12 resultados para Coverage probabilites

em eResearch Archive - Queensland Department of Agriculture


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Field trials and laboratory bioassays were undertaken to compare the performance and efficacy (mortality of diamondback moth larvae) of insecticides applied to cabbages with three high volume hydraulic knapsack sprayers (NS-16, PB-20 and Selecta 12V) and a controlled droplet application (CDA) sprayer. In field experiments, the high volume knapsack sprayers (application rate 500-600 L ha-') provided better spray coverage on the upper and lower surfaces of inner leaves, the upper surfaces of middle and outer leaves, and greater biological efficacy than the CDA sprayer (application rate 20~40 L ha-'). The PB-20 provided better spray coverage on the upper surface of middle leaves and both Surfaces of outer leaves when compared with the Selecta I2V. However, its biological efficacy in the field was not significantly different from that of the other high volume sprayers. Increasing the application rate from 20 to 40 L ha - ' for the CDA sprayer significantly increased droplet density but had no impact on test insect mortality. Laboratory evaluations of biological efficacy yielded higher estimates than field evaluations and there was no significant difference between the performance of the PB-20 and the CDA sprayer. Significant positive relationships were detected between insect mortality and droplet density deposited for both the PB-20 and the CDA sprayers

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Detailed data on seagrass distribution, abundance, growth rates and community structure information were collected at Orman Reefs in March 2004 to estimate the above-ground productivity and carbon assimilated by seagrass meadows. Seagrass meadows were re-examined in November 2004 for comparison at the seasonal extremes of seagrass abundance. Ten seagrass species were identified in the meadows on Orman Reefs. Extensive seagrass coverage was found in March (18,700 ha) and November (21,600 ha), with seagrass covering the majority of the intertidal reef-top areas and a large proportion of the subtidal areas examined. There were marked differences in seagrass above-ground biomass, distribution and species composition between the two surveys. Major changes between March and November included a substantial decline in biomass for intertidal meadows and an expansion in area of subtidal meadows. Changes were most likely a result of greater tidal exposure of intertidal meadows prior to November leading to desiccation and temperature-related stress. The Orman Reef seagrass meadows had a total above-ground productivity of 259.8 t DW day-1 and estimated carbon assimilation of 89.4 t C day-1 in March. The majority of this production came from the intertidal meadows which accounted for 81% of the total production. Intra-annual changes in seagrass species composition, shoot density and size of meadows measured in this study were likely to have a strong influence on the total above-ground production during the year. The net estimated above-ground productivity of Orman Reefs meadows in March 2004 (1.19 g C m-2 day-1) was high compared with other tropical seagrass areas that have been studied and also higher than many other marine, estuarine and terrestrial plant communities.

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The genus Corymbia is closely related to the genus Eucalyptus, and like Eucalyptus contains tree species that are important for sub-tropical forestry. Corymbia's close relationship with Eucalyptus suggests genetic studies in Corymbia should benefit from transfer of genetic information from its more intensively studied relatives. Here we report a genetic map for Corymbia spp. based on microsatellite markers identified de novo in Corymbia sp or transferred from Eucalyptus. A framework consensus map was generated from an outbred F 2 population (n = 90) created by crossing two unrelated Corymbia torelliana x C. citriodora subsp. variegata F1 trees. The map had a total length of 367 cM (Kosambi) and was composed of 46 microsatellite markers distributed across 13 linkage groups (LOD 3). A high proportion of Eucalyptus microsatellites (90%) transferred to Corymbia. Comparative analysis between the Corymbia map and a published Eucalyptus map identified eight homeologous linkage groups in Corymbia with 13 markers mapping on one or both maps. Further comparative analysis was limited by low power to detect linkage due to low genome coverage in Corymbia, however, there was no convincing evidence for chromosomal structural differences because instances of non-synteny were associated with large distances on the Eucalyptus map. Segregation distortion was primarily restricted to a single linkage group and due to a deficit of hybrid genotypes, suggesting that hybrid inviability was one factor shaping the genetic composition of the F2 population in this inter-subgeneric hybrid. The conservation of microsatellite loci and synteny between Corymbia and Eucalyptus suggests there will be substantial value in exchanging information between the two groups.

