Zm-CML322-REFERENCE-NAM-1.0 genome assembly
   Project Details        Metadata        Browser        

The NAM parents sequencing project


NAM Consortium website: https://nam-genomes.org/


Currently, many or most forms of sequence analyses are referenced to the single B73 inbred. Beyond B73, some of the most extensively researched maize lines are the core set of 25 inbreds known as the NAM founder lines, which represent a broad cross-section of modern maize diversity. Prior data show that gene content can differ by more than 5% across lines and that as much as half of the functional genetic information lies outside of genes in highly variable intergenic spaces. To capture and utilize this variation, the NAM founder inbreds have been sequenced and assembled by the NAM Consortium using PacBio long reads a mate-pair strategy. Scaffolds were validated by BioNano optical mapping, and ordered and oriented using linkage and pan-genome marker data. RNA-seq data from multiple tissues were used to annotate each genome using a pipeline that includes BRAKER, Mikado, and PASA. These data will help the maize community assess the role of structural variation such as presence-absence variation and copy number variation in the determination of agronomic traits.


Hosting status: (January, 2020)

  • FASTA for all genome assemblies and annotations are available in the MaizeGDB downloads section.
  • JBrowse instances for all assemblies are available here. All genomes are listed in the "Genome" menu on the top bar.
  • BLAST targets for all genome assemblies and annotations are available in the MaizeGDB BLAST tool
  • Genome assembly pages available for all NAM founders. See the list under "+ NAM founders" here.
  • Gene model pages available for all NAM founders. See the Gene/Gene Model data center.


All NAM assemblies and stock:
Assembly name GRIN stock accession
Zm-B97-REFERENCE-NAM-1.0 PI 564682
Zm-CML52-REFERENCE-NAM-1.0 PI 595561
Zm-CML69-REFERENCE-NAM-1.0 Ames 28184
Zm-CML103-REFERENCE-NAM-1.0 Ames 27081
Zm-CML228-REFERENCE-NAM-1.0 Ames 27088
Zm-CML247-REFERENCE-NAM-1.0 PI 595541
Zm-CML277-REFERENCE-NAM-1.0 PI 595550
Zm-CML322-REFERENCE-NAM-1.0 Ames 27096
Zm-CML333-REFERENCE-NAM-1.0 Ames 27101
Zm-HP301-REFERENCE-NAM-1.0 PI 587131
Zm-Il14H-REFERENCE-NAM-1.0 Ames 27118
Zm-Ki3-REFERENCE-NAM-1.0 Ames 27123
Zm-Ki11-REFERENCE-NAM-1.0 Ames 27124
Zm-Ky21-REFERENCE-NAM-1.0 Ames 27130
Zm-M37W-REFERENCE-NAM-1.0 Ames 27133
Zm-M162W-REFERENCE-NAM-1.0 Ames 27134
Zm-Mo18W-REFERENCE-NAM-1.0 PI 550441
Zm-Ms71-REFERENCE-NAM-1.0 PI 587137
Zm-NC350-REFERENCE-NAM-1.0 Ames 27171
Zm-NC358-REFERENCE-NAM-1.0 Ames 27175
Zm-Oh7B-REFERENCE-NAM-1.0 Ames 19323
Zm-Oh43-REFERENCE-NAM-1.0 Ames 19288
Zm-P39-REFERENCE-NAM-1.0 Ames 28186
Zm-Tx303-REFERENCE-NAM-1.0 Ames 19327
Zm-Tzi8-REFERENCE-NAM-1.0 PI 506246

FAQs
General Information about Nested Association Mapping (first developed in Maize!): https://en.wikipedia.org/wiki/Nested_association_mapping

First report of the maize NAM population: https://science.sciencemag.org/content/325/5941/737

Genetic Design and Statistical Power of NAM in Maize: https://www.ncbi.nlm.nih.gov/pmc/articles/PMC2206100/

How to Order NAM lines: http://maizecoop.cropsci.uiuc.edu/nam-rils.php


Coming soon to MaizeGDB

January 9th, 2020

Tracks

  • TE annotations
  • Structural Variations
  • SNPs used with the NAM RILs
  • SNPs used for IBM and LHRF RILs
  • Core Bin Markers
  • Insertion data
  • HapMap5
  • Ab initio gene models
  • B73v5 methylome
  • HiC data

Page updates

  • Core Bin Marker Pages
  • Additional functional annotations for NAM gene models
  • JBrowse snapshots within gene model pages
  • Pan-gene information on gene pages
  • Adding physical coordinates for each NAM line to NAM genetic map page

Tools

  • MaizeMine update to include v5 annotations
  • qTeller update to include NAM RNA-seq data

Features

  • Pangenome and syntenic ortholog information
  • External links to Apollo instances for manual structural annotations
  • V5 gene models linked to gene data
  • Current v5 gene models are evidence-based. Ab initio gene models will be added when available
  • Create links between GBrowse and JBrowse instances at MaizeGDB
  • Deploy JBrowse plugins to combine bigWig tracks