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Breeding crops with delayed senescence could plausibly increase grain yield. Here the authors show that variation at the rice SGR locus contributes to differences in senescence between indica and japonica subspecies and show that introgression can increase yield in an elite indica rice variety.

A map of fitness consequence scores is generated for 246 rice genome region classes inferred from nine functional genomic and epigenomic datasets, which illuminates the evolutionary forces associated with genome diversity and guides crop breeding.

Michael Purugganan reflects on a 100-year-old publication by Nikolai Vavilov, which postulated a new law of genetics from which key evolutionary insights emerged and which guided future molecular genetic investigations.

Analysis of the bracteatus pineapple genome provides insight into fiber production, color formation, sugar accumulation and fruit maturation. Resequencing of 89 Ananas genomes supports the coexistence of sexual recombination and a ‘one-step operation’ during domestication.

Phenotypic selection analysis is used to estimate the type and strength of selection that acts on more than 15,000 transcripts in rice (Oryza sativa), which provides insight into the adaptive evolutionary role of selection on gene expression.

Setaria pan-genome constructed using genome assemblies of 110 representative accessions and variation analyses provides insights into foxtail millet domestication and the genetic basis for crop improvement.

A population genomics study reveals a high similarity between a New World landrace of African rice and an Ivory Coast landrace. Together with diaries from captains of slave ships, the evidence presented traces the ancestry of the New World rice to its African origin.

Date palm is an important fruit crop in the Middle East and North Africa. Here, the authors report an improved genome assembly of this species and perform GWAS mapping of sex determining region and 21 fruit traits using high density SNP data generated from re-sequencing of the mapping population.

The domestication of African rice, Oryza glaberrima, occurred separately from that of the much more widespread Asian rice species Oryza sativa. Analysis of the whole-genome sequence for O. glaberrima shows the extent to which the same genes were involved in these distinct but parallel evolutionary events.

The transcription factor CONSTANS regulates the timing of flowering in Arabidopsis. Rosas et al. report that genetic variation in the cis-regulatory regions of this gene contributes to natural phenotypic variation in flowering time.

Asian rice cultivation has remained within consistent thermal limits for 9000 years while areas in Asia’s rice-producing nations exceeding these thresholds could expand 10-30 times by 2100, as revealed by contemporary, archaeological, and climate projection data.

A reconstruction of the genomic history of japonica and indica rice over 9,000 yr with geographic, environmental, archaeobotanical and paleoclimate data.

Date palm is a perennial fruit tree crop that thrives in arid environments of North Africa and the Middle East. Here Hazzouriet al. analyze the date palm germplasm by re-sequencing 62 different varieties and uncover selection signatures and candidate genes associated with important agronomic traits.

The recent improvement in technologies to identify genetic variants linked with quantitative traits has allowed the identification of variants that are associated with crop domestication. This Review considers these approaches and their application to the study of crop domestication.

Complementary single-cell and single-nucleus transcriptomic analyses of Zea mays, Sorghum bicolor and Setaria viridis root cells provide insights into the evolution of cell types and gene modules that control key traits in these important crop species.

Genetic diversity in social genes is expected to be shaped by conflict. Here, the authors show that in Dictyostelium discoideum, social genes in fact exhibit diversification patterns consistent with relaxed purifying selection, likely due to their expression only in intermittent social generations.

This Perspective on crop genomics discusses the promises of new technologies and approaches to help minimize food insecurity and to lay the foundation for sustainable agricultural systems needed to feed the world.

Rachel Meyer and colleagues use whole-genome resequencing of 93 African rice landraces to generate a SNP map used for population analysis and a genome-wide association study for salt tolerance traits. They find 11 significant loci, some with signatures of positive selection, and evidence for a population bottleneck beginning around 15,000 years ago.

Genomic technologies are helping researchers to understand the natural genetic variation that exists in wild and cultivated rice populations. Harnessing this genetic variation will be key to developing Green Super Rice varieties with high yield and low environmental costs.