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Background: Sorghum genome mapping based on DNA markers began in the early 1990s and numerous genetic linkage maps of sorghum have been published in the last decade, based initially on RFLP markers with more recent maps including AFLPs and SSRs and very recently, Diversity Array Technology (DArT) markers. It is essential to integrate the rapidly growing body of genetic linkage data produced through DArT with the multiple genetic linkage maps for sorghum generated through other marker technologies. Here, we report on the colinearity of six independent sorghum component maps and on the integration of these component maps into a single reference resource that contains commonly utilized SSRs, AFLPs, and high-throughput DArT markers. Results: The six component maps were constructed using the MultiPoint software. The lengths of the resulting maps varied between 910 and 1528 cM. The order of the 498 markers that segregated in more than one population was highly consistent between the six individual mapping data sets. The framework consensus map was constructed using a "Neighbours" approach and contained 251 integrated bridge markers on the 10 sorghum chromosomes spanning 1355.4 cM with an average density of one marker every 5.4 cM, and were used for the projection of the remaining markers. In total, the sorghum consensus map consisted of a total of 1997 markers mapped to 2029 unique loci ( 1190 DArT loci and 839 other loci) spanning 1603.5 cM and with an average marker density of 1 marker/0.79 cM. In addition, 35 multicopy markers were identified. On average, each chromosome on the consensus map contained 203 markers of which 58.6% were DArT markers. Non-random patterns of DNA marker distribution were observed, with some clear marker-dense regions and some marker-rare regions. Conclusion: The final consensus map has allowed us to map a larger number of markers than possible in any individual map, to obtain a more complete coverage of the sorghum genome and to fill a number of gaps on individual maps. In addition to overall general consistency of marker order across individual component maps, good agreement in overall distances between common marker pairs across the component maps used in this study was determined, using a difference ratio calculation. The obtained consensus map can be used as a reference resource for genetic studies in different genetic backgrounds, in addition to providing a framework for transferring genetic information between different marker technologies and for integrating DArT markers with other genomic resources. DArT markers represent an affordable, high throughput marker system with great utility in molecular breeding programs, especially in crops such as sorghum where SNP arrays are not publicly available.

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Management of the commercial harvest of kangaroos relies on quotas set annually as a proportion of regular estimates of population size. Surveys to generate these estimates are expensive and, in the larger states, logistically difficult; a cheaper alternative is desirable. Rainfall is a disappointingly poor predictor of kangaroo rate of increase in many areas, but harvest statistics (sex ratio, carcass weight, skin size and animals shot per unit time) potentially offer cost-effective indirect monitoring of population abundance (and therefore trend) and status (i.e. under-or overharvest). Furthermore, because harvest data are collected continuously and throughout the harvested areas, they offer the promise of more intensive and more representative coverage of harvest areas than aerial surveys do. To be useful, harvest statistics would need to have a close and known relationship with either population size or harvest rate. We assessed this using longterm (11-22 years) data for three kangaroo species (Macropus rufus, M. giganteus and M. fuliginosus) and common wallaroos (M. robustus) across South Australia, New South Wales and Queensland. Regional variation in kangaroo body size, population composition, shooter efficiency and selectivity required separate analyses in different regions. Two approaches were taken. First, monthly harvest statistics were modelled as a function of a number of explanatory variables, including kangaroo density, harvest rate and rainfall. Second, density and harvest rate were modelled as a function of harvest statistics. Both approaches incorporated a correlated error structure. Many but not all regions had relationships with sufficient precision to be useful for indirect monitoring. However, there was no single relationship that could be applied across an entire state or across species. Combined with rainfall-driven population models and applied at a regional level, these relationships could be used to reduce the frequency of aerial surveys without compromising decisions about harvest management.

