OBPC Symposium: Maize 2004 &; beyond—Plant regeneration,gene discovery,and genetic engineering of plants for crop improvement

Summary The development of robust plant regeneration technology in cereals, dicots and ornamentals that is in turn coupled to a high-frequency DNA transfer technology is reported. Transgenic cereals that include maize, Tripsacum, sorghum, Festuca and Lolium, in addition to dicots that include soybean, cotton and various ornamentals such as petunia, begonia, and geranium have been produced following either somatic embryogenesis or direct organogenesis independent of genotype. Coupled with these regeneration protocols, we have also identified several interesting genes and promoters for incorporation into various crops and ornamentals. In addition, the phenomenon of direct in vitro flowering from cotyledonary nodes in soybean is described. In in vitro flowering, the formation of a plant body is suppressed and the cells of the cotyledonary node produce complete flowers from which fertile seed is recovered. This in vitro flowering technology serves as a complementary tool to chloroplast transformation for developing a new transgenic pollen containment strategy for crop species. Recently, the center has undertaken to screen the expression response of the 24 000 Arabidopsis genes to nitric oxide. This signaling molecule upregulated 342 genes and downregulated 80 genes. The object here was to identify a population of promoters that can be manipulated by using a signaling molecule. In addition, in keeping with the mission of enhancing greenhouse profitability for North West Ohio growers, we cloned a number of genes responsive for disease resistance from ornamentals that play an important role in disease management and abiotic stress. We have constructed a plant transformation vector with CBF3 gene under the rd29A promoter for engineering cold and freezing tolerance in petunia. Leaf dises of Petunia×hybrida v26 were used for Agrobacterium-mediated transformation, and 44 hygromycin-resistant T0 plants were obtained. The presence of CBF3 gene was confirmed in all the transgenic plants by PCR and Southern analyses.     

Whole genome sequencing of cotton—a new chapter in cotton genomics

<正>A Cotton Genome Consortium led by the Cotton Research Institute,Chinese Academy of Agricultural Sciences,with scientists from Peking University,Wuhan University,BGI and US Department of Agriculture Southern Plains Research Center has completed the genome sequence of the allotetraploid G.hirsutum(At Dt)by using the second-generation high-throughput sequencing technology     

Developments in coffee biotechnology—in vitro plant propagation and crop improvement

Coffee is an important plantation crop grown in about 80 countries across the globe. In recent years, coffee attained lot of attention in the biotechnology research area. Since last three decades, there has been a steady flow of information on coffee biotechnology and now it is entering into the genomic era. Major milestones in coffee biotech research are successful in vitro manipulation and multiplication of coffee, development of gene transfer protocols and generation of transgenic coffee plants with specific traits. The isolation of genes involved in caffeine biosynthetic pathway has opened up new avenues for generating caffeine free transgenic coffee. With the initiation of international coffee genomics initiatives, the genomic research in coffee is expected to reach new dimensions. The IPR issues may play crucial role in sharing of benefits during international collaborations in near future. This review focuses on the basic and applied aspects of coffee biotechnology for newer potentials.     

Biotechnological detoxification: an unchanging source–sink balance strategy for crop improvement

The wide occurrence of natural phytotoxins renders many crops unfit for human consumption. To overcome this problem and produce detoxified crop varieties, we propose the use of biotechnological strategies that can enhance the harvest index without the need to increase crop biomass or alter whole plant architecture.     

Plant improvement for tolerance to aluminum in acid soils – a review

Development of acid soils that limit crop production is an increasing problem worldwide. Many factors contribute to phytotoxicity of these soils, however, in acid soils with a high mineral content, aluminum (Al) is the major cause of toxicity. The target of Al toxicity is the root tip, in which Al exposure causes inhibition of cell elongation and cell division, leading to root stunting accompanied by reduced water and nutrient uptake. Natural variation for Al tolerance has been identified in many crop species and in some crops tolerance to Al has been introduced into productive, well-adapted varieties. Aluminum tolerance appears to be a complex multigenic trait. Selection methodology remains a limiting factor in variety development as all methods have particular drawbacks. Molecular markers have been associated with Al tolerance genes or quantitative trait loci in Arabidopsis and in several crops, which should facilitate development of additional tolerant varieties. A variety of genes have been identified that are induced or repressed upon Al exposure. Most induced genes characterized so far are not specific to Al exposure but are also induced by other stress conditions. Ectopic over-expression of some of these genes has resulted in enhanced Al tolerance. Additionally, expression of genes involved in organic acid synthesis has resulted in enhanced production of organic acids and an associated increase in Al tolerance. This review summarizes the three main approaches that have been taken to develop crops with Al tolerance: recurrent selection and breeding, development of Al tolerant somaclonal variants and ectopic expression of transgenes to reduce Al uptake or limit damage to cells by Al.     

