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Stable isotope biochemistry (δ¹³C and δ¹⁵N) and radiocarbon dating of ancient human and animal bone document 2 distinct phases of plant and animal domestication at the Dadiwan site in northwest China. The first was brief and nonintensive: at various times between 7900 and 7200 calendar years before present (calBP) people harvested and stored enough broomcorn millet (Panicum miliaceum) to provision themselves and their hunting dogs (Canis sp.) throughout the year. The second, much more intensive phase was in place by 5900 calBP: during this time both broomcorn and foxtail (Setaria viridis spp. italica) millets were cultivated and made significant contributions to the diets of people, dogs, and pigs (Sus sp.). The systems represented in both phases developed elsewhere: the earlier, low-intensity domestic relationship emerged with hunter-gatherers in the arid north, while the more intensive, later one evolved further east and arrived at Dadiwan with the Yangshao Neolithic. The stable isotope methodology used here is probably the best means of detecting the symbiotic human-plant-animal linkages that develop during the very earliest phases of domestication and is thus applicable to the areas where these connections first emerged and are critical to explaining how and why agriculture began in East Asia.

Tolpyralate is a new 4-hydroxyphenyl-pyruvate dioxygenase (HPPD)–inhibiting herbicide for weed control in corn. Previous research has reported efficacy of tolpyralate + atrazine on several annual grass and broadleaf weed species; however, no studies have evaluated weed control of tolpyralate + atrazine depending on time-of-day (TOD) of application. Six field experiments were conducted over a 2-yr period (2018, 2019) near Ridgetown, ON, to determine if there is an effect of TOD of application on tolpyralate + atrazine efficacy on common annual grass and broadleaf weeds. An application was made at 3-h intervals beginning at 06:00 h with the last application at 24:00 h. There was a slight TOD effect on velvetleaf, pigweed species, and common ragweed control with tolpyralate + atrazine; however, the magnitude of change throughout the day was ≤3% at 2, 4, or 8 wk after application (WAA). There was no effect of TOD of tolpyralate + atrazine on the control of lambsquarters, barnyardgrass, and green foxtail. All weed species were controlled ≥88% at 8 WAA. There was no effect of TOD of tolpyralate + atrazine application on corn yield. Results of this study show no evidence of a TOD effect on weed control efficacy with tolpyralate + atrazine. Nomenclature: Atrazine; tolpyralate; barnyardgrass; Echinochloa crus-galli (L.) P. Beauv.; common ragweed; Ambrosia artemisiifolia L.; green foxtail; Setaria viridis (L.) P. Beauv; hemp sesbania; Sesbania herbacea (Mill.) McVaugh; lambsquarters; Chenopodium album L.; redroot pigweed; Amaranthus retroflexus L.; sicklepod; Senna obtusifolia (L.) H.S. Irwin & Barneby; velvetleaf; Abutilon theophrasti Medik.; corn; Zea mays L.

The weedy Setaria species (giant, green, yellow, knotroot, and bristly foxtail) compose one of the worst weed groups interfering with world agriculture and in other disturbed and managed habitats. These species, together with their crop counterparts (foxtail millet, korali), form the foxtail species-group (spp.-gp). Five successive waves of Setaria spp. invasion from preagricultural times to the present have resulted in widespread infestation of the disturbed, arable, temperate regions of the earth. These invasions have resulted in considerable economic and environmental costs. The success of the Setaria spp.-gp is because of their intimate evolutionary relationship with humans, disturbance, agriculture, and land management. The ability to adapt rapidly to local conditions is the hallmark of this weedy group. Genotypic and phenotypic biodiversity provides this spp.-gp with traits that allow it to invade, colonize, adapt to, and endure in a wide range of habitats around the world. The phenotypic life-history traits important to the success of weedy Setaria spp. begin with the induction of dormancy in seed during embryogenesis. The formation of long-lived, heterogeneous seed pools in the soil is the inevitable consequence of the dormant seed rain. In soil seed pools, after-ripening, the occurrence and timing of seedling emergence, and the induction of secondary (summer) dormancy are regulated by seasonally and diurnally varying soil oxygen, water, and temperature signals. Precise and variable timing of seedling emergence ensures Setaria a dominant place in disturbed and managed communities during the growth and reproductive phases that follow. Once established in a community, phenotypic plasticity inherent in an individual weedy Setaria sp. allows it to maximize its growth, form, and reproduction to the specific local conditions it encounters, including competitive interactions with neighbors. Traits controlling the plastic development of plant architecture include the ability to form one or more tillering shoots whose stature and number are precisely sized to local conditions. A complex pattern of branching, from plant to spikelet, provides diverse microenvironments within which different levels of dormancy are induced in individual seeds on a panicle and among panicles on a common plant. Traits for adaptation to stress in weedy Setaria spp. include tolerance to many inhibitory chemicals (e.g., herbicides, salt), mechanical damage, and drought. Genetic traits such as self-pollination and small genome size contribute to a highly diverse collection of locally adapted genotypes and phenotypes ready to exploit any opportunities provided by a cropping system. Self-pollinating Setaria spp. exist in wild, weed, and crop variants, an ideal genetic condition ensuring both long-term stability and novelty. Weedy Setaria spp. populations have low to exceedingly low amounts of total genetic variation, unusually low intrapopulation genetic diversity, and unusually high genetic diversity between populations compared with an average plant species. These traits result spatially in local populations that are unusually homogeneous, typically consisting of a single multilocus genotype. Either a generally or a specifically adapted genotype of an individual species might predominate in that local population. Across the landscape, different single-genotype populations dominate particular local sites, providing novel genetics to the region by dispersal and gene flow when conditions change. Across North America, populations of green foxtail and knotroot foxtail are genetically differentiated along a north–south gradient. The history of invasion and colonization, the successful life histories of locally adapted weedy Setaria spp., and the evolutionary potential of this weed group emphasize the need for accurate prediction of its behavior. Weedy Setaria spp. management is the management of local selection pressure and consequent adaptation. Farmers, land managers, policy makers and regulators, homeowners, and consumers need accurate information about weedy Setaria spp. to predict and guide management decisions based on economics, risk, and environmental sustainability. Nomenclature: Green foxtail, Setaria viridis, subspecies viridis (L.) Beauv. SETVI; foxtail millet, Setaria viridis, subspecies italica SETIT; korali = yellow foxtail, Setaria pumila (Poir) Roem. & Schult. = Setaria glauca (L.) Beauv. SETLU; giant foxtail, Setaria faberi Herrm. SETFA; bristly foxtail, Setaria verticillata (L.) Beauv. SETVE; knotroot foxtail, Setaria geniculata (Lam.) Beauv. SETGE.

