A modified TILLING approach to detect induced mutations in tetraploid and hexaploid wheat

Background  

Wheat (Triticum ssp.) is an important food source for humans in many regions around the world. However, the ability to understand and modify gene function for crop improvement is hindered by the lack of available genomic resources. TILLING is a powerful reverse genetics approach that combines chemical mutagenesis with a high-throughput screen for mutations. Wheat is specially well-suited for TILLING due to the high mutation densities tolerated by polyploids, which allow for very efficient screens. Despite this, few TILLING populations are currently available. In addition, current TILLING screening protocols require high-throughput genotyping platforms, limiting their use.     

Life cycle inventory modelling of land use induced by crop consumption

Background, Aims and Scope  

The actual land use consequences of crop consumption are not very well reflected in existing life cycle inventories. The state of the art is that such inventories typically include data from crop production in the country in which the crop is produced, and consequently the inventories do not necessarily consider the land ultimately affected in the systems being studied. The aims of this study are to analyse the mechanisms influencing the long-term land use consequences of changes in crop demand and to propose a methodological framework for identifying these consequences within a global scope.     

Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source-sink tissues in a segregating potato population

Background  

With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potato genome sequence to differentiate between cis- and trans-acting eQTLs in relation to gene subfunctionalization.     

Identification and characterisation of seed storage protein transcripts from Lupinus angustifolius

Background  

In legumes, seed storage proteins are important for the developing seedling and are an important source of protein for humans and animals. Lupinus angustifolius (L.), also known as narrow-leaf lupin (NLL) is a grain legume crop that is gaining recognition as a potential human health food as the grain is high in protein and dietary fibre, gluten-free and low in fat and starch.     

CWRML: representing crop wild relative conservation and use data in XML

Background  

Crop wild relatives are wild species that are closely related to crops. They are valuable as potential gene donors for crop improvement and may help to ensure food security for the future. However, they are becoming increasingly threatened in the wild and are inadequately conserved, both in situ and ex situ. Information about the conservation status and utilisation potential of crop wild relatives is diverse and dispersed, and no single agreed standard exists for representing such information; yet, this information is vital to ensure these species are effectively conserved and utilised. The European Community-funded project, European Crop Wild Relative Diversity Assessment and Conservation Forum, determined the minimum information requirements for the conservation and utilisation of crop wild relatives and created the Crop Wild Relative Information System, incorporating an eXtensible Markup Language (XML) schema to aid data sharing and exchange.     

Development and mapping of Simple Sequence Repeat markers for pearl millet from data mining of Expressed Sequence Tags

Background  

Pearl millet [Pennisetum glaucum (L.) R. Br.] is a staple food and fodder crop of marginal agricultural lands of sub-Saharan Africa and the Indian subcontinent. It is also a summer forage crop in the southern USA, Australia and Latin America, and is the preferred mulch in Brazilian no-till soybean production systems. Use of molecular marker technology for pearl millet genetic improvement has been limited. Progress is hampered by insufficient numbers of PCR-compatible co-dominant markers that can be used readily in applied breeding programmes. Therefore, we sought to develop additional SSR markers for the pearl millet research community.     

Behavior of Buff-Breasted Sandpipers (Tryngites subruficollis) during Migratory Stopover in Agricultural Fields

Background

Understanding the behavior of birds in agricultural habitats can be the first step in evaluating the conservation implications of birds'' use of landscapes shaped by modern agriculture. The existence and magnitude of risk from agricultural practices and the quality of resources agricultural lands provide will be determined largely by how birds use these habitats. Buff-breasted Sandpipers (Tryngites subruficollis) are a species of conservation concern. During spring migration large numbers of Buff-breasted Sandpipers stopover in row crop fields in the Rainwater Basin region of Nebraska. We used behavioral observations as a first step in evaluating how Buff-breasted Sandpipers use crop fields during migratory stopover.

Methodology/Principal Findings

We measured behavior during migratory stopover using scan and focal individual sampling to determine how birds were using crop fields. Foraging was the most frequent behavior observed, but the intensity of foraging changed over the course of the day with a distinct mid-day low point. Relative to other migrating shorebirds, Buff-breasted Sandpipers spent a significant proportion of their time in social interactions including courtship displays.