Whole genome and exome sequencing of monozygotic twins discordant for Crohn’s disease

Background

Crohn’s disease (CD) is an inflammatory bowel disease caused by genetic and environmental factors. More than 160 susceptibility loci have been identified for IBD, yet a large part of the genetic variance remains unexplained. Recent studies have demonstrated genetic differences between monozygotic twins, who were long thought to be genetically completely identical.

Results

We aimed to test if somatic mutations play a role in CD etiology by sequencing the genomes and exomes of directly affected tissue from the bowel and blood samples of one and the blood-derived exomes of two further monozygotic discordant twin pairs. Our goal was the identification of mutations present only in the affected twins, pointing to novel candidates for CD susceptibility loci. We present a thorough genetic characterization of the sequenced individuals but detected no consistent differences within the twin pairs. An estimate of the CD susceptibility based on known CD loci however hinted at a higher mutational load in all three twin pairs compared to 1,920 healthy individuals.

Conclusion

Somatic mosaicism does not seem to play a role in the discordance of monozygotic CD twins. Our study constitutes the first to perform whole genome sequencing for CD twins and therefore provides a valuable reference dataset for future studies. We present an example framework for mosaicism detection and point to the challenges in these types of analyses.

Electronic supplementary material

The online version of this article (doi:10.1186/1471-2164-15-564) contains supplementary material, which is available to authorized users.     

Can improvement in photosynthesis increase crop yields?

The yield potential (Y_p) of a grain crop is the seed mass per unit ground area obtained under optimum growing conditions without weeds, pests and diseases. It is determined by the product of the available light energy and by the genetically determined properties: efficiency of light capture (?_i), the efficiency of conversion of the intercepted light into biomass (?_c) and the proportion of biomass partitioned into grain (η). Plant breeding brings η and ?_i close to their theoretical maxima, leaving ?_c, primarily determined by photosynthesis, as the only remaining major prospect for improving Y_p. Leaf photosynthetic rate, however, is poorly correlated with yield when different genotypes of a crop species are compared. This led to the viewpoint that improvement of leaf photosynthesis has little value for improving Y_p. By contrast, the many recent experiments that compare the growth of a genotype in current and future projected elevated [CO₂] environments show that increase in leaf photosynthesis is closely associated with similar increases in yield. Are there opportunities to achieve similar increases by genetic manipulation? Six potential routes of increasing ?_c by improving photosynthetic efficiency were explored, ranging from altered canopy architecture to improved regeneration of the acceptor molecule for CO₂. Collectively, these changes could improve ?_c and, therefore, Y_p by c. 50%. Because some changes could be achieved by transgenic technology, the time of the development of commercial cultivars could be considerably less than by conventional breeding and potentially, within 10–15 years.     

Agricultural biotechnology for crop improvement in a variable climate: hope or hype?

Developing crops that are better adapted to abiotic stresses is important for food production in many parts of the world today. Anticipated changes in climate and its variability, particularly extreme temperatures and changes in rainfall, are expected to make crop improvement even more crucial for food production. Here, we review two key biotechnology approaches, molecular breeding and genetic engineering, and their integration with conventional breeding to develop crops that are more tolerant of abiotic stresses. In addition to a multidisciplinary approach, we also examine some constraints that need to be overcome to realize the full potential of agricultural biotechnology for sustainable crop production to meet the demands of a projected world population of nine billion in 2050.     

Plant hydraulic lift of soil water – implications for crop production and land restoration