Setaria viridis (L.) P. Beauv. and its domesticated form, S. italica (L.) P. Beauv., have been developed over the past few years as model systems for C 4 photosynthesis and for the analysis of bioenergy traits. S. viridis is native to Eurasia, but is now a ubiquitous weed. An analysis of the population structure of a set of 232 S. viridis lines, mostly from North America but also comprising some accessions from around the world, using 11 SSR markers, showed that S. viridis populations in the US largely separate by latitude and/or climatic zone. S. viridis populations from the Northern US and Canada (north of 44°N) group with accessions from Western Europe, while populations in the Mid and Southern US predominantly group with accessions from Turkey and Iran. We hypothesize that S. viridis in the US was most likely introduced from Europe, and that introductions were competitive only in regions that had climatic conditions that were similar to those in the regions of origins. This hypothesis is supported by the fact that Canadian S. viridis lines were fast cycling and undersized when grown in the Mid-Western and Southern US compared to their morphology in their native environment. A comparison of the population structure obtained with 11 SSR markers and ~40,000 single nucleotide polymorphisms (SNPs) in a common set of S. viridis germplasm showed that both methods essentially yielded the same groupings, although admixture was identified at a higher frequency in the SNP analysis. Small numbers of SSR markers can thus be used effectively to discern the population structure in this inbreeding species.

Different plant species within the grasses were parallel targets of domestication, giving rise to crops with distinct evolutionary histories and traits 1 . Key traits that distinguish these species are mediated by specialized cell types 2 . Here we compare the transcriptomes of root cells in three grass species— Zea mays , Sorghum bicolor and Setaria viridis . We show that single-cell and single-nucleus RNA sequencing provide complementary readouts of cell identity in dicots and monocots, warranting a combined analysis. Cell types were mapped across species to identify robust, orthologous marker genes. The comparative cellular analysis shows that the transcriptomes of some cell types diverged more rapidly than those of others—driven, in part, by recruitment of gene modules from other cell types. The data also show that a recent whole-genome duplication provides a rich source of new, highly localized gene expression domains that favour fast-evolving cell types. Together, the cell-by-cell comparative analysis shows how fine-scale cellular profiling can extract conserved modules from a pan transcriptome and provide insight on the evolution of cells that mediate key functions in crops. 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.

Wild and weedy relatives of domesticated crops harbor genetic variants that can advance agricultural biotechnology. Here we provide a genome resource for the wild plant green millet (Setaria viridis), a model species for studies of C4 grasses, and use the resource to probe domestication genes in the close crop relative foxtail millet (Setaria italica). We produced a platinum-quality genome assembly of S. viridis and de novo assemblies for 598 wild accessions and exploited these assemblies to identify loci underlying three traits: response to climate, a ‘loss of shattering’ trait that permits mechanical harvest and leaf angle, a predictor of yield in many grass crops. With CRISPR–Cas9 genome editing, we validated Less Shattering1 (SvLes1) as a gene whose product controls seed shattering. In S. italica, this gene was rendered nonfunctional by a retrotransposon insertion in the domesticated loss-of-shattering allele SiLes1-TE (transposable element). This resource will enhance the utility of S. viridis for dissection of complex traits and biotechnological improvement of panicoid crops.Sequencing wild relatives of millet identifies genes that regulate yield and harvesting traits.

