Whole-genome sequencing reveals untapped genetic potential in Africa’s indigenous cereal crop sorghum

Sorghum is a food and feed cereal crop adapted to heat and drought and a staple for 500 million of the world’s poorest people. Its small diploid genome and phenotypic diversity make it an ideal C4 grass model as a complement to C3 rice. Here we present high coverage (16-45 × ) resequenced genomes of 44 sorghum lines representing the primary gene pool and spanning dimensions of geographic origin, end-use and taxonomic group. We also report the first resequenced genome of S. propinquum, identifying 8 M high-quality SNPs, 1.9 M indels and specific gene loss and gain events in S. bicolor. We observe strong racial structure and a complex domestication history involving at least two distinct domestication events. These assembled genomes enable the leveraging of existing cereal functional genomics data against the novel diversity available in sorghum, providing an unmatched resource for the genetic improvement of sorghum and other grass species.

Managing glyphosate resistance in Australian cotton farming: modelling shows how to delay evolution and maintain long-term population control

Glyphosate resistance is a rapidly developing threat to profitability in Australian cotton farming. Resistance causes an immediate reduction in the effectiveness of in-crop weed control in glyphosate-resistant transgenic cotton and summer fallows. Although strategies for delaying glyphosate resistance and those for managing resistant populations are qualitatively similar, the longer resistance can be delayed, the longer cotton growers will have choice over which tactics to apply and when to apply them. Effective strategies to avoid, delay, and manage resistance are thus of substantial value. We used a model of glyphosate resistance dynamics to perform simulations of resistance evolution in Sonchus oleraceus (common sowthistle) and Echinochloa colona (awnless barnyard grass) under a range of resistance prevention, delaying, and management strategies. From these simulations, we identified several elements that could contribute to effective glyphosate resistance prevention and management strategies. (i) Controlling glyphosate survivors is the most robust approach to delaying or preventing resistance. High-efficacy, high-frequency survivor control almost doubled the useful lifespan of glyphosate from 13 to 25 years even with glyphosate alone used in summer fallows. (ii) Two non-glyphosate tactics in-crop plus two in-summer fallows is the minimum intervention required for long-term delays in resistance evolution. (iii) Pre-emergence herbicides are important, but should be backed up with non-glyphosate knockdowns and strategic tillage; replacing a late-season, pre-emergence herbicide with inter-row tillage was predicted to delay glyphosate resistance by 4 years in awnless barnyard grass. (iv) Weed species' ecological characteristics, particularly seed bank dynamics, have an impact on the effectiveness of resistance strategies; S. oleraceus, because of its propensity to emerge year-round, was less exposed to selection with glyphosate than E. colona, resulting in an extra 5 years of glyphosate usefulness (18 v. 13 years) even in the most rapid cases of resistance evolution. Delaying tactics are thus available that can provide some or many years of continued glyphosate efficacy. If glyphosate-resistant cotton cropping is to remain profitable in Australian farming systems in the long-term, however, growers must adapt to the probability that they will have to deal with summer weeds that are no longer susceptible to glyphosate. Robust resistance management systems will need to include a diversity of weed control options, used appropriately.

Control by glyphosate and its alternatives of glyphosate-susceptible and glyphosate-resistant Echinochloa colona in the fallow phase of crop rotations in subtropical Australia

Echinochloa colona is the most common grass weed of summer fallows in the grain-cropping systems of the subtropical region of Australia. Glyphosate is the most commonly used herbicide for summer grass control in fallows in this region. The world's first population of glyphosate-resistant E. colona was confirmed in Australia in 2007 and, since then, >70 populations have been confirmed to be resistant in the subtropical region. The efficacy of alternative herbicides on glyphosate-susceptible populations was evaluated in three field experiments and on both glyphosate-susceptible and glyphosate-resistant populations in two pot experiments. The treatments were knockdown and pre-emergence herbicides that were applied as a single application (alone or in a mixture) or as part of a sequential application to weeds at different growth stages. Glyphosate at 720 g ai ha−1 provided good control of small glyphosate-susceptible plants (pre- to early tillering), but was not always effective on larger susceptible plants. Paraquat was effective and the most reliable when applied at 500 g ai ha−1 on small plants, irrespective of the glyphosate resistance status. The sequential application of glyphosate followed by paraquat provided 96–100% control across all experiments, irrespective of the growth stage, and the addition of metolachlor and metolachlor + atrazine to glyphosate or paraquat significantly reduced subsequent emergence. Herbicide treatments have been identified that provide excellent control of small E. colona plants, irrespective of their glyphosate resistance status. These tactics of knockdown herbicides, sequential applications and pre-emergence herbicides should be incorporated into an integrated weed management strategy in order to greatly improve E. colona control, reduce seed production by the sprayed survivors and to minimize the risk of the further development of glyphosate resistance.

