Setaria Research Articles

Residual weeds in winter wheat in Manitoba

Cavalieri, A., Lewis, D. W. and Gulden, R. H. 2013. Residual weeds in winter wheat in Manitoba. Can. J. Plant Sci. 93: 1195-1200. Winter wheat production has increased from a few thousand to several hundred thousand acres in Manitoba over the past decade. In the summer of 2009, a mid-season weed survey was conducted to establish a benchmark of the residual weed community in winter wheat in three ecoregions in Manitoba. Field histories and herbicide management practices were also recorded for all 84 fields surveyed. Traditionally important weeds in other field crops such as green foxtail [Setaria viridis (L.) Beauv.], wild oats (Avena fatua L.) and wild buckwheat (Polygonum convolvulus L.) were also the most abundant weeds in winter wheat. A species never observed in production fields, waterpod [Ellisia nyctelea (L.) L.] was documented. Neither Japanese brome grass (Bromus japonicum L.) nor downy brome (Bromus tectorum L.), winter annuals often prevalent in winter wheat, were found.

Phytolith production in wetland plants of the Hangzhou Xixi Wetlands ecosystem

Phytoliths，also referred to as plant opal，are silicified features that form as a result of biomineralization within plants and plays an important role in terrestrial biogeochemical cycles of carbon and silicon. This study selected 18 different plant species at the Xixi Wetlands in Zhejiang Province，to determine the phytolith content and its production flux using microwave，Walkley-Black digestion，and a correlation analysis. The main purpose of this study is to provide scientific reference for understanding the role of phytoliths in biogeochemical cycles of silicon and carbon. Results showed strong variation in phytolith content among the 18 plants：Cortaderia selloana（7.7%），Setaria viridis（7.6%），Digitaria ternata（6.9%），and Phragmites australis （6.6%）were higher than Salvinia natans（1.3%），Halerpestes cymbalaria（1.1%），and Canna indica L.（1.0%）. A positive correlation between phytolith content and total SiO2 in the 18 plants（R2=0.663 3，P＜0.01）was also found. Phytolith production flux was 4.48-129.92 gm-2a-1；phytolith sequestration of atmospheric CO2 was 0.16-1.03 gm-2a-1；and the phytolith sequestration rate of atmospheric CO2 was 8.29 ta-1. So，it is very important to improve the flux of aboveground plant phytolith production in wetlands ecosystems by selecting a plant with high-phytolith（silicon）content and high-ANPP（aboveground net primary production）yields for the plant Phragmites australis.［Ch，1 fig. 1 tab. 35 ref.］

Setaria genome sequencing: an overview

The genus Setaria includes two important C4 Panicoid grass species, namely S. italica (cultivated) and S. viridis (weed; wild ancestor), which together represent an appropriate model system for architectural, physiological, evolutionary, and genomic studies in related grasses. It is a diploid, inbreeder, self-fertile annual cereal grass having short life cycle and minimal growth requirements. There close relatedness to biofuel crops like switch grass and napier grass further signifies their importance. Further, foxtail millet is an important food and fodder grain crop grown in arid and semi-arid regions in many parts of the world. Therefore, an increasing interest in these species has led to a gradual accumulation and development of genomic data and genetic resources. Setaria genome sequencing is an outcome of such endeavors. These sequencing efforts uncovered several distinctive attributes of Setaria genome that may help in understanding its physiology, evolution and adaptation. This will not only aid in comparative genomics studies of Setaria and related crops including bioenergy grasses but also help in rapid advancements of genomics information for developing varieties with superior traits either through marker-assisted selection (MAS) or using transgenic approaches in these crops.

