OMICS_01655
Name MaizeGDB
Alternative name Maize Genetics and Genomics Database
Restrictions to use None
Community driven Yes
Data access File download, Browse
User data submission Allowed
Registration required Yes
Maintained Yes

Taxon


  • Plants and Fungi
    • Zea mays

Documentation


Maintainer


  • person_outline Carson M. Andorf

Additional information


Video tutorials: http://tutorial.maizegdb.org/

Publications for Maize Genetics and Genomics Database

MaizeGDB citations

 (107)
library_books

SNPversity: a web based tool for visualizing diversity

2018
PMCID: 5912076
PMID: 29688387
DOI: 10.1093/database/bay037

[…] With low-cost genomic technologies, increasingly more data are available to biologists, and online biological databases, such as MaizeGDB () and GrainGenes (), are being challenged by the diversity of data types that need to be curated, managed, queried, and visualized. For some data types, web-based software applications are a […]

library_books

Massive Loss of DNA Methylation in Nitrogen , but Not in Phosphorus Deficient Zea mays Roots Is Poorly Correlated With Gene Expression Differences

2018
Front Plant Sci
PMCID: 5917015
PMID: 29725341
DOI: 10.3389/fpls.2018.00497

[…] irst 4 and the last 6 basepairs of each read were then removed via the FastX-Toolkit by Hannon Lab to remove bias and get higher quality reads. As reference the Z. mays genome (AGPv3) provided by the Maize Genetics and Genomics Database () was used. The alignment was done by BS-Seeker2, which produces a reduced representation genome from the reference genome to increase mappability and accuracy of […]

library_books

Long Non Coding RNAs Responsive to Salt and Boron Stress in the Hyper Arid Lluteño Maize from Atacama Desert

2018
Genes
PMCID: 5867891
PMID: 29558449
DOI: 10.3390/genes9030170

[…] o identify the relationship of Lluteño maize with other commercial variants, we performed different sequence similarity searches against the genomic sequences from maize with genome data available at MaizeGDB []. For B73, the most used and completely sequenced maize variant, we used the genome assembly release RefGen_v3. For Palomero, we used the assembly version v1, containing 196,697 contigs. Fo […]

library_books

Map based cloning and characterization of Zea mays male sterility33 (ZmMs33) gene, encoding a glycerol 3 phosphate acyltransferase

2018
PMCID: 5945757
PMID: 29546443
DOI: 10.1007/s00122-018-3083-9

[…] To elucidate the evolutionary relationship between ZmMs33 and its close homologues, the ZmMs33 protein sequence was used in BLASTP queries in NCBI, MaizeGDB and RGAP databases. Meanwhile, we used AtATS1 and AtGPAT9 protein sequences to search for the putative sn-1 GPATs in maize and rice. Consequently, there are 18 and 20 putative GPATs in the ma […]

call_split

Evaluation of Optimized Tube Gel Methods of Sample Preparation for Large Scale Plant Proteomics

2018
Proteomes
PMCID: 5874765
PMID: 29385730
DOI: 10.3390/proteomes6010006
call_split See protocol

[…] Data were searched with X!Tandem (version 2015.04.01.1 []) against the maize genome database V5a (https://ftp.maizegdb.org/MaizeGDB/FTP/) and a homemade database containing standard contaminants. Trypsin digestion was set in strict mode with one authorized missed cleavage. Cysteine carbamidomethylation was se […]

library_books

Genome wide association analysis and QTL mapping reveal the genetic control of cadmium accumulation in maize leaf

2018
BMC Genomics
PMCID: 5785805
PMID: 29370753
DOI: 10.1186/s12864-017-4395-x

[…] Expression profiles of eight candidate genes were examined in maize B73 under non-limiting growth conditions. Using online transcriptome data from maize B73 (MaizeGDB), an expression heatmap was constructed for these candidate genes in different tissues from 8 developmental stages (Fig. ). The results showed that the expression patterns of different candid […]

Citations

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MaizeGDB institution(s)
USDA-ARS Corn Insects and Crop Genetics Research Unit, Iowa State University, Ames, IA, USA; Department of Computer Science, Iowa State University, Ames, IA, USA; Department of Electrical and Computer Engineering, Iowa State University, Ames, IA, USA; Department of Genetics, Development and Cell Biology, Iowa State University, Ames, IA, USA; School of Plant Sciences, University of Arizona, Tucson, AZ, USA; USDA-ARS Plant Genetics Research Unit, University of Missouri, Columbia, MO, USA; Division of Plant Sciences, Department of Agronomy, University of Missouri, Columbia, MO, USA; Department of Agronomy, Iowa State University, Ames, IA, USA; Bioinformatics and Computational Biology, Iowa State University, Ames, IA, USA; Interdepartmental Genetics and Genomics, Iowa State University, Ames, IA, USA
MaizeGDB funding source(s)
Supported by the United States Department of Agriculture, Agricultural Re- search Service (USDA-ARS) as well as the National Corn Growers Association and National Science Foundation [IOS #1027527 and #1238142].

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