Comparison of compost and a sandy loam as turf underlay materials on salt-affected parkland

Turfgrasses range from extremely salt sensitive to highly salt tolerant. However, the selection of a salt tolerant turf is not a 'silver bullet' solution to successful turf growth on salt-affected parklands. Interactions between factors such as cultivar, construction practices, establishment, and maintenance can be complex and should not be considered in isolation of one another. Taking this holistic approach, a study investigating cultivar evaluation for salt-affected sites also included a comparison of topsoil materials as turf underlay, as well as pre-treatment of the sod. The turf species and cultivars used in the study were: Cynodon dactylon, cultivar 'Oz Tuff (I) '; Paspalum vaginatum, cultivars 'Sea Isle 1 (I) ' and 'Velvetene (I) '; Zoysia matrella cultivar 'A-1 (I) '; and Zoysia japonica, cultivar 'Empire (I) '. The two underlay materials were compost (100%) or a sandy clay topsoil each applied above a coastal sand profile to a depth of 10 cm. Rooting depth or root dry weight did not significantly differ among turf cultivars. Compost profile treatment had significantly greater root mass than the topsoil among all turf cultivars. This higher root production was reflected by improved quality of all turf at the final evaluation. Turfgrass grown on compost had a higher normalised difference vegetation index (NDVI), regardless of whether full sod or bare-rooted turfgrass was used. The use of a quality underlay was paramount to the successful growth of the turf cultivars investigated. While each cultivar had superior performance in sub-optimal conditions, the key to success was the selection of the right species and cultivar for each situation combined with proper establishment and maintenance of each turf grass.

The effect of pasture utilization rate on stocks of soil organic carbon and total nitrogen in a semi-arid tropical grassland

The influence of grazing management on total soil organic carbon (SOC) and soil total nitrogen (TN) in tropical grasslands is an issue of considerable ecological and economic interest. Here we have used linear mixed models to investigate the effect of grazing management on stocks of SOC and TN in the top 0.5 m of the soil profile. The study site was a long-term pasture utilization experiment, 26 years after the experiment was established for sheep grazing on native Mitchell grass (Astrebla spp.) pasture in northern Australia. The pasture utilization rates were between 0% (exclosure) and 80%, assessed visually. We found that a significant amount of TN had been lost from the top 0.1 m of the soil profile as a result of grazing, with 80% pasture utilization resulting in a loss of 84 kg ha−1 over the 26-year period. There was no significant effect of pasture utilization rate on TN when greater soil depths were considered. There was no significant effect of pasture utilization rate on stocks of SOC and soil particulate organic carbon (POC), or the C:N ratio at any depth; however, visual trends in the data suggested some agreement with the literature, whereby increased grazing pressure appeared to: (i) decrease SOC and POC stocks; and, (ii) increase the C:N ratio. Overall, the statistical power of the study was limited, and future research would benefit from a more comprehensive sampling scheme. Previous studies at the site have found that a pasture utilization rate of 30% is sustainable for grazing production on Mitchell grass; however, given our results, we conclude that N inputs (possibly through management of native N2-fixing pasture legumes) should be made for long-term maintenance of soil health, and pasture productivity, within this ecosystem.

Harvest weed seed control: is there a role in northern region farming systems?