Novel genomes and genome constitutions identified by GISH and 5S rDNA and knotted1 genomic sequences in the genus Setaria

BackgroundThe Setaria genus is increasingly of interest to researchers, as its two species, S. viridis and S. italica, are being developed as models for understanding C4 photosynthesis and plant functional genomics. The genome constitution of Setaria species has been studied in the diploid species S. viridis, S. adhaerans and S. grisebachii, where three genomes A, B and C were identified respectively. Two allotetraploid species, S. verticillata and S. faberi, were found to have AABB genomes, and one autotetraploid species, S. queenslandica, with an AAAA genome, has also been identified. The genomes and genome constitutions of most other species remain unknown, even though it was thought there are approximately 125 species in the genus distributed world-wide.ResultsGISH was performed to detect the genome constitutions of Eurasia species of S. glauca, S. plicata, and S. arenaria, with the known A, B and C genomes as probes. No or very poor hybridization signal was detected indicating that their genomes are different from those already described. GISH was also performed reciprocally between S. glauca, S. plicata, and S. arenaria genomes, but no hybridization signals between each other were found. The two sets of chromosomes of S. lachnea both hybridized strong signals with only the known C genome of S. grisebachii. Chromosomes of Qing 9, an accession formerly considered as S. viridis, hybridized strong signal only to B genome of S. adherans. Phylogenetic trees constructed with 5S rDNA and knotted1 markers, clearly classify the samples in this study into six clusters, matching the GISH results, and suggesting that the F genome of S. arenaria is basal in the genus.ConclusionsThree novel genomes in the Setaria genus were identified and designated as genome D (S. glauca), E (S. plicata) and F (S. arenaria) respectively. The genome constitution of tetraploid S. lachnea is putatively CCC’C’. Qing 9 is a B genome species indigenous to China and is hypothesized to be a newly identified species. The difference in genome constitution and origin of S. verticillata and S. faberi is also discussed. The new genomes and the genome constitutions of Setaria species identified in this report provide useful information for Setaria germplasm management, foxtail millet breeding, grass evolution and the development of S. viridis and S. italica as a new model for functional genomics.

Fenoxaprop for control of yellow bristle grass in pasture and its efficacy on other C<sub>4</sub> grasses

The efficacy of the herbicide fenoxaprop for control of yellow bristle grass (Setaria pumila) in pasture was evaluated in two field trials Additionally glasshouse experiments investigated its phytotoxicity on seven annual and four perennial C4 grass species Results of the field trials showed good control of yellow bristle grass and consequently a very high (up to 98) reduction in seed head production Fenoxaprop had no measurable effect on clover yield but the removal of yellow bristle grass resulted in higher production of perennial ryegrass (Lolium perenne) Fenoxaprop killed all the annual C4 species tested viz yellow bristle grass summer grass (Digitaria sanguinalis) witchgrass (Panicum capillare) smooth witchgrass (Panicum dichotomiflorum) barnyard grass (Echinochloa crusgalli) broom corn millet (Panicum miliaceum) and crowfoot grass (Eleusine indica) but was less effective on the perennial C4 grass species viz Indian doab (Cynodon dactylon) Kikuyu grass (Cenchrus clandestinus) Mercer grass (Paspalum distichum) and paspalum (Paspalum dilatatum)

Construction of a foxtail millet linkage map and mapping of spikelet-tipped bristles 1(stb1) by using transposon display markers and simple sequence repeat markers with genome sequence information

We attempted genetic analysis and mapping of a gene responsible for the trait “spikelet-tipped bristles” (stb) in foxtail millet, Setaria italica (L.) P.Beauv., as the first step in positional cloning of the gene. This trait is important not only in grain yield such as grain number per panicle of this millet but also in the evolutionary development of the “bristle grass” clade including genera Setaria, Pennisetum and Cenchrus in subfamily Panicoideae. First of all, we confirmed that this trait is controlled by a single recessive gene, using two populations of F2 plants; one was a cross combination between two Taiwanese landraces and the other was a combination between a Taiwanese landrace and a Japanese landrace. Using the latter of the two F2 populations, with transposon display (TD) markers and simple sequence repeat (SSR) markers developed previously, we constructed a genetic map with 13 linkage groups and mapped the responsible gene (stb1) on chromosome 2. We also developed novel SSR markers by using foxtail millet genome sequence information, and we finally constructed nine linkage groups corresponding to nine chromosomes with a total length of 1287.5 cM, and mapped stb1 more precisely on chromosome 2. This work suggests that the foxtail millet genome sequences recently published are useful for developing genome-wide SSR markers for constructing linkage maps and mapping genes in this millet.

