Repetitive part of the banana (<Emphasis Type="Italic">Musa acuminata</Emphasis>) genome investigated by low-depth 454 sequencing

Background  

Bananas and plantains (Musa spp.) are grown in more than a hundred tropical and subtropical countries and provide staple food for hundreds of millions of people. They are seed-sterile crops propagated clonally and this makes them vulnerable to a rapid spread of devastating diseases and at the same time hampers breeding improved cultivars. Although the socio-economic importance of bananas and plantains cannot be overestimated, they remain outside the focus of major research programs. This slows down the study of nuclear genome and the development of molecular tools to facilitate banana improvement.     

Cryopreserved storage of clonal germplasm in the USDA National Plant Germplasm System

The US Department of Agriculture-Agricultural Research Service (USDA-ARS), National Plant Germplasm System (NPGS) plant collections are a critical source of genetic diversity for breeding and selection of improved crops, including vegetatively propagated plants. Information on these collections is readily accessible to breeders and researchers on the internet from the Germplasm Resources Information Network (GRIN). The clonal collections are at risk for loss due in part to their genetic diversity that makes growing them in one location a challenge, but also because it is difficult to have duplicate collections without incurring great expense. The development of cryopreservation techniques during the last two decades provides a low maintenance form of security backup for these collections. National plant collections for vegetatively propagated crop plants and their wild relatives are maintained by the USDA-ARS, NPGS at 15 sites across the country. These sites include various combinations of field, greenhouse, screenhouse, and in vitro collections. Cryopreserved backup collections in liquid nitrogen storage were instituted in the 1990s, increased greatly in the 2000s with the advent of new techniques, and are continuing today. Collections of dormant buds of temperate trees, shoot tips of in vitro cultures of many crops, and embryonic axes of some large seeded or recalcitrant seeded plants are all part of the clonal backup storage system.     

Critical evaluation of strategies for mineral fortification of staple food crops

Staple food crops, in particular cereal grains, are poor sources of key mineral nutrients. As a result, the world’s poorest people, generally those subsisting on a monotonous cereal diet, are also those most vulnerable to mineral deficiency diseases. Various strategies have been proposed to deal with micronutrient deficiencies including the provision of mineral supplements, the fortification of processed food, the biofortification of crop plants at source with mineral-rich fertilizers and the implementation of breeding programs and genetic engineering approaches to generate mineral-rich varieties of staple crops. This review provides a critical comparison of the strategies that have been developed to address deficiencies in five key mineral nutrients—iodine, iron, zinc, calcium and selenium—and discusses the most recent advances in genetic engineering to increase mineral levels and bioavailability in our most important staple food crops.     

Induction,rapid fixation and retention of mutations in vegetatively propagated banana

Mutation discovery technologies have enabled the development of reverse genetics for many plant species and allowed sophisticated evaluation of the consequences of mutagenesis. Such methods are relatively straightforward for seed‐propagated plants. To develop a platform suitable for vegetatively propagated species, we treated isolated banana shoot apical meristems with the chemical mutagen ethyl methanesulphonate, recovered plantlets and screened for induced mutations. A high density of GC‐AT transition mutations were recovered, similar to that reported in seed‐propagated polyploids. Through analysis of the inheritance of mutations, we observed that genotypically heterogeneous stem cells resulting from mutagenic treatment are rapidly sorted to fix a single genotype in the meristem. Further, mutant genotypes are stably inherited in subsequent generations. Evaluation of natural nucleotide variation showed the accumulation of potentially deleterious heterozygous alleles, suggesting that mutation induction may uncover recessive traits. This work therefore provides genotypic insights into the fate of totipotent cells after mutagenesis and suggests rapid approaches for mutation‐based functional genomics and improvement of vegetatively propagated crops.     

A further study of microsatellite on apomixis in cassava

Cassava is the main staple crop in the tropics. It is vegetatively propagated by stem cuttings that maintain superior genotypes, but favors disease accumulation. In this report we present the results of the screening of the progeny and the second generation of the clone UnB 307 for apomixis using microsatellites. A total of 29 plants were screened, representing the maternal plant, its first and second generations, that were left to open pollination. About 20% of the offspring were rated as genetically identical plants. This result confirms the facultative apomictic nature of cassava, with high environment effect.     

