OBITUARY Heinrich Rohrer, pioneer of scanning tunnelling microscopy, remembered p.30 GENES US Supreme Court patent rulings set a higher bar for innovation p.29 ART Exhibition revels in the power of unconstrained thought p.28 SPACE An elegy for the disappearing dark, banished by science p.26 Feeding the future We must mine the biodiversity in seed banks to help to overcome food shortages, urge Susan McCouch and colleagues. The International Center for Tropical Agriculture in Colombia holds 65,000 crop samples from 141 countries.

BackgroundThe expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplification and insertion of the 5-enolpyruvylshikimate-3-phosphate synthase (EPSPS) gene across the genome. Increased EPSPS gene copy numbers results in higher titers of the EPSPS enzyme, the target of glyphosate, and confers resistance to glyphosate treatment. To understand the genomic unit and mechanism of EPSPS gene copy number proliferation, we developed and used a bacterial artificial chromosome (BAC) library from a highly resistant biotype to sequence the local genomic landscape flanking the EPSPS gene.ResultsBy sequencing overlapping BACs, a 297 kb sequence was generated, hereafter referred to as the “EPSPS cassette.” This region included several putative genes, dense clusters of tandem and inverted repeats, putative helitron and autonomous replication sequences, and regulatory elements. Whole genome shotgun sequencing (WGS) of two biotypes exhibiting high and no resistance to glyphosate was performed to compare genomic representation across the EPSPS cassette. Mapping of sequences for both biotypes to the reference EPSPS cassette revealed significant differences in upstream and downstream sequences relative to EPSPS with regard to both repetitive units and coding content between these biotypes. The differences in sequence may have resulted from a compounded-building mechanism such as repetitive transpositional events. The association of putative helitron sequences with the cassette suggests a possible amplification and distribution mechanism. Flow cytometry revealed that the EPSPS cassette added measurable genomic content.ConclusionsThe adoption of glyphosate resistant cropping systems in major crops such as corn, soybean, cotton and canola coupled with excessive use of glyphosate herbicide has led to evolved glyphosate resistance in several important weeds. In Amaranthus palmeri, the amplification of the EPSPS cassette, characterized by a complex array of repetitive elements and putative helitron sequences, suggests an adaptive structural genomic mechanism that drives amplification and distribution around the genome. The added genomic content not found in glyphosate sensitive plants may be driving evolution through genome expansion.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-016-3336-4) contains supplementary material, which is available to authorized users.

The angiosperm family Brassicaceae contains both the research model Arabidopsis (Arabidopsis thaliana) and the agricultural genus Brassica. Comparative genomics in the Brassicaceae has largely focused on direct comparisons between Arabidopsis and the species of interest. However, the reduced genome size and chromosome number (n 5 5) of Arabidopsis complicates comparisons. Arabidopsis shows extensive genome and chromosome reshuffling compared to its close relatives Arabidopsis lyrata and Capsella rubella, both with n 5 8. To facilitate comparative genomics across the Brassicaceae we recently outlined a system of 24 conserved chromosomal blocks based on their positions in an ancestral karyotype of n 5 8, rather than by their position in Arabidopsis. In this report we use this system as a tool to understand genome structure and evolution in Boechera stricta (n 5 7). B. stricta is a diploid, sexual, and highly self-fertilizing species occurring in mostly montane regions of western North America. We have created an F 2 genetic map of B. stricta based on 192 individuals scored at 196 microsatellite and candidate gene loci. Single-nucleotide polymorphism genotyping of 94 of the loci was done simultaneously using an Illumina bead array. The total map length is 725.8 cM, with an average marker spacing of 3.9 cM. There are no gaps greater than 19.3 cM. The chromosomal reduction from n 5 8 to n 5 7 and other genomic changes in B. stricta likely involved a pericentric inversion, a chromosomal fusion, and two reciprocal translocations that are easily visualized using the genomic blocks. Our genetic map will facilitate the analysis of ecologically relevant quantitative variation in Boechera.Comparative genetic mapping between related organisms within a phylogenetic framework is a powerful method for understanding genome evolution. Comparative mapping in the grass family (Poaceae) has been successful in detecting collinear genomic regions between a number of domesticated cereal and forage crops, leading to the formulation of the crop circle with rice (Oryza sativa) at the center (Moore et al., 1995;Devos, 2005). Rice was selected as the reference point because of its small genome and vast genomic resources, and not because it was phylogenetically well positioned to facilitate comparisons within the family. An analogous situation occurs in the dicot family Brassicaceae, which contains both the model species Arabidopsis (Arabidopsis thaliana) as well as the domesticated Brassica species. To date, most comparative genomics in the Brassicaceae has largely focused on direct comparisons between Arabidopsis and the species of interest. However, several of the factors that made Arabidopsis ideal for genome sequencing, particularly its reduced genome size and chromosome number (157 Mb, n 5 5; AGI, 2000;Johnston et al., 2005), complicate its use as a standard in comparative genomics. Recent phylogenetic results have demonstrated that genome and chromosome reduction in Arabidopsis are derived characteristics from its close relatives with...

Weedy red rice (Oryza sativa) is a problematic weed in cultivated rice. About 50% of US rice is produced in Arkansas and 60% of these fields have some red rice infestation. Red rice populations are morphologically and phenologically diverse. We hypothesise that red rice in Arkansas has high genetic diversity, which underlies its wide phenotypic diversity, and that some alleles from cultivated rice have been introgressed into red rice during more than a century of coexistence. We tested 137 red rice accessions from four ecological zones in Arkansas and 36 cultivars that have been grown in Arkansas in the past century. Twenty-seven rice microsatellite primers, distributed across 12 chromosomes, were used to generate molecular markers. The overall NeiÕs genetic distance (GD) of red rice accessions was 0.70. Rice grown in the last century had an overall GD of 0.26. The awnless strawhull red rice was genetically distant from blackhull (GD = 0.55) and brownhull (GD = 0.60) red rice types. NeiÕs GD between blackhull and brownhull red rice was 0.42. Brownhull and blackhull formed one genotypic cluster, whereas the majority of strawhull red rice formed another cluster. Within blackhull red rice, the GD was 0.76, whereas for awnless strawhull it was 0.68, 0.75 for awned strawhull and 0.80 for brownhull types. The gene diversity of blackhull and strawhull correlated with zone of origin. A quarter of the red rice accessions share common alleles with cultivated rice. A diverse complex of weedy populations has evolved in a region devoid of other weedy and wild Oryza species.