Разнообразие фитолитов видов р. Setaria на юге Западной Сибири

Разнообразие фитолитов видов р. Setaria на юге Западной Сибири

Classification of Green Bristle Grass, Yellow Foxtail and Chinese Pennisetum Seeds via HATR-FT-IR Combined with Chemometrics

Fourier transform infrared (FT-IR) and horizontal attenuated total reflectance (HATR) technique are used to obtain the FT-IR spectra of the seed of green bristle grass (the seed fromSetaria viridis(L.) Beauv), yellow foxtail seed (the seed fromSetaria glauca(L.) Beauv), and the Chinese pennisetum seed (the seed fromSetaria faberiiHerrum). In order to extrude the difference among them, cluster analysis is considered to identify the three kinds of plant seeds. Because they belong to the sibling plant seeds, and have similar chemical components and close FT-IR spectra. The result of Cluster analysis is not satisfactory. The discrete wavelet transformation (DWT) and a support vector machine (SVM) were used for further study. The compression detail 3 and 4 in DWT are used to extract the feature vectors, which are used to train SVM. The trained SVM is used to classify seed of green bristle grass, yellow foxtail seed and Chinese pennisetum seed. The seed samples are collected from different places around the country. With 40 testing samples we could effectively identify the sibling plants, seed of green bristle grass, yellow foxtail seed and Chinese pennisetum seed by FT-IR with discrete wavelet feature extraction and SVM classification.

Gradients in fracture force and grazing resistance across canopy layers in seven tropical grass species

AbstractIn reproductive swards, stems can act as a barrier that affects the grazing behaviour of ruminant livestock. The barrier effect of stems is closely associated with both the force required to fracture the stems and the density of these stems (in combination, these make up grazing resistance), and these factors need to be considered when making predictions about the forage intake of ruminants grazing reproductive pastures. Differences in grazing resistance between sward canopy layers of different grass species are thought to affect bite dimensions, but data are scarce. In this study, we assessed the grazing resistance for three canopy layers of seven tropical grass species. Species differed significantly in grazing resistance for every canopy layer, with a general ranking order for grazing resistance, in ascending order: Cenchrus ciliaris (‘American' buffel), Digitaria milanjiana (‘Jarra’ finger grass), Setaria surgens (annual pigeon grass), Setaria sphacelata (‘Narok’ setaria), Dichanthium sericeum (Queensland bluegrass), Chloris gayana (‘Callide’ Rhodes grass). In the top canopy layer, grazing resistance did not appear to create a barrier for any of the species, but in the bottom canopy layer, it did for all species. Species also differed in the relative contribution of fracture force and density to grazing resistance. The results highlight the importance of managing the grazing systems to minimize the barrier effect of the stems, which can be done by controlling the phenological stage of the pasture and the grass species and animal size used in the system.

Reference genome sequence of the model plant Setaria

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).

Subconjunctival infestation with Setaria

Abstract Most cases of human subconjunctival infestations with nematodes described in the literature belong to the genus Dirofilaria. This is a report of subconjunctival setariasis in a 65 years old man, diagnosed 2 years after a travel to Singapore. The parasite was removed immediately from the subconjunctival space and the patient was administered topical antibiotic and anti-inflammatory eye drops. The complete remission of symptoms and signs was noted. The parasite was identified on optical microscopy as belonging to the genus Setaria. The life cycle of the parasite and the accidental human contamination are described. The presence of a moving worm under the human conjunctiva is a rare condition that requires urgent action, in order to prevent its migration into less accessible locations. Since the human subject is a dead-end host who does not allow the multiplication of the parasite, its surgical removal is the only cure.