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The requirement for Queensland, Northern Territory and Western Australian jurisdictions to ensure sustainable harvest of fish resources and their optimal use relies on robust information on the resource status. For grey mackerel (Scomberomorus semifasciatus) fisheries, each of these jurisdictions has their own management regime in their corresponding waters. The lack of information on stock structure of grey mackerel, however, means that the appropriate spatial scale of management is not known. As well, fishers require assurance of future sustainability to encourage investment and long-term involvement in a fishery that supplies lucrative overseas markets. These management and fisher-unfriendly circumstances must be viewed in the context of recent 3-fold increases in catches of grey mackerel along the Queensland east coast, combined with significant and increasing catches in other parts of the species' northern Australian range. Establishing the stock structure of grey mackerel would also immensely improve the relevance of resource assessments for fishery management of grey mackerel across northern Australia. This highlighted the urgent need for stock structure information for this species. The impetus for this project came from the strategic recommendations of the FRDC review by Ward and Rogers (2003), "Northern mackerel (Scombridae: Scomberomorus): current and future research needs" (Project No. 2002/096), which promoted the urgency for information on the stock structure of grey mackerel. In following these recommendations this project adopted a multi-technique and phased sampling approach as carried out by Buckworth et al (2007), who examined the stock structure of Spanish mackerel, Scomberomorus commerson, across northern Australia. The project objectives were to determine the stock structure of grey mackerel across their northern Australian range, and use this information to define management units and their appropriate spatial scales. We used multiple techniques concurrently to determine the stock structure of grey mackerel. These techniques were: genetic analyses (mitochondrial DNA and microsatellite DNA), otolith (ear bones) isotope ratios, parasite abundances, and growth parameters. The advantage of using this type of multi-technique approach was that each of the different methods is informative about the fish’s life history at different spatial and temporal scales. Genetics can inform about the evolutionary patterns as well as rates of mixing of fish from adjacent areas, while parasites and otolith microchemistry are directly influenced by the environment and so will inform about the patterns of movement during the fishes lifetime. Growth patterns are influenced by both genetic and environmental factors. Due to these differences the use of these techniques concurrently increases the likelihood of detecting different stocks where they exist. We adopted a phased sampling approach whereby sampling was carried out at broad spatial scales in the first year: east coast, eastern Gulf of Carpentaria (GoC), western GoC, and the NW Northern Territory (NW NT). By comparing the fish samples from each of these locations, and using each of the techniques, we tested the null hypothesis that grey mackerel were comprised of a single homogeneous population across northern Australia. Having rejected the null hypothesis we re-sampled the 1st year locations to test for temporal stability in stock structure, and to assess stock structure at finer spatial scales. This included increased spatial coverage on the east coast, the GoC, and WA. From genetic approaches we determined that there at least four genetic stocks of grey mackerel across northern Australia: WA, NW NT (Timor/Arafura), the GoC and the east Grey mackerel management units in northern Australia ix coast. All markers revealed concordant patterns showing WA and NW NT to be clearly divergent stocks. The mtDNA D-loop fragment appeared to have more power to resolve stock boundaries because it was able to show that the GoC and east coast QLD stocks were genetically differentiated. Patterns of stock structure on a finer scale, or where stock boundaries are located, were less clear. From otolith stable isotope analyses four major groups of S. semifasciatus were identified: WA, NT/GoC, northern east coast and central east coast. Differences in the isotopic composition of whole otoliths indicate that these groups must have spent their life history in different locations. The magnitude of the difference between the groups suggests a prolonged separation period at least equal to the fish’s life span. The parasite abundance analyses, although did not include samples from WA, suggest the existence of at least four stocks of grey mackerel in northern Australia: NW NT, the GoC, northern east coast and central east coast. Grey mackerel parasite fauna on the east coast suggests a separation somewhere between Townsville and Mackay. The NW NT region also appears to comprise a separate stock while within the GoC there exists a high degree of variability in parasite faunas among the regions sampled. This may be due to 1. natural variation within the GoC and there is one grey mackerel stock, or 2. the existence of multiple localised adult sub-stocks (metapopulations) within the GoC. Growth parameter comparisons were only possible from four major locations and identified the NW NT, the GoC, and the east coast as having different population growth characteristics. Through the use of multiple techniques, and by integrating the results from each, we were able to determine that there exist at least five stocks of grey mackerel across northern Australia, with some likelihood of additional stock structuring within the GoC. The major management units determined from this study therefore were Western Australia, NW Northern Territory (Timor/Arafura), the Gulf of Carpentaria, northern east Queensland coast and central east Queensland coast. The management implications of these results indicate the possible need for management of grey mackerel fisheries in Australia to be carried out on regional scales finer than are currently in place. In some regions the spatial scales of management might continue as is currently (e.g. WA), while in other regions, such as the GoC and the east coast, managers should at least monitor fisheries on a more local scale dictated by fishing effort and assess accordingly. Stock assessments should also consider the stock divisions identified, particularly on the east coast and for the GoC, and use life history parameters particular to each stock. We also emphasise that where we have not identified different stocks does not preclude the possibility of the occurrence of further stock division. Further, this study did not, nor did it set out to, assess the status of each of the stocks identified. This we identify as a high priority action for research and development of grey mackerel fisheries, as well as a management strategy evaluation that incorporates the conclusions of this work. Until such time that these priorities are addressed, management of grey mackerel fisheries should be cognisant of these uncertainties, particularly for the GoC and the Queensland east coast.