Conclusions/Significance

Our results show that the primary use of upland agricultural fields by migrating Buff-breasted Sandpipers is foraging while wetlands are used for maintenance and resting. The importance of foraging in row crop fields suggests that both the quality of food resources available in fields and the possible risks from dietary exposure to agricultural chemicals will be important to consider when developing conservation plans for Buff-breasted Sandpipers migrating through the Great Plains.     

Development and characterization of an oat TILLING-population and identification of mutations in lignin and β-glucan biosynthesis genes

Background  

Oat, Avena sativa is the sixth most important cereal in the world. Presently oat is mostly used as feed for animals. However, oat also has special properties that make it beneficial for human consumption and has seen a growing importance as a food crop in recent decades. Increased demand for novel oat products has also put pressure on oat breeders to produce new oat varieties with specific properties such as increased or improved β-glucan-, antioxidant- and omega-3 fatty acid levels, as well as modified starch and protein content. To facilitate this development we have produced a TILLING (Targeting Induced Local Lesions IN Genomes) population of the spring oat cultivar SW Belinda.     

Agricultural use of wetlands: opportunities and limitations

Background

Wetlands are species-rich habitats performing valuable ecosystem services such as flood protection, water quality enhancement, food chain support and carbon sequestration. Worldwide, wetlands have been drained to convert them into agricultural land or industrial and urban areas. A realistic estimate is that 50 % of the world''s wetlands have been lost.

Scope

This paper reviews the relationship between wetlands and agriculture with the aim to identify the successes and failures of agricultural use in different types of wetlands, with reference to short-term and long-term benefits and issues of sustainability. It also addresses a number of recent developments which will lead to pressure to reclaim and destroy natural wetlands, i.e. the continuous need for higher production to feed an increasing world population and the increasing cultivation of energy crops. Finally, attention is paid to the development of more flood-tolerant crop cultivars.

Conclusions

Agriculture has been carried out in several types of (former) wetlands for millennia, with crop fields on river floodplain soils and rice fields as major examples. However, intensive agricultural use of drained/reclaimed peatlands has been shown to lead to major problems because of the oxidation and subsidence of the peat soil. This does not only lead to severe carbon dioxide emissions, but also results in low-lying land which needs to be protected against flooding. Developments in South-East Asia, where vast areas of tropical peatlands are being converted into oil palm plantations, are of great concern in this respect. Although more flood-tolerant cultivars of commercial crop species are being developed, these are certainly not suitable for cultivation in wetlands with prolonged flooding periods, but rather will survive relatively short periods of waterlogging in normally improved agricultural soils. From a sustainability perspective, reclamation of peatlands for agriculture should be strongly discouraged. The opportunities for agriculture in naturally functioning floodplains should be further investigated. The development and use of crop cultivars with an even stronger flood tolerance could form part of the sustainable use of such floodplain systems. Extensive use of wetlands without drastic reclamation measures and without fertilizer and pesticides might result in combinations of food production with other wetland services, with biodiversity remaining more or less intact. There is a need for research by agronomists and environmental scientists to optimize such solutions.Key words: Wetlands, sustainable agriculture, peat subsidence, floodplains, rice fields, water use, irrigation     

TriMEDB: A database to integrate transcribed markers and facilitate genetic studies of the tribe Triticeae

Background  

The recent rapid accumulation of sequence resources of various crop species ensures an improvement in the genetics approach, including quantitative trait loci (QTL) analysis as well as the holistic population analysis and association mapping of natural variations. Because the tribe Triticeae includes important cereals such as wheat and barley, integration of information on the genetic markers in these crops should effectively accelerate map-based genetic studies on Triticeae species and lead to the discovery of key loci involved in plant productivity, which can contribute to sustainable food production. Therefore, informatics applications and a semantic knowledgebase of genome-wide markers are required for the integration of information on and further development of genetic markers in wheat and barley in order to advance conventional marker-assisted genetic analyses and population genomics of Triticeae species.     