The rise and rise of emerging infectious fungi challenges food security and ecosystem health

This article highlights some of the more notable persistent fungal diseases of our times. It draws attention to the emergence of new fungal pathotypes infecting food staple crops, due largely to modern agricultural practices, and to nascent fungal diseases decimating frog populations worldwide and killing hibernating bats in Northern USA. We invoke use of the basic disease triangle concept to highlight the “missing” data, with regards to pathogen and host biology and to the various environmental parameters which may dictate disease spread. Given these data “voids” we comment on the implementation of policy. We conclude with a series of recommendations for improved disease surveillance and reporting, the need for greater public awareness of these issues and a call for greater funding for fungal research. In so doing, we have exploited Magnaporthe oryzae and Batrachochytrium dendrobatidis as exemplar emerging infectious fungi. Our aim is to highlight the impact of emerging and emergent fungi on food security and, more broadly, ecosystem health.     

Virus disease in wheat predicted to increase with a changing climate

Current atmospheric CO₂ levels are about 400 μmol mol^?1 and are predicted to rise to 650 μmol mol^?1 later this century. Although the positive and negative impacts of CO₂ on plants are well documented, little is known about interactions with pests and diseases. If disease severity increases under future environmental conditions, then it becomes imperative to understand the impacts of pathogens on crop production in order to minimize crop losses and maximize food production. Barley yellow dwarf virus (BYDV) adversely affects the yield and quality of economically important crops including wheat, barley and oats. It is transmitted by numerous aphid species and causes a serious disease of cereal crops worldwide. This study examined the effects of ambient (aCO₂; 400 μmol mol^?1) and elevated CO₂ (eCO₂; 650 μmol mol^?1) on noninfected and BYDV‐infected wheat. Using a RT‐qPCR technique, we measured virus titre from aCO₂ and eCO₂ treatments. BYDV titre increased significantly by 36.8% in leaves of wheat grown under eCO₂ conditions compared to aCO₂. Plant growth parameters including height, tiller number, leaf area and biomass were generally higher in plants exposed to higher CO₂ levels but increased growth did not explain the increase in BYDV titre in these plants. High virus titre in plants has been shown to have a significant negative effect on plant yield and causes earlier and more pronounced symptom expression increasing the probability of virus spread by insects. The combination of these factors could negatively impact food production in Australia and worldwide under future climate conditions. This is the first quantitative evidence that BYDV titre increases in plants grown under elevated CO₂ levels.     

Molecular analysis of apomixis in cassava

Cassava is the main staple for more than 800 million people in the tropics. It is propagated vegetatively by stem cuttings, which maintains superior genotypes but favors disease accumulation and spread. In this report, we present the results of the screening of the progeny and the second generation of the clone UnB 307 for apomixes using microsatellites. A total of 29 plants were screened, representing the maternal plant, its first and second generations that were left to open pollination. About 20% of the offspring were rated as genetically identical plants. This result confirms the facultative apomictic nature of cassava, with high environmental effect.     

Field testing and exploitation of genetically modified cassava with low-amylose or amylose-free starch in Indonesia

The development and testing in the field of genetically modified -so called- orphan crops like cassava in tropical countries is still in its infancy, despite the fact that cassava is not only used for food and feed but is also an important industrial crop. As traditional breeding of cassava is difficult (allodiploid, vegetatively propagated, outbreeding species) it is an ideal crop for improvement through genetic modification. We here report on the results of production and field testing of genetically modified low-amylose transformants of commercial cassava variety Adira4 in Indonesia. Twenty four transformants were produced and selected in the Netherlands based on phenotypic and molecular analyses. Nodal cuttings of these plants were sent to Indonesia where they were grown under biosafety conditions. After two screenhouse tests 15 transformants remained for a field trial. The tuberous root yield of 10 transformants was not significantly different from the control. Starch from transformants in which amylose was very low or absent showed all physical and rheological properties as expected from amylose-free cassava starch. The improved functionality of the starch was shown for an adipate acetate starch which was made into a tomato sauce. This is the first account of a field trial with transgenic cassava which shows that by using genetic modification it is possible to obtain low-amylose cassava plants with commercial potential with good root yield and starch quality.     