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In 2002, AFL Queensland and the Brisbane Lions Football Club approached the Department of Primary Industries and Fisheries (Queensland) for advice on improving their Premier League sports fields. They were concerned about player safety and dissatisfaction with playing surfaces, particularly uneven turf cover and variable under-foot conditions. They wanted to get the best from new investments in ground maintenance equipment and irrigation infrastructure. Their sports fields were representative of community-standard, multi-use venues throughout Australia; generally ‘natural’ soil fields, with low maintenance budgets, managed by volunteers. Improvements such as reconstruction, drainage, or regular re-turfing are generally not affordable. Our project aimed to: (a) Review current world practice and performance benchmarks; (b) Demonstrate best-practice management for community-standard fields; (c) Adapt relevant methods for surface performance testing; (d) Assess current soils, and investigate useful amendments; (e) Improve irrigation system performance; and (e) Build industry capacity and encourage patterns for ongoing learning. Most global sports field research focuses on elite, sand-based fields. We adjusted elite standards for surface performance (hardness, traction, soil moisture, evenness, sward cover/height) and maintenance programs, to suit community-standard fields with lesser input resources. In regularly auditing ground conditions across 12 AFLQ fields in SE QLD, we discovered surface hardness (measured by Clegg Hammer) was the No. 1 factor affecting player safety and surface performance. Other important indices were turf coverage and surface compaction (measured by penetrometer). AFLQ now runs regularly audits affiliated fields, and closes grounds with hardness readings greater than 190 Gmax. Aerating every two months was the primary mechanical practice improving surface condition and reducing hardness levels to < 110 Gmax on the renovated project fields. With irrigation installation, these fields now record surface conditions comparable to elite fields. These improvements encouraged many other sporting organisations to seek advice / assistance from the project team. AFLQ have since substantially invested in an expanded ground improvement program, to cater for this substantially increased demand. In auditing irrigation systems across project fields, we identified low maintenance (with < 65% of sprinklers operating optimally) as a major problem. Retrofitting better nozzles and adjusting sprinklers improved irrigation distribution uniformity to 75-80%. Research showed that reducing irrigation frequency to weekly, and preparedness to withhold irrigation longer after rain, reduced irrigation requirement by 30-50%, compared to industry benchmarks of 5-6 ML/ha/annum. Project team consultation with regulatory authorities enhanced irrigation efficiency under imposed regional water restrictions. Laboratory studies showed incorporated biosolids / composts, or topdressed crumb rubber, improved compaction resistance of soils. Field evaluations confirmed compost incorporation significantly reduced surface hardness of high wear areas in dry conditions, whilst crumb rubber assisted turf persistence into early winter. Neither amendment was a panacea for poor agronomic practices. Under the auspices of the project Trade Mark Sureplay®, we published > 80 articles, and held > 100 extension activities involving > 2,000 participants. Sureplay® has developed a multi-level curator training structure and resource materials, subject to commercial implementation. The partnerships with industry bodies (particularly AFLQ), frequent extension activities, and engagement with government/regulatory sectors have been very successful, and are encouraged for any future work. Specific aspects of sports field management for further research include: (a) Understanding of factors affecting turf wear resistance and recovery, to improve turf persistence under wear; (b) Simple tests for pinpointing areas of fields with high hardness risk; and (c) Evaluation of new irrigation infrastructure, ‘water-saving’ devices, and irrigation protocols, in improving water use and turf cover outcomes.