A high-throughput method for the detection of homoeologous gene deletions in hexaploid wheat

Background  

Mutational inactivation of plant genes is an essential tool in gene function studies. Plants with inactivated or deleted genes may also be exploited for crop improvement if such mutations/deletions produce a desirable agronomical and/or quality phenotype. However, the use of mutational gene inactivation/deletion has been impeded in polyploid plant species by genetic redundancy, as polyploids contain multiple copies of the same genes (homoeologous genes) encoded by each of the ancestral genomes. Similar to many other crop plants, bread wheat (Triticum aestivum L.) is polyploid; specifically allohexaploid possessing three progenitor genomes designated as 'A', 'B', and 'D'. Recently modified TILLING protocols have been developed specifically for mutation detection in wheat. Whilst extremely powerful in detecting single nucleotide changes and small deletions, these methods are not suitable for detecting whole gene deletions. Therefore, high-throughput methods for screening of candidate homoeologous gene deletions are needed for application to wheat populations generated by the use of certain mutagenic agents (e.g. heavy ion irradiation) that frequently generate whole-gene deletions.     

Life cycle human health impacts of 875 pesticides

Purpose

Residues in field crops grown and harvested for human consumption are the main contributor to overall human exposure toward agricultural pesticides for the general population. However, exposure from crop residues is currently not considered in life cycle assessment practice. We therefore present a consistent framework for characterizing human toxicological impacts associated with pesticides applied to agricultural crops in the frame of life cycle impact assessment based on state-of-the-art data and methods.

Methods

We combine a dynamic multicrop plant uptake model designed for evaluating human exposure to residues for a wide range of pesticide-crop combinations with latest findings of pesticide dissipation kinetics in crops and post-harvest food processing. Outcome is a set of intake fractions and characterization factors for 875 organic pesticides and six major food crops along with specific confidence intervals for each factor.

Results and discussion

Intake fractions aggregating exposure via crop residues and exposure via fractions lost to air and soil for pesticides applied to agricultural crops vary between 10^?8 and 10^?1 kg intake per kilogram applied as a function of pesticide and crop. Intake fractions are typically highest for lettuce and tomato and lowest for potato due to differences in application times before crop harvest and soil as additional barrier for uptake into potato tubers. Uncertainty in intake fractions is mainly associated with dissipation dynamics in crops, where results demonstrate that using pesticide- and crop-specific data is crucial. Combined with the uncertainty in effect modeling, characterization factors per pesticide and crop show squared geometric mean standard deviations ranging from 38 to 15,560 over a variability range across pesticide-crop combinations of 10 orders of magnitude.

Conclusions

Our framework is operational for use in current life cycle impact assessment models, is made available for USEtox, and closes an important gap in the assessment of human exposure to pesticides. For ready use in life cycle assessment studies, we present pesticide-crop combination-specific characterization factors normalized to pesticide mass applied and provide default data for application times and loss due to post-harvest food processing. When using our data, we emphasize the need to consult current pesticide regulation, since each pesticide is registered for use on certain crops only, which varies between countries.

     

Generation and analysis of 9792 EST sequences from cold acclimated oat, <Emphasis Type="Italic">Avena sativa</Emphasis>

Background  

Oat is an important crop in North America and northern Europe. In Scandinavia, yields are limited by the fact that oat cannot be used as a winter crop. In order to develop such a crop, more knowledge about mechanisms of cold tolerance in oat is required.     

Extracting samples of high diversity from thematic collections of large gene banks using a genetic-distance based approach

Background  

Breeding programs are usually reluctant to evaluate and use germplasm accessions other than the elite materials belonging to their advanced populations. The concept of core collections has been proposed to facilitate the access of potential users to samples of small sizes, representative of the genetic variability contained within the gene pool of a specific crop. The eventual large size of a core collection perpetuates the problem it was originally proposed to solve. The present study suggests that, in addition to the classic core collection concept, thematic core collections should be also developed for a specific crop, composed of a limited number of accessions, with a manageable size.     

Deciphering the complexities of the wheat flour proteome using quantitative two-dimensional electrophoresis,three proteases and tandem mass spectrometry

Background  

Wheat flour is one of the world's major food ingredients, in part because of the unique end-use qualities conferred by the abundant glutamine- and proline-rich gluten proteins. Many wheat flour proteins also present dietary problems for consumers with celiac disease or wheat allergies. Despite the importance of these proteins it has been particularly challenging to use MS/MS to distinguish the many proteins in a flour sample and relate them to gene sequences.     