Zinc deficiency is a well-documented problem in food crops, causing decreased crop yields and nutritional quality. Generally, the regions in the world with Zn-deficient soils are also characterized by widespread Zn deficiency in humans. Recent estimates indicate that nearly half of world population suffers from Zn deficiency. Cereal crops play an important role in satisfying daily calorie intake in developing world, but they are inherently very low in Zn concentrations in grain, particularly when grown on Zn-deficient soils. The reliance on cereal-based diets may induce Zn deficiency-related health problems in humans, such as impairments in physical development, immune system and brain function. Among the strategies being discussed as major solution to Zn deficiency, plant breeding strategy (e.g., genetic biofortification) appears to be a most sustainable and cost-effective approach useful in improving Zn concentrations in grain. The breeding approach is, however, a long-term process requiring a substantial effort and resources. A successful breeding program for biofortifying food crops with Zn is very much dependent on the size of plant-available Zn pools in soil. In most parts of the cereal-growing areas, soils have, however, a variety of chemical and physical problems that significantly reduce availability of Zn to plant roots. Hence, the genetic capacity of the newly developed (biofortified) cultivars to absorb sufficient amount of Zn from soil and accumulate it in the grain may not be expressed to the full extent. It is, therefore, essential to have a short-term approach to improve Zn concentration in cereal grains. Application of Zn fertilizers or Zn-enriched NPK fertilizers (e.g., agronomic biofortification) offers a rapid solution to the problem, and represents useful complementary approach to on-going breeding programs. There is increasing evidence showing that foliar or combined soil+foliar application of Zn fertilizers under field conditions are highly effective and very practical way to maximize uptake and accumulation of Zn in whole wheat grain, raising concentration up to 60 mg Zn kg⁻¹. Zinc-enriched grains are also of great importance for crop productivity resulting in better seedling vigor, denser stands and higher stress tolerance on potentially Zn-deficient soils. Agronomic biofortification strategy appears to be essential in keeping sufficient amount of available Zn in soil solution and maintaining adequate Zn transport to the seeds during reproductive growth stage. Finally, agronomic biofortification is required for optimizing and ensuring the success of genetic biofortification of cereal grains with Zn. In case of greater bioavailability of the grain Zn derived from foliar applications than from soil, agronomic biofortification would be a very attractive and useful strategy in solving Zn deficiency-related health problems globally and effectively.     

How can we harness quantitative genetic variation in crop root systems for agricultural improvement?

Root systems are a black box obscuring a comprehensive understanding of plant function,from the ecosystem scale down to the individual. In particular,a lack of knowledge about the genetic mechanisms and environmental effects that condition root system growth hinders our ability to develop the next generation of crop plants for improved agricultural productivity and sustainability. We discuss how the methods and metrics we use to quantify root systems can affect our ability to understand them,how we can bridge knowledge gaps and accelerate the derivation of structurefunction relationships for roots,and why a detailed mechanistic understanding of root growth and function will be important for future agricultural gains.     

Metabolomics platforms for genome wide association studies—linking the genome to the metabolome

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Highlights► Genome-wide association studies with metabolomics constitute mGWAS. ► mGWAS provide insights into genetic and environmental impact on metabolic processes. ► We review essential strategies for mGWAS. ► Examples of mGWAS in large cohort studies are discussed.     

Wild barley: a source of genes for crop improvement in the 21st century?

The development of new barleys tolerant of abiotic and biotic stresses is an essential part of the continued improvement of the crop. The domestication of barley, as in many crops, resulted in a marked truncation of the genetical variation present in wild populations. This process is significant to agronomists and scientists because a lack of allelic variation will prevent the development of adapted cultivars and hinder the investigation of the genetic mechanisms underlying performance. Wild barley would be a useful source of new genetic variation for abiotic stress tolerance if surveys identify appropriate genetic variation and the development of marker-assisted selection allows efficient manipulation in cultivar development. There are many wild barley collections from all areas of its natural distribution, but the largest are derived from the Mediterranean region. The results of a range of assays designed to explore abiotic stress tolerance in barley are reported in this paper. The assays included; sodium chloride uptake in wild barley and a mapping population, effects for delta 13C and plant dry weight in wheat aneuploids, effects of photoperiod and vernalization in wild barley, and measurements of root length in wild barley given drought and nitrogen starvation treatments in hydroponic culture. There are examples of the use of wild barley in breeding programmes, for example, as a source of new disease resistance genes, but the further exploration of the differences between wild barley and cultivars is hampered by the lack of good genetic maps. In parallel to the need for genetic studies there is also a need for the development of good physiological models of crop responses to the environment. Given these tools, wild barley offers the prospect of a 'goldmine' of untapped genetic reserves.     

Plant genome editing in the European Union—to be or not to be—a GMO

New plant-breeding techniques have been boosting plant breeding, since only a few years but already first promising products are pushing to the market. In contrast to this, in many countries, the current Directives regulating genetically modified organisms have been established more than 25 years ago, especially in the European Union being based on clear differentiation between transgenic plants and conventional breeding. Therefore, the question arises if these Directives are suitable to face the new challenge of genetic engineering or if there is a need for updated regulations.     

A decade after the first full human genome sequencing: when will we understand our own genome?

The contrast between the pomp of celebrating the first full human genome sequencing in 2000 and the cautious tone of recollections a decade thereafter could hardly be greater. The promises with regard to medical cures and biotechnology applications have been realized not even nearly to the expectations. Understanding the human genomes means knowing the genes' and proteins' functions and their interconnectedness via biomolecular mechanisms. This articles estimates how long will it take to achieve this goal if we extrapolate from the previous decade (indeed, a century!) and the possible disruptive trends in science, technology and society that may accelerate the pace of progress dramatically.