Harvest weed seed control (HWSC) is a new approach which targets weed seed removal and/or destruction during the crop harvest operation. The success of HWSC is dependant upon weed seed retention at harvest. To identify and define the potential value of HWSC in northern farming systems, we conducted a field survey. In total 1400 transects across 70 paddocks assessed weed distribution, density and seed production at harvest time in wheat, chickpea and sorghum crops. Seventy weed species were identified, of which many had large seed numbers retained at crop harvest. The most prevalent included common sowthistle, flaxleaf fleabane, awnless barnyard grass, wild oat, and African turnip weed. Our field survey has shown there is a role for HWSC in the northern farming system. Therefore the efficacy of specific HWSC systems on problematic weeds should be evaluated in the northern region.

Digestion of forages in the rumen is increased by the amount but not the type of protein supplement

Three polyester bag experiments were conducted with fistulated Bos indicus steers to determine the effect of the amount and type of nitrogen (N) supplement on the digestion rate of forages different in quality. In Experiment 1, test substrates were incubated in polyester bags in the rumen of steers fed ryegrass, pangola grass, speargrass and Mitchell grass hays in a 4 by 4 Latin-square design. In Experiment 2, test substrates were incubated in polyester bags in the rumen of steers fed speargrass hay supplemented with urea and ammonium sulfate (US), branched-chain amino acids with US (USAA), casein, cottonseed meal, yeast and Chlorella algae in a 7 by 3 incomplete Latin-square design. In Experiment 3, test substrates were incubated in polyester bags in the rumen of steers fed Mitchell grass hay supplemented with increasing amounts of US or Spirulina algae (Spirulina platensis). The test substrates used in all experiments were speargrass, Mitchell grass, pangola grass or ryegrass hays. Digestion rate of the ryegrass substrate was higher than that of the speargrass substrate (P < 0.05) in Experiment 1. Supplementation with various N sources increased the degradation rate and effective degradability of all incubated substrates above that apparent in Control steers (P < 0.05; Experiment 2). Supplementation of US and Spirulina increased degradation rate and effective degradability of ryegrass, pangola grass and Mitchell grass substrates above that apparent in Control steers (P < 0.05; Experiment 3). However, there was no further response on digestion rate of the substrates in increasing supplementation levels either for US or Spirulina. In conclusion, rate of digestion was affected by forage physical and anatomical properties. Supplementation with various N sources increased rate of digestion when the Control forage ration was very low in N but once a minimum level of N supplementation was reached, irrespective of form of N or other potential growth factors, there was no further increase in rate of digestion.

Immediate, cumulative and residual effects of short- and long-term low plane of nutrition on milk protein and casein composition

Immediate and residual effects of two lengths of low plane of nutrition (PON) on the synthesis of milk protein and protein fractions were studied at the Mutdapilly Research Station, in south-east Queensland. Thirty-six multiparous Holstein-Friesian cows, between 46 and 102 days in milk (DIM) initially, were used in a completely randomised design experiment with three treatments. All cows were fed on a basal diet of ryegrass pasture (7.0 kg DM/cow.day), barley-sorghum concentrate mix (2.7 kg DM/cow.day) and a canola meal-mineral mix (1.3 kg DM/cow.day). To increase PON, 5.0 kg DM/cow.day supplemental maize and forage sorghum silage was added to the basal diet. The three treatments were (C) high PON (basal diet + supplemental silage); (L9) low PON (basal diet only) for a period of 9 weeks; and (L3) low PON (basal diet only) for a period of 3 weeks. The experiment comprised three periods (1) covariate – high PON, all groups (5 weeks), (2) period of low PON for either 3 weeks (L3) or 9 weeks (L9), and (3) period of high PON (all groups) to assess ability of cows to recover any production lost as a result of treatments (5 weeks). The low PON treatment periods for L3 and L9 were end-aligned so that all treatment groups began Period 3 together. Although there was a significant effect of L9 on yields of milk, protein, fat and lactose, and concentrations of true protein, whey protein and urea, these were not significantly different from L3. There were no residual effects of L3 or L9 on protein concentration or nitrogen distribution after 5 weeks of realimentation. There was no significant effect of low PON for 3 or 9 weeks on casein concentration or composition.

