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Maize originated in southern Mexico from domestication of the wild grass teosinte, and diffused throughout the Americas. Sequenced DNA from archaeological samples spanning 6,000 years, documents the diffusion route and reveals the genes that were specifically selected for climatic and cultural adaptation to the US Southwest.

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.

Pan-cistrome of the maize leaf under well-watered and drought conditions profiled by haplotype-specific MOA-seq highlights the relevance of transcription factor binding QTLs for understanding phenotypic diversity in maize.

With a changing climate and a growing population, the world increasingly needs more-productive and resilient crops. But improving them requires a knowledge of what actually works in the field.

We must mine the biodiversity in seed banks to help to overcome food shortages, urge Susan McCouch and colleagues.

John Doebley and colleagues have identified a transposon insertion in the maize domestication gene, tb1, that acts as a regulatory enhancer. The transposon insertion appears to be a causative variant that partially explains major changes in plant architecture during maize domestication.

This study reports the genomic changes underlying the convergent and divergent agronomic improvement of the female and male heterotic groups during modern hybrid maize breeding, laying a foundation for the dissection and utilization of maize heterosis.

An example of hybrid incompatibility between maize and teosinte reveals a selfish toxin–antidote system mediated by small RNAs that may have contributed to the origin of maize.

The increased availability of reference genomes and the ability to obtain resequencing data in larger quantities are changing the capabilities of crop comparative genomics. Insights into the genetic basis of domestication and agriculturally important traits are emerging, and improved genomic tools have implications for crop breeders and evolutionary biologists.

A high-density genomic variation map from 744 genomes encompassing maize and all wild taxa of the genus Zea reveals evidence of adaptive variation and provides a genus-wide resource of genetic diversity in Zea.

Variation and evolution of DNA methylation during maize domestication remain largely unknown. Here, the authors generate genome and methylome sequencing data as well as HiChIP-based interactome data to investigate the adaptive and phenotypic consequences of methylation variations in maize.

Comparative genomics revealed similar distribution patterns of deleterious mutations in maize and sorghum but a post-domestication reduction of genetic load in sorghum, which is probably caused by sorghum’s high selfing rate and unique domestication history.

A study using population genomic data of domesticated and wild maize shows that purifying selection plays a major role in shaping maize diversity, and the efficacy of purifying selection increased following post-domestication population expansion.

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.

Structural variations in crop genomes are thought to be responsible for significant differences in phenotype and they can be well-represented by a ‘pan-genome’. Here, Lu et al.develop an approach to genetically map pan-genome sequence anchors using 14,129 inbred lines of maize, showing structural variation is a significant source of adaptive variation.

Genome-wide association analysis for morphological traits across 350 elite maize inbred lines in Chinese and US germplasm identifies loci and genomic regions representing the targets of selection during modern maize breeding.

Davide Sosso and colleagues show that SWEET4 hexose transporters are essential for grain filling in both maize and rice, and were likely selected during domestication to enhance sugar import into the endosperm.

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.