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 genetic variation. 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

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

Information about assembly Zm-M162W-REFERENCE-NAM-1.0