The rise and rise of emerging infectious fungi challenges food security and ecosystem health

This article highlights some of the more notable persistent fungal diseases of our times. It draws attention to the emergence of new fungal pathotypes infecting food staple crops, due largely to modern agricultural practices, and to nascent fungal diseases decimating frog populations worldwide and killing hibernating bats in Northern USA. We invoke use of the basic disease triangle concept to highlight the “missing” data, with regards to pathogen and host biology and to the various environmental parameters which may dictate disease spread. Given these data “voids” we comment on the implementation of policy. We conclude with a series of recommendations for improved disease surveillance and reporting, the need for greater public awareness of these issues and a call for greater funding for fungal research. In so doing, we have exploited Magnaporthe oryzae and Batrachochytrium dendrobatidis as exemplar emerging infectious fungi. Our aim is to highlight the impact of emerging and emergent fungi on food security and, more broadly, ecosystem health.     

Chinese chestnut production in the United States: Practice,problems, and possible solutions

There are fewer than 162 ha of commercial Chinese chestnut orchards in the United States, with approximately half of these in the Southeast. Large numbers of Chinese chestnut seedlings are planted annually in the United States for home and game food production; however, knowledge about chestnut propagation, fertilization, pests, harvest, storage and marketing is not adequate. There is little commercial marketing of U.S.-grown Chinese chestnuts through roadside markets and local farmers’ markets as the supply is low and unpredictable. However, we yearly import 4.5 mill kg of European chestnuts to satisfy the U.S. market. Successful chestnut orchards will require vegetatively propagated selections, intensive management, mechanical harvesting, and control of insect and disease pests.     

Optimal antiviral switching to minimize resistance risk in HIV therapy

The development of resistant strains of HIV is the most significant barrier to effective long-term treatment of HIV infection. The most common causes of resistance development are patient noncompliance and pre-existence of resistant strains. In this paper, methods of antiviral regimen switching are developed that minimize the risk of pre-existing resistant virus emerging during therapy switches necessitated by virological failure. Two distinct cases are considered; a single previous virological failure and multiple virological failures. These methods use optimal control approaches on experimentally verified mathematical models of HIV strain competition and statistical models of resistance risk. It is shown that, theoretically, order-of-magnitude reduction in risk can be achieved, and multiple previous virological failures enable greater success of these methods in reducing the risk of subsequent treatment failures.     

Proteome wide identification of iron binding proteins of <Emphasis Type="Italic">Xanthomonas translucens</Emphasis> pv. <Emphasis Type="Italic">undulosa</Emphasis>: focus on secretory virulent proteins

Xanthomonas translucens pv. undulosa (Xtu) causes Bacterial Leaf Streak disease in the staple food crops such as wheat and barley. The survival strategies of pathogen and host are determined by the complex interactions occurring between the host plants and the pathogenic microbes. Iron binding proteins are important in the plant–microbe interactions as they are indulged in enzyme catalysis, virulence, metabolic and transport activities. In the presented study, we have identified that ~9.8% of Xtu proteome possess iron binding sequence motifs. Further, the analysis of Xtu proteome for secretory iron binding virulent proteins (IBVPs) revealed the fact that iron co-regulate the function of secretory proteins in virulence. We have found 26 secretory IBVPs and observed that these proteins are diverse in their biological functions ranging from transport to antimicrobial resistance, Reactive oxygen species detoxification and carbohydrate catabolism. The inferences may instigate to design the new strategies to combat and control the microbial diseases of staple food crops.     

Metabolic engineering of carotenoid accumulation by creating a metabolic sink

Carotenoids are highly beneficial for human nutrition and health because they provide essential nutrients and important antioxidants in our diets. However, many food crops, especially the major staple crops contain only trace to low amounts of carotenoids. Although significant progress has been made in developing food crops rich in carotenoids by altering the expression of carotenoid biosynthetic genes, in many cases it has proved to be difficult to reach the desired levels of carotenoid enrichment. The recent identification and characterization of a novel gene mutation in cauliflower reveals that creating a metabolic sink to sequester carotenoids is an important mechanism to control carotenoid accumulation in plants. The successful demonstration of increased carotenoid accumulation in association with the formation of sink structures in transgenic crops offers a new and alternative approach to increase carotenoid content. Manipulation of the formation of metabolic sink along with the catalytic activity of the pathway may represent a promising strategy for maximally improving the nutritional quality of food crops.     