Assessment of Genetic Relationship of Foxtail Millet with Its Wild Ancestor and Close Relatives by ISSR Markers

Inter simple sequence repeat (ISSR) analysis was applied to samples of foxtail millet and its wild ancestor and other close relatives of the genus Setaria in order to detect domestication-related geographical structure and phylogenetic relationship of those species. Eighty-one accessions of nine Setaria species that originated from different regions were used in this study. Fourteen out of the 27 ISSR primers screened amplified successfully and a total of 156 markers were scored for all the accessions, with a high level of polymorphism being detected. The dendrogram based on UPGMA cluster analysis showed clear geographic structure among foxtail millet and its wild ancestor green foxtail, which implies that northern China is the domestication center for both the Chinese and European foxtail millet landraces used in this study. This result did not support the hypothesis that China and Europe are independent domestication centers for foxtail millet proposed by several previous studies based on morphological and isozyme data. The dendrogram also clearly classified the Setaria sample used into two groups, a viridis and a pumila groups. The viridis group was composed of S. viridis, S. italica, S. faberii, S. verticillata, S. leucopila, and S. queenslandica, and the pumila group consisted of S. parviflora and S. pumila, which is consistent with the recently proposed hypothesis of multiple origin of Setaria species. The phylogenetic relationships among different species are discussed.

Elemental dispersive spectrophotometer analysis and morpho-anatomical characterization of Panicum species from Pakistan

The present study was conducted to identify, evaluate and compare the anatomical data and elemental composition of the Panicum species present in Pakistan. The study is based on the six species of the genus Setaria represented in Pakistan. The elemental dispersive spectrophotometer (EDS) detector was used for the first time in Pakistan for quantitative and qualitative determinations of the elements present in the phytoliths of grasses. Leaf epidermal anatomy was found taxonomically useful, which helps at the species level and showed that in all the six species of the genus, leaf is bifacial. Epidermal cells show the difference in shape of silica bodies, prickles, micro hairs and macro hairs. A lot of variation was observed in the silica bodies of the genus Panicum showing it as a new taxonomical tool during EDS analysis. Key words: Elemental dispersive spectrophotometer, morpho-anatomical characterization,Panicum spp.

Influence of summer dung deposition on estimated yellow bristle grass (<i>Setaria pumila</i>) seed production

A study was carried out to investigate the impact of dung pats on seeding by yellow bristle grass (Setaria pumila) Fresh cow dung was placed on dairy pasture as uniform pats in summer at two sites in Waikato New Zealand and changes in pasture attributes and earthworm abundance monitored over three grazing rotations A zone of repugnance where dairy cows avoided grazing formed out to 40 cm from the centre of the pat It was still evident at 60 days The site with highest yellow bristle grass incidence had taller and bigger yellow bristle grass seed heads in the zone resulting in over twice as much seed as control pasture Earthworm abundance was markedly higher under dung than control pasture the main species being Aporrectodea caliginosa Onfarm management strategies that may accelerate the return of the zone of repugnance to full utilization by stock and minimise weed exploitation are discussed

Changes in yellow bristle grass (<i>Setaria pumila</i>) incidence in Waikato dairy pastures over 4 years

Thirtynine Waikato dairy pastures have been surveyed annually each February for 5 years to quantify changes in cover of yellow bristle grass and to determine if management factors influence this After a severe drought yellow bristle grass ground cover increased from 4 to 11 (2008 to 2009) and has since remained at this level Ryegrass cover declined after the drought and has not returned to predrought levels while clover cover has increased There was a much higher than average 2011/2012 summer rainfall possibly causing the reduced summer grass and broadleaf weed cover measured in February 2012 By the end of the survey period there was no reduction of yellow bristle grass cover from any of the following farm practices aimed to improve pasture performance summer cropping undersowing oversowing and nonselective herbicide applied during summer

Resistance of New Zealand dairy pastures to ingress of summer-active annual grass weeds