Early recovery signs of an Australian grassland following the management of Parthenium hysterophorus L

Parthenium weed (Parthenium hysterophorus L.) is believed to reduce the above- and below-ground plant species diversity and the above-ground productivity in several ecosystems. We quantified the impact of this invasive weed upon species diversity in an Australian grassland and assessed the resulting shifts in plant community composition following management using two traditional approaches. A baseline plant community survey, prior to management, showed that the above-ground community was dominated by P. hysterophorus, stoloniferous grasses, with a further high frequency of species from Malvaceae, Chenopodiaceae and Amaranthaceae. In heavily invaded areas, P. hysterophorus abundance and biomass was found to negatively correlate with species diversity and native species abundance. Digitaria didactyla Willd. was present in high abundance when P. hysterophorus was not, with these two species, contributing most to the dissimilarity seen between areas. The application of selective broad leaf weed herbicides significantly reduced P. hysterophorus biomass under ungrazed conditions, but this management did not yet result in an increase in species diversity. In the above-ground community, P. hysterophorus was partly replaced by the introduced grass species Cynodon dactylon L. (Pers.) 1 year after management began, increasing the above-ground forage biomass production, while D. didactyla replaced P. hysterophorus in the below-ground community. This improvement in forage availability continued to strengthen over the time of the study resulting in a total increase of 80% after 2 years in the ungrazed treatment, demonstrating the stress that grazing was imposing upon this grassland-based agro-ecosystem and showing that it is necessary to remove grazing to obtain the best results from the chemical management approach.

Legume pastures can reduce N2O emissions intensity in subtropical cereal cropping systems

Alternative sources of N are required to bolster subtropical cereal production without increasing N2O emissions from these agro-ecosystems. The reintroduction of legumes in cereal cropping systems is a possible strategy to reduce synthetic N inputs but elevated N2O losses have sometimes been observed after the incorporation of legume residues. However, the magnitude of these losses is highly dependent on local conditions and very little data are available for subtropical regions. The aim of this study was to assess whether, under subtropical conditions, the N mineralised from legume residues can substantially decrease the synthetic N input required by the subsequent cereal crop and reduce overall N2O emissions during the cereal cropping phase. Using a fully automated measuring system, N2O emissions were monitored in a cereal crop (sorghum) following a legume pasture and compared to the same crop in rotation with a grass pasture. Each crop rotation included a nil and a fertilised treatment to assess the N availability of the residues. The incorporation of legumes provided enough readily available N to effectively support crop development but the low labile C left by these residues is likely to have limited denitrification and therefore N2O emissions. As a result, N2O emissions intensities (kgN2O-N yield-1ha-1) were considerably lower in the legume histories than in the grass. Overall, these findings indicate that the C supplied by the crop residue can be more important than the soil NO3 - content in stimulating denitrification and that introducing a legume pasture in a subtropical cereal cropping system is a sustainable practice from both environmental and agronomic perspectives.

Effect of crop establishment methods and weed control treatments on weed management, and rice yield

Lower water availability coupled with labor shortage has resulted in the increasing inability of growers to cultivate puddled transplanted rice (PTR). A field study was conducted in the wet season of 2012 and dry season of 2013 to evaluate the performance of five rice establishment methods and four weed control treatments on weed management, and rice yield. Grass weeds were higher in dry-seeded rice (DSR) as compared to PTR and nonpuddled transplanted rice (NPTR). The highest total weed density (225-256plantsm-2) and total weed biomass (315-501gm-2) were recorded in DSR while the lowest (102-129plantsm-2 and 75-387gm-2) in PTR. Compared with the weedy plots, the treatment pretilachlor followed by fenoxaprop plus ethoxysulfuron plus 2,4-D provided excellent weed control. This treatment, however, had a poor performance in NPTR. In both seasons, herbicide efficacy was better in DSR and wet-seeded rice. PTR and DSR produced the maximum rice grain yields. The weed-free plots and herbicide treatments produced 84-614% and 58-504% higher rice grain yield, respectively, than the weedy plots in 2012, and a similar trend was observed in 2013.