Saving land to feed a growing population: consequences for consumption of crop and livestock products

Purpose

The expected increase in demand for food raises concerns about the expansion of agricultural land worldwide. To avoid expansion, we need to focus on increasing land productivity, reducing waste, and shifting human diets. Studies exploring diet shifts so far have ignored competition for land between humans and animals. Our objective was to study the relation between land use, the share of animal protein in the human diet, population size, and land availability and quality.

Methods

We used linear programming to determine minimum land required to feed a population a diet with 0–80 % of the protein derived from terrestrial domestic animals. Populations ranged from 15 million to the maximum number of people that could be supported by the system. The agricultural system in the Netherlands was used as illustration, assuming no import and export of feed and food. Daily energy and protein requirements of humans were fulfilled by a diet potentially consisting of grain (wheat), root and tuber crops (potato, sugar beet), oil crops (rapeseed), legumes (brown bean), and animal protein from ruminants (milk and meat) and monogastrics (pork).

Results and discussion

Land is used most efficiently if people would derive 12 % of dietary protein from animals (% PA), especially milk. The role of animals in such a diet is to convert co-products from crop production and the human food industry into protein-rich milk and meat. Below 12 % PA, human-inedible products were wasted (i.e., not used for food production), whereas above 12 % PA, additional crops had to be cultivated to feed livestock. Large populations (40 million or more) could be sustained only if animal protein was consumed. This results from the fact that at high population sizes, land unsuitable for crop production was necessary to meet dietary requirements of the population, and contributed to food production by providing animal protein without competing for land with crops.

Conclusions

A land use optimization model including crop and animal production enables identification of the optimal % PA in the diet. Land use per capita was lowest at 12 % PA. At this level, animals optimally consume co-products from food production. Larger populations, furthermore, can be sustained only with diets relatively high in % PA, as land unsuitable for crop production is needed to fulfil their food demand. The optimal % PA in the human diet depended on population size and the relative share of land unsuitable for crop production.

     

A Meta-Analysis of the Impacts of Genetically Modified Crops

Background

Despite the rapid adoption of genetically modified (GM) crops by farmers in many countries, controversies about this technology continue. Uncertainty about GM crop impacts is one reason for widespread public suspicion.

Objective

We carry out a meta-analysis of the agronomic and economic impacts of GM crops to consolidate the evidence.

Data Sources

Original studies for inclusion were identified through keyword searches in ISI Web of Knowledge, Google Scholar, EconLit, and AgEcon Search.

Study Eligibility Criteria

Studies were included when they build on primary data from farm surveys or field trials anywhere in the world, and when they report impacts of GM soybean, maize, or cotton on crop yields, pesticide use, and/or farmer profits. In total, 147 original studies were included.

Synthesis Methods

Analysis of mean impacts and meta-regressions to examine factors that influence outcomes.

Results

On average, GM technology adoption has reduced chemical pesticide use by 37%, increased crop yields by 22%, and increased farmer profits by 68%. Yield gains and pesticide reductions are larger for insect-resistant crops than for herbicide-tolerant crops. Yield and profit gains are higher in developing countries than in developed countries.

Limitations

Several of the original studies did not report sample sizes and measures of variance.

Conclusion

The meta-analysis reveals robust evidence of GM crop benefits for farmers in developed and developing countries. Such evidence may help to gradually increase public trust in this technology.     

Development of ESTs from chickpea roots and their use in diversity analysis of the <Emphasis Type="Italic">Cicer</Emphasis>genus

Background  

Chickpea is a major crop in many drier regions of the world where it is an important protein-rich food and an increasingly valuable traded commodity. The wild annual Cicer species are known to possess unique sources of resistance to pests and diseases, and tolerance to environmental stresses. However, there has been limited utilization of these wild species by chickpea breeding programs due to interspecific crossing barriers and deleterious linkage drag. Molecular genetic diversity analysis may help predict which accessions are most likely to produce fertile progeny when crossed with chickpea cultivars. While, trait-markers may provide an effective tool for breaking linkage drag. Although SSR markers are the assay of choice for marker-assisted selection of specific traits in conventional breeding populations, they may not provide reliable estimates of interspecific diversity, and may lose selective power in backcross programs based on interspecific introgressions. Thus, we have pursued the development of gene-based markers to resolve these problems and to provide candidate gene markers for QTL mapping of important agronomic traits.