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Panzea specifications

Information


Unique identifier OMICS_03293
Name Panzea
Restrictions to use None
Maintained Yes

Taxon


  • Plants and Fungi
    • Zea mays

Maintainer


  • person_outline Jeffrey C. Glaubitz

Publications for Panzea

Panzea citations

 (28)
library_books

Parallel altitudinal clines reveal trends in adaptive evolution of genome size in Zea mays

2018
PLoS Genet
PMCID: 5944917
PMID: 29746459
DOI: 10.1371/journal.pgen.1007162

[…] s a random effect to control for the population structure []. The genetic relatedness matrix was calculated using GEMMA [] from publicly available GBS genotyping for these lines (AllZeaGBSv2.7 at www.panzea.org, []). In the calculation, we used 349,167 biallelic SNPs after removing SNPs with minor allele frequency <0.01 and missing rate >0.6 using PLINK []. […]

library_books

SNPversity: a web based tool for visualizing diversity

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

[…] The data sets are from Panzea (). Panzea is a project focused on understanding the connection between phenotype and genotype for complex traits in maize and its wild relative teosinte. SNPversity has four data sets in total […]

library_books

Analysis of Extreme Phenotype Bulk Copy Number Variation (XP CNV) Identified the Association of rp1 with Resistance to Goss's Wilt of Maize

2018
Front Plant Sci
PMCID: 5812337
PMID: 29479358
DOI: 10.3389/fpls.2018.00110

[…] WGS data of the Maize 282 Association Panel were downloaded from iplant shared from the Panzea research group. Among all WGS sequenced lines, 239 maize lines were phenotyped in this study. Sequencing reads were trimmed and aligned to the B73 reference genome (B73Ref2; Schnable et al., ) […]

library_books

Genome wide association study in Asia adapted tropical maize reveals novel and explored genomic regions for sorghum downy mildew resistance

2018
Sci Rep
PMCID: 5762920
PMID: 29321632
DOI: 10.1038/s41598-017-18690-3

[…] Illumina HiSeq. 2000. SNP calling was performed using the TASSEL-GBS pipeline with B73 as the reference genome to generate a comprehensive genotype collection, the AllZeaGBSv2.7 Production Build (www.panzea.org). The TASSEL-GBS pipeline is optimized for low sequencing depth (0.5 to 3×) over a large number of markers in a large sample of individuals. This collection included genotypes of more than […]

library_books

Plant Phylogeny and Life History Shape Rhizosphere Bacterial Microbiome of Summer Annuals in an Agricultural Field

2017
Front Microbiol
PMCID: 5732146
PMID: 29321763
DOI: 10.3389/fmicb.2017.02414

[…] ic distances among maize lines found in previous studies using chloroplast markers (). Genetic distance matrices for the ten NAM inbred lines were constructed using GBS markers build 2.7 available at panzea.org. Distance matrices were estimated using TASSEL version 5 (). […]

library_books

Incomplete dominance of deleterious alleles contributes substantially to trait variation and heterosis in maize

2017
PLoS Genet
PMCID: 5633198
PMID: 28953891
DOI: 10.1371/journal.pgen.1007019

[…] mbl.gramene.org/Zea_mays/Tools/AssemblyConverter?db=core).To compare GERP scores (for all SNPs with GERP > 0) to recombination rate and allele frequencies, we obtained the NAM genetic map [] from the Panzea website (http://www.panzea.org/) and allele frequencies from the > 1,200 maize lines sequenced as part of HapMap3.2 []. To compare the burden of deleterious alleles in modern inbred lines to la […]


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Panzea institution(s)
Cold Spring Harbor Laboratory, Cold Spring Harbor NY, USA; Genetics Department, University of Wisconsin-Madison Madison, WI, USA; Institute for Genomic Diversity, Cornell University Ithaca, NY, USA; USDA-ARS NAA Plant, Soil & Nutrition Laboratory Research Unit Tower Road, Ithaca, NY, USA; Department of Ecology and Evolutionary Biology, University of California-Irvine, USA; Crop Science Department, North Carolina State University Raleigh, NC, USA; USDA-ARS, Plant Science Research Unit Raleigh, NC, USA; Department of Agronomy, University of Missouri-Columbia Columbia, MO, USA; USDA-ARS, Plant Genetics Research Unit Columbia, MO, USA

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