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An improved reference genome for maize, using single-molecule sequencing and high-resolution optical mapping, enables characterization of structural variation and repetitive regions, and identifies lineage expansions of transposable elements that are unique to maize.

The nucleotide diversity present in maize exceeds that in humans by an order of magnitude, and it has been challenging to characterize the high levels of diversity in this important crop. Doreen Ware and colleagues have identified 55 million SNPs in 103 domesticated and pre-domestication Zea mays varieties, as well as in a representative from the sister genus Tripsacum.

Inflorescence architecture affects crop grain yield. Here, the authors deploy whole-genome sequencing-based bulk segregant analysis to identify the causal gene of a sorghum multi-seeded (msd) mutant and suggest MSD1 regulating the fertility of the pedicellate spikelets through jasmonic acid pathway.

MaizeCODE maps active regulatory regions tied to maize domestication traits in a diverse panel of tissues and inbreds. It reveals bi-directional enhancer RNAs and the molecular conflicts between activity and silencing of non-coding regions.

Genome assemblies of 13 domesticated and wild rice relatives reveal salient features of genome evolution across the genus Oryza, especially rapid species diversification and turnover of transposons. This study also releases a complete long-read assembly of IR 8 ‘Miracle Rice’.

Sequence depth and read length determine the quality of genome assembly. Here, the authors leverage a set of PacBio reads to develop guidelines for sequencing and assembly of complex plant genomes in order to allocate finite resources using maize as an example.

An almost-complete, sequence-verified collection of Arabidopsis thaliana root stele transcription factors is reported. The authors use it in the enhanced yeast-one hybrid (eY1H) assay to map gene regulatory interactions in the plant. Also in this issue, Reece-Hoyes et al. describe the eY1H pipeline.

Zea mays is an important crop species and genetic model but uncertainties remain regarding the structure of the transcriptome. Here Wang et al. use single-molecule sequencing and size-fractionated libraries to identify novel transcripts and isoforms illustrating the complexity of maize mRNA.

Trait introgression requires universal markers, but cross-species transferability of current SNP markers can be as low as 2%. Here, the authors use an AmpSeq haplotype strategy targeting the collinear core genome for marker development and show transferability increases to 91.4% in the Vitis genus.

Sequencing and de novo assembly of the maize W22 reference genome enable accurate placement of Mutator (Mu) and Dissociation (Ds) transposable element insertions, providing a foundation for maize functional genomics and transposon biology.

Sorghum is an African grass that is grown for food, animal feed and fuel. The current paper presents an initial analysis of the ∼730 megabase genome of Sorghum bicolor. Genome analysis and its comparison with maize and rice shed light on grass genome evolution and also provide insights into the evolution of C₄ photosynthesis, as well as protein coding genes and miRNAs that might contribute to sorghum's drought tolerance.

The de novo genome assembly of maize line Mo17 and comparative analysis with other sequenced maize lines show extensive gene-order variations. This study provides insights into maize evolution and has implications for improving maize hybrid lines.

The yeast one-hybrid network for nitrogen-associated metabolism in Arabidopsis reveals the transcription factors that regulate the architecture of root and shoot systems under conditions of changing nitrogen availability.

This paper reports the genome sequence of domesticated tomato, a major crop plant, and a draft sequence for its closest wild relative; comparative genomics reveal very little divergence between the two genomes but some important differences with the potato genome, another important food crop in the genus Solanum.

Jeff Ross-Ibarra and colleagues report a population genomic analysis of maize evolution. They analyze genome-wide evidence for selection during the initial domestication of wild maize and during the improvement of landraces to modern inbred breeds. Their findings suggest stronger selection during domestication compared to improvement.

James Holland and colleagues report a genome-wide association study for resistance to Southern Leaf Blight (SLB) in the maize nested association mapping population. Linkage mapping identified 32 QTLs linked to SLB resistance, and association tests showed that 51 SNPs, many located within the QTL intervals, are significantly associated with SLB resistance.

Bo Wang et al. report an isoform-level phasing study in maize using long-read cDNA sequencing and a new method, IsoPhase, to annotate allele-specific, gene-level and isoform-level expression. They identify novel gene isoforms, imprinted genes, and variation in cis- and trans-regulatory effects.