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We investigated the effects of annual burning since 1952, triennial burning since 1973, fire exclusion since 1946 and infrequent wildfire (one fire in 61 years) on woody understorey vegetation in a dry sclerophyll eucalypt forest, south-eastern Queensland, Australia. We determined the influence of these treatments, and other site variables (rainfall, understorey density, topsoil C : N ratio, tree basal area, distance to watercourse and burn coverage) on plant taxa density, richness and composition. The richness of woody understorey taxa 0–1 m in height was not affected by burning treatments, but richness of woody plants 1–7.5 m in height was lower in the annually burnt treatment than in the triennially burnt treatment from 1989 to 2007. Fire frequency and other site variables explained 34% of the variation in taxa composition (three taxon groups and 10 species), of which 33% of the explained variance was explained by fire treatment and 46% was explained by other site variables. Annual burning between 1974 and 1993 was associated with lower understorey densities mainly due to reduced densities of eucalypts 1–7.5 m in height. Triennial burning during the same period was associated with higher densities of eucalypts 0–7.5 m in height relative to the annually burnt and unburnt treatments. Most woody taxa persisted in the frequently burnt treatments through resprouting mechanisms (e.g. lignotuberous regeneration), and fire patchiness associated with low-intensity burning was also found to be important. Persistence of plants <1 m tall demonstrates the resilience of woody taxa to repeated burning in this ecosystem, although they mainly exist in a suppressed growth state under annual burning.

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The Rhipicephalus micro plus genome is large and complex in structure, making it difficult to assemble a genome sequence and costly to resource the required bioinformatics. In light of this, a consortium of international collaborators was formed to pool resources to begin sequencing this genome. We have acquired and assembled genomic DNA into contigs that represent over 1.8 Gigabase pairs of DNA from gene-enriched regions of the R. micro plus genome. We also have several datasets containing transcript sequences from a number of gene expression experiments conducted by the consortium. A web-based resource was developed to enable the scientific community to access our datasets and conduct analysis through a web-based bioinformatics environment called YABI. The collective bioinformatics resource is termed CattleTickBase. Our consortium has acquired genomic and transcriptomic sequence data at approximately 0.9X coverage of the gene-coding regions of the R. microplus genome. The YABI tool will facilitate access and manipulation of cattle tick genome sequence data as the genome sequencing of R. microplus proceeds. During this process the CattleTickBase resource will continue to be updated. Published by Elsevier Ltd. on behalf of Australian Society for Parasitology Inc.