Spirulina (Spirulina platensis) algae supplementation increases microbial protein production and feed intake and decreases retention time of digesta in the rumen of cattle

Cattle consuming pastures low in protein have low liveweight gain due to low rumen degradable protein (RDP) supply and thus low microbial crude protein (MCP) production and efficiency of MCP production [EMCP, g MCP/kg digestible organic matter (DOM)]. Nitrogen supplements can increase MCP production and EMCP of cattle grazing low protein pastures. The objective of this study was to compare the effects of supplementation with a non-protein-N source (NPN), in this case urea and ammonium sulfate (US), with a single-cell algal protein source (Spirulina platensis), on intake, microbial protein supply and digestibility in cattle. Nine cannulated Bos indicus steers [initial liveweight 250.1 ± 10.86 (s.d.) kg] were fed Mitchell grass hay (Astrebla spp; 6.1 g N, 746 g NDF/kg DM) ad libitum and were supplied with increasing amounts of US (0, 6, 13, 19 and 33 g US DM/kg hay DM) or Spirulina 0, 0.5, 1.4, 2.5 and 6.1 g Spirulina DM/kg W.day in an incomplete Latin square design. The response of MCP production and EMCP to increasing amounts of the two supplements was different, with a greater response to Spirulina evident. The MCP production was predicted to peak at 140 and 568 g MCP/day (0.64 and 2.02 g MCP/kg W.day) for the US and Spirulina supplements, respectively. The highest measured EMCP were 92 and 166 g MCP/kg DOM for the US and Spirulina treatments at 170 and 290 g RDP/kg DOM, respectively, or a Spirulina intake of 5.7 g DM/kg W.day. Increasing RDP intake from US and Spirulina resulted in an increase in Mitchell grass hay intake and rumen NH3-N concentration and reduced the retention time of liquid and particulate markers and digesta DM, NDF and lignin in the rumen with greater changes due to Spirulina. Total DM intake peaked at a Spirulina supplement level of 4.6 g Spirulina DM/kg W.day with a 2.3-fold higher DOM intake than Control steers. Rumen NH3-N concentrations reached 128 and 264 mg NH3-N/L for the US and Spirulina treatments with a significant increase in the concentration of branched-chain fatty acids for the Spirulina treatment. The minimum retention time of liquid (Cr-EDTA; 23 and 13 h) and particulate (Yb; 34 and 22 h) markers in the rumen were significantly lower for Spirulina compared with US and lower than unsupplemented animals at 24 and 34 h for Cr-EDTA and Yb, respectively. Spirulina could be provided safely at much higher N intakes than NPN supplements. The results suggest that, at an equivalent RDP supply, Spirulina provided greater increases than US in MCP production, EMCP and feed intake of Bos indicus cattle consuming low protein forage and could also be fed safely at higher levels of N intake.

A field investigation into a suspected outbreak of pyrrolizidine alkaloid toxicosis in horses in western Queensland

A disease outbreak investigation was conducted in western Queensland to investigate a rare suspected outbreak of pyrrolizidine alkaloid (PA) toxicosis in horses. Thirty five of 132 horses depastured on five properties on the Mitchell grass plains of western Queensland died in the first six months of 2010. Clinical–pathological findings were consistent with PA toxicosis. A local variety of Crotalaria medicaginea was the only hepatotoxic plant found growing on affected properties. Pathology reports and departure and arrival dates of two brood mares provided evidence of a pre wet season exposure period. All five affected properties experienced a very dry spring and early summer preceded by a large summer wet season. The outbreak was characterised as a point epidemic with a sudden peak of deaths in March followed by mortalities steadily declining until the end of June. The estimated morbidity (serum IGG > 50 IU/L) rate was 76%. Average crude mortality was 27% but higher in young horses (67%) and brood mares (44%). Logistic regression analysis showed that young horses and brood mares and those grazing denuded pastures in December were most strongly associated with dying whereas those fed hay and/or grain based supplements were less likely to die. This is the first detailed study of an outbreak of PA toxicosis in central western Queensland and the first to provide evidence that environmental determinants were associated with mortality, that the critical exposure period was towards the end of the dry season, that supplementary feeding is protective and that denuded pastures and the horses physiological protein requirement are risk factors.

