Zm-NC350-REFERENCE-NAM-1.0 genome assembly
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The NAM parents sequencing project


NAM Consortium website: https://nam-genomes.github.io/


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, B73 and 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.

Learn more about maize genome sequencing here. Explore the NAM assemblies at the whole genome level here.

Important note: The NAM founders genome assemblies were released with a preliminary annotation. The official annotations are sufficiently different from the preliminary annotations that they have been given new names and gene models were given new identifiers. For example, the preliminary annotation for B97, Zm00018a.1 was replaced with annotation Zm00018ab.1. The new identifiers are numbered in sequential order.

Cross-reference files that translate between the preliminary and official annotations can be found in the MaizeGDB downloads and are linked in the table below.


The publication is available here:
De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes. Hufford et al., 2021


Data hosted at MaizeGDB:

  • FASTA for all genome assemblies and the official 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.
  • NAM genetic maps: 1 2 3 4 5 6 7 8 9 10

Additional data is available here.

B73 v5 assembly and stock
Assembly name GRIN stock accession Downloads Cross Reference
Zm-B73-REFERENCE-NAM-5.0 PI 677128 MaizeGDB Zm00001e.1->Zm00001eb.1


All NAM founder assemblies and stock:
Assembly name GRIN stock accession Downloads Cross Reference Subpopulation Stock GenBank
Zm-B97-REFERENCE-NAM-1.0 PI 692135 MaizeGDB Zm00018a.1->Zm00018ab.1 Non-stiff-stalk MaizeGDB GCA_902167075
Zm-CML52-REFERENCE-NAM-1.0 PI 692137 MaizeGDB Zm00019a.1->Zm00019ab.1 Tropical MaizeGDB GCA_902373975
Zm-CML69-REFERENCE-NAM-1.0 PI 692138 MaizeGDB Zm00020a.1->Zm00020ab.1 Tropical MaizeGDB GCA_902167135
Zm-CML103-REFERENCE-NAM-1.0 PI 692139 MaizeGDB Zm00021a.1->Zm00021ab.1 Tropical MaizeGDB GCA_902167055
Zm-CML228-REFERENCE-NAM-1.0 PI 692140 MaizeGDB Zm00022a.1->Zm00022ab.1 Tropical MaizeGDB GCA_902167155
Zm-CML247-REFERENCE-NAM-1.0 PI 692141 MaizeGDB Zm00023a.1->Zm00023ab.1 Tropical MaizeGDB GCA_902166975
Zm-CML277-REFERENCE-NAM-1.0 PI 692142 MaizeGDB Zm00024a.1->Zm00024ab.1 Tropical MaizeGDB GCA_902166985
Zm-CML322-REFERENCE-NAM-1.0 PI 692143 MaizeGDB Zm00025a.1->Zm00025ab.1 Tropical MaizeGDB GCA_902167095
Zm-CML333-REFERENCE-NAM-1.0 PI 692144 MaizeGDB Zm00026a.1->Zm00026ab.1 Tropical MaizeGDB GCA_902167025
Zm-HP301-REFERENCE-NAM-1.0 PI 692145 MaizeGDB Zm00027a.1->Zm00027ab.1 Popcorn MaizeGDB GCA_902167085
Zm-Il14H-REFERENCE-NAM-1.0 PI 692146 MaizeGDB Zm00028a.1->Zm00028ab.1 Sweet corn MaizeGDB GCA_902167065
Zm-Ki3-REFERENCE-NAM-1.0 PI 692147 MaizeGDB Zm00029a.1->Zm00029ab.1 Tropical MaizeGDB GCA_902167105
Zm-Ki11-REFERENCE-NAM-1.0 PI 692148 MaizeGDB Zm00030a.1->Zm00030ab.1 Tropical MaizeGDB GCA_902167115
Zm-Ky21-REFERENCE-NAM-1.0 PI 692149 MaizeGDB Zm00031a.1->Zm00031ab.1 Non-stiff-stalk MaizeGDB GCA_902167045
Zm-M37W-REFERENCE-NAM-1.0 PI 692150 MaizeGDB Zm00032a.1->Zm00032ab.1 Temporate/tropical mix MaizeGDB GCA_902167175
Zm-M162W-REFERENCE-NAM-1.0 PI 692151 MaizeGDB Zm00033a.1->Zm00033ab.1 Non-stiff-stalk MaizeGDB GCA_902166995
Zm-Mo18W-REFERENCE-NAM-1.0 PI 692152 MaizeGDB Zm00034a.1->Zm00034ab.1 Temporate/Tropical mix MaizeGDB GCA_902167165
Zm-Ms71-REFERENCE-NAM-1.0 PI 692153 MaizeGDB Zm00035a.1->Zm00035ab.1 Non-stiff-stalk MaizeGDB GCA_902167375
Zm-NC350-REFERENCE-NAM-1.0 PI 692154 MaizeGDB Zm00036a.1->Zm00036ab.1 Tropical MaizeGDB GCA_902167005
Zm-NC358-REFERENCE-NAM-1.0 PI 692155 MaizeGDB Zm00037a.1->Zm00037ab.1 Tropical MaizeGDB GCA_902167035
Zm-Oh7B-REFERENCE-NAM-1.0 PI 692156 MaizeGDB Zm00038a.1->Zm00038ab.1 Non-stiff-stalk MaizeGDB GCA_902166955
Zm-Oh43-REFERENCE-NAM-1.0 PI 692157 MaizeGDB Zm00039a.1->Zm00039ab.1 Non-stiff-stalk MaizeGDB GCA_902167015
Zm-P39-REFERENCE-NAM-1.0 PI 692158 MaizeGDB Zm00040a.1->Zm00040ab.1 Sweet corn MaizeGDB GCA_902166965
Zm-Tx303-REFERENCE-NAM-1.0 PI 692159 MaizeGDB Zm00041a.1->Zm00041ab.1 Temporate/tropical mixed MaizeGDB GCA_902167205
Zm-Tzi8-REFERENCE-NAM-1.0 PI 692160 MaizeGDB Zm00042a.1->Zm00042ab.1 Tropical MaizeGDB GCA_902167185

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