Yellow bristle grass (Setaria pumila) and summer grass (Digitaria sanguinalis) are summer-active annual grass weeds which infest temperate dairy pastures. A study was undertaken over 2 years to compare hand-sown yellow bristle and summer grass establishment, survival, and seed production in pastures grazed by dairy cows and based on (i) tetraploid perennial ryegrass (Lolium perenne), (ii) tetraploid perennial ryegrass and white clover (Trifolium repens), and (iii) tall fescue (Festuca arundinacea) and white clover, to determine which pasture type offered the greatest resistance to these grass weeds. Ingress of grass weeds was similar in all three pasture types. Total dry matter production was similar for all pasture types for the first year and lower in tall fescue + clover than perennial ryegrass pasture in the second year. All pasture types had a similar distribution of microsite types (bare ground ± canopy, basal cover ± canopy) in both years. The annual grass weeds were most prevalent in bare ground + canopy microsites, which were also the most frequent of the four microsite types. In the first year, <5% of microsites were occupied within 2 months of sowing, whereas in the second year, microsite occupation remained >13% for all assessments. In the first year, panicle production of yellow bristle and summer grass was similar (averaging 4.1 panicles plant–1); in the second year, panicle production was greater for summer grass (0.80 v. 0.16 panicles plant–1, respectively). Where present, these annual grass weeds are likely to spread in dryland dairy pastures sown with either perennial ryegrass or tall fescue. Variability in their panicle production between years shows how their impact on pasture performance and consequent need for control measures will also vary from year to year.

Minimum tillage and vegetable crop rotation

Soil quality improvement by reducing soil tillage is one tool of sustainable agriculture. Covers crops left on soil surface prevent soil erosion, reduces evapotranspiration and weeds, and improves soil infi ltration; key factors for a successful vegetable production on heavy clay soils. The objective of this research was to evaluate the effect of cover crops plus ridge tillage on soil water content, soil, physico-chemical and biological properties and on vegetable yield. In 2005 at INIA Las Brujas Research Station was established a fi eld experiment on a Typic Argiudoll soil, of silty clay loam texture with a 3% slope. Conventional treatment with fallow periods was compared with sustainable treatment included cover crops and minimum tillage. Onion ( Allium cepa L.), cabagge ( Brassica oleracea, Capitata group), carrot ( Daucus carota ), sweet potato ( Ipomoea batata ) and squash ( Cucurbita moschata x C. maxima ) crops were included in the study. Black oat ( Avena strigosa ), foxtail millet ( Setaria italica ) and forage sorghum ( Sorghum sudanense x S. bicolor ) were the cover crops. Soil water content was measured by time domain refl ectometry on soil surface and by neutron probe in depth. Weed population was evaluated by number and dry weight. Soil biological activity was determined by soil respiration. Weed population and weight of weeds were reduced with minimum tillage as compared to conventional treatment. Soil water content was higher at certain periods on minimum tillage and biological activity was better on minimum tillage. Vegetable crop yields were similar on both treatments.

Problems with the control of perennial weeds in a simplified cultivation system of maize crops in the conditions of Lower SilesiaProblemy ograniczania chwastów wieloletnich w uproszczonej uprawie kukurydzy w warunkach Dolnego Śląska