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The off-site transport of agricultural chemicals, such as herbicides, into freshwater and marine ecosystems is a world-wide concern. The adoption of farm management practices that minimise herbicide transport in rainfall-runoff is a priority for the Australian sugarcane industry, particularly in the coastal catchments draining into the World Heritage listed Great Barrier Reef (GBR) lagoon. In this study, residual herbicide runoff and infiltration were measured using a rainfall simulator in a replicated trial on a brown Chromosol with 90–100% cane trash blanket cover in the Mackay Whitsunday region, Queensland. Management treatments included conventional 1.5 m spaced sugarcane beds with a single row of sugarcane (CONV) and 2 m spaced, controlled traffic sugarcane beds with dual sugarcane rows (0.8 m apart) (2mCT). The aim was to simulate the first rainfall event after the application of the photosynthesis inhibiting (PSII) herbicides ametryn, atrazine, diuron and hexazinone, by broadcast (100% coverage, on bed and furrow) and banding (50–60% coverage, on bed only) methods. These events included heavy rainfall 1 day after herbicide application, considered a worst case scenario, or rainfall 21 days after application. The 2mCT rows had significantly (P < 0.05) less runoff (38%) and lower peak runoff rates (43%) than CONV rows for a rainfall average of 93 mm at 100 mm h−1 (1:20 yr Average Return Interval). Additionally, final infiltration rates were higher in 2mCT rows than CONV rows, with 72 and 52 mm h−1 respectively. This resulted in load reductions of 60, 55, 47, and 48% for ametryn, atrazine, diuron and hexazinone from 2mCT rows, respectively. Herbicide losses in runoff were also reduced by 32–42% when applications were banded rather than broadcast. When rainfall was experienced 1 day after application, a large percentage of herbicides were washed off the cane trash. However, by day 21, concentrations of herbicide residues on cane trash were lower and more resistant to washoff, resulting in lower losses in runoff. Consequently, ametryn and atrazine event mean concentrations in runoff were approximately 8 fold lower at day 21 compared with day 1, whilst diuron and hexazinone were only 1.6–1.9 fold lower, suggesting longer persistence of these chemicals. Runoff collected at the end of the paddock in natural rainfall events indicated consistent though smaller treatment differences to the rainfall simulation study. Overall, it was the combination of early application, banding and controlled traffic that was most effective in reducing herbicide losses in runoff. Crown copyright © 2012

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Background Next-generation sequencing technology is an important tool for the rapid, genome-wide identification of genetic variations. However, it is difficult to resolve the ‘signal’ of variations of interest and the ‘noise’ of stochastic sequencing and bioinformatic errors in the large datasets that are generated. We report a simple approach to identify regional linkage to a trait that requires only two pools of DNA to be sequenced from progeny of a defined genetic cross (i.e. bulk segregant analysis) at low coverage (<10×) and without parentage assignment of individual SNPs. The analysis relies on regional averaging of pooled SNP frequencies to rapidly scan polymorphisms across the genome for differential regional homozygosity, which is then displayed graphically. Results Progeny from defined genetic crosses of Tribolium castaneum (F4 and F19) segregating for the phosphine resistance trait were exposed to phosphine to select for the resistance trait while the remainders were left unexposed. Next generation sequencing was then carried out on the genomic DNA from each pool of selected and unselected insects from each generation. The reads were mapped against the annotated T. castaneum genome from NCBI (v3.0) and analysed for SNP variations. Since it is difficult to accurately call individual SNP frequencies when the depth of sequence coverage is low, variant frequencies were averaged across larger regions. Results from regional SNP frequency averaging identified two loci, tc_rph1 on chromosome 8 and tc_rph2 on chromosome 9, which together are responsible for high level resistance. Identification of the two loci was possible with only 5-7× average coverage of the genome per dataset. These loci were subsequently confirmed by direct SNP marker analysis and fine-scale mapping. Individually, homozygosity of tc_rph1 or tc_rph2 results in only weak resistance to phosphine (estimated at up to 1.5-2.5× and 3-5× respectively), whereas in combination they interact synergistically to provide a high-level resistance >200×. The tc_rph2 resistance allele resulted in a significant fitness cost relative to the wild type allele in unselected beetles over eighteen generations. Conclusion We have validated the technique of linkage mapping by low-coverage sequencing of progeny from a simple genetic cross. The approach relied on regional averaging of SNP frequencies and was used to successfully identify candidate gene loci for phosphine resistance in T. castaneum. This is a relatively simple and rapid approach to identifying genomic regions associated with traits in defined genetic crosses that does not require any specialised statistical analysis.

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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.