Papaya Ring Spot Virus: An Understanding of a Severe Positive-Sense Single Stranded RNA Viral Disease and Its Management

Viral diseases have been studied in-depth for reducing quality, yield, health and longevity of the fruit, to highlight the economic losses. Positive-sense single-stranded RNA viruses are more devastating among all viruses that infect fruit trees. One of the best examples is papaya ringspot virus (PRSV). It belongs to the genus Potyvirus and it is limited to cause diseases on the family Chenopodiaceae, Cucurbitaceae and Caricaceae. This virus has a serious threat to the production of papaya, which is famous for its high nutritional and pharmaceutical values. The plant parts such as leaves, latex, seeds, fruits, bark, peel and roots may contain the biological compound that can be isolated and used in pharmaceutical industries as a disease control. Viral disease symptoms consist of vein clearing and yellowing of young leaves. Distinctive ring spot patterns with concentric rings and spots on fruit reduce its quality and taste. The virus has two major strains P and W. The former cause disease in papaya while the later one in papaya. Virion comprises 94.4% protein, including a 36 kDa coat protein which is a component responsible for a non-persistent transmission through aphids, and 5.5% nucleic acid. Cross protection, development of transgenic crops, exploring the resistant sources and induction of pathogen derived resistance have been recorded as effective management of PRSV. Along with these practices reduced aphid population through insecticides and plant extracts have been found ecofriendly approaches to minimize the disease incidence. Adoption of transgenic crops is a big challenge for the success of disease resistant papaya crops. The aim of this review is to understand the genomic nature of PRSV, detection methods and the different advanced control methods. This review article will be helpful in developing the best management strategies for controlling PRSV.     

Ex-Ante Economic Impact Assessment of Genetically Modified Banana Resistant to Xanthomonas Wilt in the Great Lakes Region of Africa

Background

Credible empirical evidence is scanty on the social implications of genetically modified (GM) crops in Africa, especially on vegetatively propagated crops. Little is known about the future success of introducing GM technologies into staple crops such as bananas, which are widely produced and consumed in the Great Lakes Region of Africa (GLA). GM banana has a potential to control the destructive banana Xanthomonas wilt disease.

Objective

To gain a better understanding of future adoption and consumption of GM banana in the GLA countries which are yet to permit the production of GM crops; specifically, to evaluate the potential economic impacts of GM cultivars resistant to banana Xanthomonas wilt disease.

Data Sources

The paper uses data collected from farmers, traders, agricultural extension agents and key informants in the GLA.

Analysis

We analyze the perceptions of the respondents about the adoption and consumption of GM crop. Economic surplus model is used to determine future economic benefits and costs of producing GM banana.

Results

On the release of GM banana for commercialization, the expected initial adoption rate ranges from 21 to 70%, while the ceiling adoption rate is up to 100%. Investment in the development of GM banana is economically viable. However, aggregate benefits vary substantially across the target countries ranging from US$ 20 million to 953 million, highest in countries where disease incidence and production losses are high, ranging from 51 to 83% of production.

Conclusion

The findings support investment in the development of GM banana resistant to Xanthomonas wilt disease. The main beneficiaries of this technology development are farmers and consumers, although the latter benefit more than the former from reduced prices. Designing a participatory breeding program involving farmers and consumers signifies the successful adoption and consumption of GM banana in the target countries.     

Insights on the evolution of a vegetatively propagated crop species

The opportunity for gene flow between a vegetatively propagated crop and its wild relatives is expected to be much lower than for seed-propagated crops, since sexual reproduction in the crop occurs only infrequently. A study by Duputié and colleagues now demonstrates evidence of sexual reproduction between a vegetatively propagated crop and a closely related wild congener. Working in French Guiana, these workers have documented a hybrid zone arising from introgression between cassava (Manihot esculenta ssp. esculenta, Euphorbiaceae), which is propagated by stem cuttings, and wild Manihot populations growing in close proximity. Patterns of heterozygosity suggest that there are little-to-no barriers to reproduction between the crop and these wild populations. Previous work by these researchers has documented the importance of occasional sexual reproduction for the development of cassava varieties in traditional Amerindian farming systems. Taken together with their previous work, these new findings suggest that gene flow between wild Manihot populations and cassava plants could potentially play a much greater role in the crop's evolution than previously thought.     