Completion of genome sequences for the diploid Setaria italica reveals features of C 4 photosynthesis that could enable improvement of the polyploid biofuel crop switchgrass ( Panicum virgatum ). The genetic basis of biotechnologically relevant traits, including drought tolerance, photosynthetic efficiency and flowering control, is also highlighted. We generated a high-quality reference genome sequence for foxtail millet ( Setaria italica ). The ∼400-Mb assembly covers ∼80% of the genome and >95% of the gene space. The assembly was anchored to a 992-locus genetic map and was annotated by comparison with >1.3 million expressed sequence tag reads. We produced more than 580 million RNA-Seq reads to facilitate expression analyses. We also sequenced Setaria viridis , the ancestral wild relative of S. italica , and identified regions of differential single-nucleotide polymorphism density, distribution of transposable elements, small RNA content, chromosomal rearrangement and segregation distortion. The genus Setaria includes natural and cultivated species that demonstrate a wide capacity for adaptation. The genetic basis of this adaptation was investigated by comparing five sequenced grass genomes. We also used the diploid Setaria genome to evaluate the ongoing genome assembly of a related polyploid, switchgrass ( Panicum virgatum ).

* Mesophyll conductance (g sub(m)) is an important factor limiting rates of C sub(3) photosynthesis. However, its role in C sub(4) photosynthesis is poorly understood because it has been historically difficult to estimate. * We use two methods to derive the temperature responses of g sub(m) in C sub(4) species. The first ( Delta super(18)O) combines measurements of gas exchange with models and measurements of super(18)O discrimination. The second method (in vitro V sub(pmax)) derives g sub(m) by retrofitting models of C sub(4) photosynthesis and super(13)C discrimination with gas exchange, kinetic constants and in vitro V sub(pmax) measurements. * The two methods produced similar g sub(m) for Setaria viridis and Zea mays. Additionally, we present the first temperature response (10-40 degree C) of C sub(4) g sub(m) in S. viridis, Z. mays and Miscanthus giganteu s. Values for g sub(m) at 25 degree C ranged from 2.90 to 7.85 mu mol m super(-2) s super(-1) Pa super(-1). * Our study demonstrated that: the two described methods are suitable to calculate g sub(m) in C sub(4) species; g sub(m) values in C sub(4) are similar to high-end values reported for C sub(3) species; and g sub(m) increases with temperature analogous to reports for C sub(3) species and the response is species specific. These results improve our mechanistic understanding of C sub(4) photosynthesis.

Bin Han and colleagues report de novo assembly of the genome of a wild progenitor ( Setaria viridis ) of foxtail millet and low-pass resequencing of 916 diverse foxtail millet varieties. They identify 0.8 million common SNPs, construct a haplotype map of foxtail millet and perform genome-wide association studies on 47 agronomic traits. Foxtail millet ( Setaria italica ) is an important grain crop that is grown in arid regions. Here we sequenced 916 diverse foxtail millet varieties, identified 2.58 million SNPs and used 0.8 million common SNPs to construct a haplotype map of the foxtail millet genome. We classified the foxtail millet varieties into two divergent groups that are strongly correlated with early and late flowering times. We phenotyped the 916 varieties under five different environments and identified 512 loci associated with 47 agronomic traits by genome-wide association studies. We performed a de novo assembly of deeply sequenced genomes of a Setaria viridis accession (the wild progenitor of S. italica ) and an S. italica variety and identified complex interspecies and intraspecies variants. We also identified 36 selective sweeps that seem to have occurred during modern breeding. This study provides fundamental resources for genetics research and genetic improvement in foxtail millet.

Many important crops are members of the Poaceae family, which develop root systems characterized by a high degree of root initiation from the belowground basal nodes of the shoot, termed the crown. Although this postembryonic shoot-borne root system represents the major conduit for water uptake, little is known about the effect of water availability on its development. Here we demonstrate that in the model C₄ grass Setaria viridis, the crown locally senses water availability and suppresses postemergence crown root growth under a water deficit. This response was observed in field and growth room environments and in all grass species tested. Luminescence-based imaging of root systems grown in soil-like media revealed a shift in root growth from crown-derived to primary root-derived branches, suggesting that primary root-dominated architecture can be induced in S. viridis under certain stress conditions. Crown roots of Zea mays and Setaria italica, domesticated relatives of teosinte and S. viridis, respectively, show reduced sensitivity to water deficit, suggesting that this response might have been influenced by human selection. Enhanced water status of maize mutants lacking crown roots suggests that under a water deficit, stronger suppression of crown roots actually may benefit crop productivity.