De novo assembly, annotation, and comparative analysis of 26 diverse maize genomes

Abstract

We report de novo genome assemblies, transcriptomes, annotations, and methylomes for the 26 inbreds that serve as the founders for the maize nested association mapping population. The number of pan-genes in these diverse genomes exceeds 103,000, with approximately a third found across all genotypes. The results demonstrate that the ancient tetraploid character of maize continues to degrade by fractionation to the present day. Excellent contiguity over repeat arrays and complete annotation of centromeres revealed additional variation in major cytological landmarks. We show that combining structural variation with single-nucleotide polymorphisms can improve the power of quantitative mapping studies. We also document variation at the level of DNA methylation and demonstrate that unmethylated regions are enriched for cis-regulatory elements that contribute to phenotypic variation.

A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean

“…A species wide record of NLR genes (called pan-NLRome) was recently reported in Arabidopsis , providing a panoramic view of important NLR genes in the model plant species 22 . More recently, 26 diverse maize genomes were sequenced, allowing for a glimpse of the haplotypic variation in the rp1 region 23 . The region exhibited drastic inter-genomic copy number variation of rp1 , but a subset of these genomes still have gaps in this region, and the structure and evolutionary processes of the rp1 region and many other NLR clusters in the genomes remain to be analyzed.…”

Maize Transformation: From Plant Material to the Release of Genetically Modified and Edited Varieties

“…In Australia, Canada, India, and the USA, these products are reviewed on a case-by-case basis, whereas in the European Union, cisgenic and intragenic plants are regulated as regular GM organisms ( Hull et al, 2021 ). Although no commercial cisgenic or intragenic maize has been launched to date, studies based on the genome-wide association and genome sequencing of maize lines will certainly lead to the identification of genes with the potential to improve cultivated genotypes using a cisgene/intragene approach ( Hufford et al, 2021 ).…”

“…Recent advances in the transformation and regulatory aspects of genetically modified/edited maize plants have encouraged academic and private facilities to provide transformation services, which has allowed small research groups and companies to test their genes and alleles. In addition, the genome sequences of several maize lines and hybrids are already available ( Hufford et al, 2021 ), which allows the design of strategies for genetic modification/edition using improved transformation protocols. These improvements will allow the evaluation of an increasing number of genes and alleles associated with desirable agronomic traits ( Portwood et al, 2019 ).…”

QTL Map of Early- and Late-Stage Perennial Regrowth in Zea diploperennis

“…The GATK Best Practices Pipeline for Germline short variant discovery was applied to call SNPs and determine SNP-index from Illumina data (DePristo et al, 2011;Poplin et al, 2017). Briefly, reads were mapped to the P39 reference (Hufford et al, 2021) using BWA MEM v0.7.15 (Li, 2013), sorted using SAMtools sort v1.3.1 (Li et al, 2009), and duplicate reads were marked using Picard 1 . HaplotypeCaller (GATK/4.0.11.0) using default settings followed by GenotypeGVCFs were used to call SNPs from "Gigi, " RG, and NRG samples and 34,235,573 raw SNPs were identified.…”

“…Segregation distortion was analyzed using the geno.table() function, however, no markers showing significant segregation distortion were found. The markers were placed in the order they occur in the P39v1 physical map (Hufford et al, 2021) and genetic map distances were estimated with the est.rf() function. The genetic distances were consistent with the ordering on the physical map.…”