Bee diseases as factors in the life and behavior of the honeybee Colony

Summary The honeybee has prospered through the years of recorded history by following a plan of life that contributes to the survival of the colony rather than to the individual. The colony is capable of air-conditioning its hive to meet changing weather and to store up food sources for adverse periods. Since it contributes to the production of fruits, seeds, vegetables and pasture crops, and produces honey, a delectable natural sweet, man has been interested in its production and care.The honeybee is subject to many diseases which affect both the adults and the developing young. Several of the diseases have caused the death or destruction of thousands of colonies annually. Fortunately, none of these diseases are transmitted to other animals. Through the natural laws of survival, certain strains of bees have developed resistance to some of the diseases and man has assisted in this by selective breeding and cultivation of the hardier strains.The most noteworthy contribution to the control of bee diseases has been the use of sulfathiazole, terramycin and other therapeutics in the food of bees in the spring and fall. By their use, at least one disease which had been considered as incurable for centuries can be prevented or controlled without the destruction of colonies or valuable equipment. The use of chemicals and antibiotics as therapeutic agents in disease control has measurably strengthened the position of the honeybee in our general economy and will save the beekeeping industry many thousands of dollars annually.     

Highly Efficient Immunodiagnosis of Episomal Banana streak MY virus Using Polyclonal Antibodies Raised Against Recombinant Viral‐Associated Protein

Banana streak MY virus (BSMYV) is the causal agent of viral leaf streak disease of banana, which leads to considerable losses in banana production in most of the banana‐growing regions worldwide. Developing high‐throughput virus detection system is essential for managing viral diseases especially in vegetatively propagated crops like banana. In this study, viral‐associated protein (VAP) coded by ORF II of BSMYV was expressed in Escherichia coli, and polyclonal antibodies were raised against purified recombinant VAP (rVAP) fusion protein in rabbits. Specificity and sensitivity of resulting antibodies were tested in Western blot, immunosorbent electron microscopy (ISEM) and enzyme‐linked immunosorbent assays (ELISAs). In direct antigen‐coated (DAC)‐ELISA, antibodies reacted specifically to BSMYV in crude sap, up to 1 : 8000 dilutions, but not to healthy leaf extracts. Using this antiserum, an immunocapture polymerase chain reaction (IC‐PCR) assay was developed and compared with DAC‐ELISA. VAP antibody‐based IC‐PCR is highly specific and could differentiate episomal virus infection from the integrated endogenous BSV (eBSV) sequences. The recombinant antibodies were validated by testing with a large number of banana germplasm conserved in the field gene bank. Field samples collected during surveys and mother cultures used in tissue culture propagation suggest that antibodies generated against rVAP are sensitive and useful for large‐scale detection of BSMYV. To the best of our knowledge, this is the first report on the production of polyclonal antiserum against recombinant VAP of BSMYV and its suitability for serology‐based testing by ELISA and IC‐PCR. This VAP‐based immunodiagnosis can be applied in quarantine, germplasm exchange and certification programmes.     

Do increases in agricultural yield spare land for nature?

Feeding a rapidly expanding human population will require a large increase in the supply of agricultural products during the coming decades. This may lead to the transformation of many landscapes from natural vegetation cover to agricultural land use, unless increases in crop yields reduce the need for new farmland. Here, we assess the evidence that past increases in agricultural yield have spared land for wild nature. We investigated the relationship between the change in the combined energy yield of the 23 most energetically important food crops over the period 1979–1999 and the change in per capita cropland area for 124 countries over the same period. Per capita area of the 23 staple crops tended to decrease in developing countries where large yield increases occurred. However, this was counteracted by a tendency for the area used to grow crops other than staples to increase in the countries where staple crop yields increased. There remained a weak tendency in developing countries for the per capita area of all cropland to decline as staple crop yield increased, a pattern that was most evident in developing countries with the highest per capita food supplies. In developed countries, there was no evidence that higher staple crop yields were associated with decreases in per capita cropland area. This may be because high agricultural subsidies in developed countries override any land-sparing pattern that might otherwise occur. Declines in the area of natural forest were smaller in countries where the yield of staple crops increased most, when the negative effects of human population increases on forest area were controlled for. Our results show that land-sparing is a weak process that occurs under a limited set of circumstances, but that it can have positive outcomes for the conservation of wild nature.