Field experiments were carried out on the reduction of weed infestation in maize grown in the rotation system on podsolic soil. As a result the following weed species were found to be dominant: barnyardgrass [Echinochloa crus-galli (L.) P. Beav.] and lambsquarters (Chenopodium album L.). A higher weed species composition and a lower soil coverage value (24%) per 1 m area were stated in the maize conventional cultivation system with plowing as compared to reduced maize tillage. Besides the dominant weeds barnyardgrass and lambsquarters the were less numerous field violet (Viola arvensis Murray), creeping speedwell (Veronica pesica L.), shepherds purse [Capsela bursa-pastoris (L.) Medik], corn chamomille (Anthemis arvensis L.), cornflower (Centaurea cyanus L). Taking into consideration the simplified system it was found that the weed species composition was dominated by barnyardgrass and lambsquarters and the coverage of 1 m soil surface amounded to 66%. There was a higher intensity of annual grass weed species barnyardgrass and green bristle grass [Setaria viridis (L.) P. Beav.] as well as perennial species in particularly quackgrass [Elymus repens (L.) Gould] and single weed plants of mugwort (Artemisia vulgaris L.) and Canada thistle [Cirsium arvense (L.) Scop.] were also recorded. The number of annual broad leaved weeds was reduced as compared to the plow cultivation system. The application of herbicides mixture rimsulfuron + dicamba with adjuvant Trend 90 EC controlled the majority of the weed species and gave the best results for this type of soil. Only quackgrass occurring numerously in the experiment as well as winter forms of mugwort and creeping speedwell were less sensitive to the applied mixture of herbicides.

Effects of biological geotextiles on aboveground biomass production in selected agro-ecosystems

Biological geotextiles have considerable potential for soil erosion control, but few studies have been completed on their effects on aboveground biomass production. Hence, field experiments were conducted to investigate the hypothesis that the use of geotextile mats would increase aboveground biomass. We investigated the crop and weed aboveground biomass at four international sites (in China, Thailand, Vietnam and Lithuania). These sites were selected due to the severity of soil erosion problems and feasibility of using biological geotextiles in highlands. In Lithuania, imported Borassus and Buriti mats and indigenous wheat straw mats were used on roadside slopes. In China, Thailand and Vietnam, both Borassus mats and other biological geotextiles were constructed using indigenous local materials (bamboo, rice straw, wheat straw and maize stalks). Results show that biomass production was ∼6 to 53% higher in plots with biological geotextiles compared with the plots with no geotextile treatment. In Lithuania, cover of Borassus and Buriti mats during 2006–2007 increased perennial grass productivity by ∼50 and 18%, respectively, compared with plots with no cover (5.29 Mg ha −1). In China, plots with contour planting covered by rice straw mats had ∼29% higher wheat yield than the plots with no geotextile treatment (1.98 Mg ha −1). Likewise, rice straw, Borassus and maize stalk mat-cover on the plots with no geotextile treatment had significant effects in increasing yields of faber bristle grass (by ∼52%) and maize by 18% and 14% in two separate experiments in China. In Thailand, results (May 2007–June 2008) showed that plots under contour planting mulched with bamboo mats had ∼40 and 26% higher ( P < 0.05) sweet corn ( Zea mays) and lablab bean ( Lablab purpureous) yields, respectively, than plots under contour planting only. Plots under contour planting (without a geotextile cover) had 2.5 and 0.61 Mg ha −1 of sweet corn and lablab bean grain yield production, respectively. In Vietnam, Borassus, maize stalk and bamboo mat cover on bare plots had ∼53, 47 and 35% higher soybean yields, respectively, than the plots with no geotextile treatment (6.6 Mg ha −1). Increased biomass in plots under biological geotextiles was due to soil and moisture conservation. Erosion rates significantly decreased by 15–20% in Lithuania and 67–98% in South-East Asia, compared with the plots with no geotextile cover. Thus, biological geotextiles significantly increased aboveground biomass production and generally contributed to decreased soil loss under diverse soil and climatic conditions.

From the modern to the archaeological: starch grains from millets and their wild relatives in China

Starch grains from 31 modern samples of millets derived from the seeds of 7 species within the genus Setaria and 2 species within the genus Panicum were analyzed to determine diagnostic morphological characteristics. Ancient starch grains recovered from a sample of broomcorn millet ( Panicum miliaceum) excavated from the Cishan site (10.0–7.6 cal yr BP) in the North China Plain were then subjected to the same analyses to determine the differences in morphologies, if any, between modern and ancient samples. The data indicate that morphological features, and particularly surface and fissure features, will allow for solid identifications of ancient millet starches, while size classes will be helpful, but will not be dependable taxonomic indicators.