Floristic composition and pasture condition of Aristida/Bothriochloa pastures in central Queensland. I. Pasture floristics

A survey was conducted in central inland Queensland, Australia of 108 sites that were deemed to contain Aristida/Bothriochloa native pastures to quantitatively describe the pastures and attempt to delineate possible sub-types. The pastures were described in terms of their floristic composition, plant density and crown cover. There were generally ~20 (range 5–33) main pasture species at a site. A single dominant perennial grass was rare with three to six prominent species the norm. Chrysopogon fallax (golden-beard grass) was the perennial grass most consistently found in all pastures whereas Aristida calycina (dark wiregrass), Enneapogon spp. (bottlewasher grasses), Brunoniella australis (blue trumpet) and Panicum effusum (hairy panic) were all regularly present. The pastures did not readily separate into broad floristic sub-groups, but three groups that landholders could recognise from a combination of the dominant tree and soil type were identified. The three groups were Eucalyptus crebra (narrow-leaved ironbark), E. melanophloia (silver-leaved ironbark) and E. populnea (poplar box). The pastures of the three main sub-groups were then characterised by the prominent presence, singly or in combination, of Bothriochloa ewartiana (desert bluegrass), Eremochloa bimaculata (poverty grass), Bothriochloa decipiens (pitted bluegrass) or Heteropogon contortus (black speargrass). The poplar box group had the greatest diversity of prominent grasses whereas the narrow-leaved ironbark group had the least. Non-native Cenchrus ciliaris (buffel grass) and Melinis repens (red Natal grass) were generally present at low densities. Describing pastures in terms of frequency of a few species or species groups sometimes failed to capture the true nature of the pasture but plant abundance for most species, as density, herbage mass of dry matter or plant crown cover, was correlated with its recorded frequency. A quantitative description of an average pasture in fair condition is provided but it was not possible to explain why some species often occur together or fail to co-exist in Aristida/Bothriochloa pastures, for example C. ciliaris and E. bimaculata rarely co-exist whereas Tragus australianus (small burrgrass) and Enneapogon spp. are frequently recorded together. Most crown cover was provided by perennial grasses but many of these are Aristida spp. (wiregrasses) and not regarded as useful forage for livestock. No new or improved categorisation of the great variation evident in the Aristida/Bothriochloa native pasture type can be given despite the much improved detail provided of the floristic composition by this survey.

Fine mapping of qGW1, a major QTL for grain weight in sorghum

Key message We detected seven QTLs for 100-grain weight in sorghum using an F 2 population, and delimited qGW1 to a 101-kb region on the short arm of chromosome 1, which contained 13 putative genes. Abstract Sorghum is one of the most important cereal crops. Breeding high-yielding sorghum varieties will have a profound impact on global food security. Grain weight is an important component of grain yield. It is a quantitative trait controlled by multiple quantitative trait loci (QTLs); however, the genetic basis of grain weight in sorghum is not well understood. In the present study, using an F2 population derived from a cross between the grain sorghum variety SA2313 (Sorghum bicolor) and the Sudan-grass variety Hiro-1 (S. bicolor), we detected seven QTLs for 100-grain weight. One of them, qGW1, was detected consistently over 2 years and contributed between 20 and 40 % of the phenotypic variation across multiple genetic backgrounds. Using extreme recombinants from a fine-mapping F3 population, we delimited qGW1 to a 101-kb region on the short arm of chromosome 1, containing 13 predicted gene models, one of which was found to be under purifying selection during domestication. However, none of the grain size candidate genes shared sequence similarity with previously cloned grain weight-related genes from rice. This study will facilitate isolation of the gene underlying qGW1 and advance our understanding of the regulatory mechanisms of grain weight. SSR markers linked to the qGW1 locus can be used for improving sorghum grain yield through marker-assisted selection.