Applying plant genomics to crop improvement

A report of the European Science Foundation-Wellcome Trust Conference on Crop Genomics, Trait Analysis and Breeding, Hinxton, UK, 8-11 November 2006.     

Strategies for engineering improved nitrogen use efficiency in crop plants via redistribution and recycling of organic nitrogen

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FACE-ing the global change: Opportunities for improvement in photosynthetic radiation use efficiency and crop yield

The earth is rapidly changing through processes such as rising [CO₂], [O₃], and increased food demand. By 2050 the projected atmospheric [CO₂] and ground level [O₃] will be 50% and 20% higher than today. To meet future agricultural demand, amplified by an increasing population and economic progress in developing countries, crop yields will have to increase by at least 50% by the middle of the century. FACE (Free Air Concentration Enrichment) experiments have been conducted for more than 20 years in various parts of world to estimate, under the most realistic agricultural conditions possible, the impact of the CO₂ levels projected for the middle of this century on crops. The stimulations of crop seed yields by the projected CO₂ levels across FACE studies are about 18% on average and up to 30% for the hybrid rice varieties and vary among crops, cultivars, nitrogen levels and soil moisture. The observed increase in crop yields under the projected CO₂ levels fall short of what would be required to meet the projected future food demand, even with the most responsive varieties. Crop biomass production and seed yield is the product of photosynthetic solar energy conversion. Improvement in photosynthetic radiation use efficiency stands as the most promising opportunity allowing for major increases in crop yield in a future that portends major changes in climate and crop growing environments. Our advanced understanding of the photosynthetic process along with rapidly advancing capabilities in functional genomics, genetic transformation and synthetic biology promises new opportunities for crop improvement by greater photosynthesis and crop yield. Traits and genes that show promise for improving photosynthesis are briefly reviewed, including enhancing leaf photosynthesis capacity and reducing photorespiration loss, manipulating plant hormones’ responses for better ideotypes, extending duration of photosynthesis, and increasing carbon partitioning to the sink to alleviate feedback inhibition of photosynthesis.     

Concurrent activation of OsAMT1;2 and OsGOGAT1 in rice leads to enhanced nitrogen use efficiency under nitrogen limitation

Nitrogen (N) is a major factor for plant development and productivity. However, the application of nitrogenous fertilizers generates environmental and economic problems. To cope with the increasing global food demand, the development of rice varieties with high nitrogen use efficiency (NUE) is indispensable for reducing environmental issues and achieving sustainable agriculture. Here, we report that the concomitant activation of the rice (Oryza sativa) Ammonium transporter 1;2 (OsAMT1;2) and Glutamate synthetase 1 (OsGOGAT1) genes leads to increased tolerance to nitrogen limitation and to better ammonium uptake and N remobilization at the whole plant level. We show that the double activation of OsAMT1;2 and OsGOGAT1 increases plant performance in agriculture, providing better N grain filling without yield penalty under paddy field conditions, as well as better grain yield and N content when plants are grown under N llimitations in field conditions. Combining OsAMT1;2 and OsGOGAT1 activation provides a good breeding strategy for improving plant growth, nitrogen use efficiency and grain productivity, especially under nitrogen limitation, through the enhancement of both nitrogen uptake and assimilation.     

Modeling long-term crop response to fertilizer and soil nitrogen

A simple nitrogen balance model to calculate long-term changes in soil organic nitrogen, nitrogen uptake by the crop and recovery of applied nitrogen, is presented. It functions with time intervals of one year or one growing season. In the model a labile and a stable pool of soil organic nitrogen are distinguished. Transfer coefficients for the various inputs of nitrogen are established that specify the fractions taken up by the crop, lost from the system, and incorporated in soil organic nitrogen. It is shown how input data, model parameters and initial pool sizes can be derived and how the model can be used for calculating long-term changes in total soil organic nitrogen and uptake by the crop. For nitrogen applied annually as fertilizer or organic material the time course of nitrogen uptake and recovery of applied nitrogen is calculated. To test the sensitivity of the model, calculations have been performed for different environmental conditions with higher or lower risks for losses. The model has also been applied to establish fertilizer recommendations for a certain target nitrogen uptake by the crop. Finally, for agricultural systems where periods of cropping alternate with peroids of green fallow the time course of nitrogen uptake by the crop is calculated.     

氮素减施对茶树光合作用和氮肥利用率的影响

为探讨当前茶园施肥水平下氮素减施对茶树的生长与氮肥利用率的影响,在大田条件下设置不施氮(空白对照CK),纯氮16 kg·667 m^-2(减氮55.6%,处理A)、纯氮26kg·667 m^-2(减氮27.8%,处理B)、纯氮36 kg·667 m^-2(常规施氮CF)4个施氮处理,研究氮素用量减施对茶树光合作用、产量、氮素吸收及其利用效率的影响。结果表明:与CF比较,处理B能提高茶树的叶绿素含量、净光合速率(P_n)、气孔导度(G_s)、蒸腾速率(T_r),降低胞间CO₂浓度(C_i)和水分利用率(WUE);各施氮肥处理中以处理B的产量最高,氮肥农学效率最高,土壤养分剩余较少,氮素的利用效率较高;CF产量较处理B增加不显著,氮肥农学效率降低,土壤未利用养分较多。因此,减氮27.8%的施肥能保证与常规施肥的茶叶产量,氮素利用率明显提升,有利于茶业的可持续发展。     

Understanding plant responses to phosphorus starvation for improvement of plant tolerance to phosphorus deficiency by biotechnological approaches

Abstract

In both prokaryotes and eukaryotes, including plants, phosphorus (P) is an essential nutrient that is involved in various biochemical processes, such as lipid metabolism and the biosynthesis of nucleic acids and cell membranes. P also contributes to cellular signaling cascades by function as mediators of signal transduction and it also serves as a vital energy source for a wide range of biological functions. Due to its intensive use in agriculture, P resources have become limited. Therefore, it is critically important in the future to develop scientific strategies that aim to increase P use efficiency and P recycling. In addition, the biologically available soluble form of P for uptake (phosphate; Pi) is readily washed out of topsoil layers, resulting in serious environmental pollution. In addition to this environmental concern, the wash out of Pi from topsoil necessitates a continuous Pi supply to maintain adequate levels of fertilization, making the situation worse. As a coping mechanism to P stress, plants are known to undergo drastic cellular changes in metabolism, physiology, hormonal balance and gene expression. Understanding these molecular, physiological and biochemical responses developed by plants will play a vital role in improving agronomic practices, resource conservation and environmental protection as well as serving as a foundation for the development of biotechnological strategies, which aim to improve P use efficiency in crops. In this review, we will discuss a variety of plant responses to low P conditions and various molecular mechanisms that regulate these responses. In addition, we also discuss the implication of this knowledge for the development of plant biotechnological applications.     

Microbial enhancement of crop resource use efficiency

Naturally occurring soil microbes may be used as inoculants to maintain crop yields despite decreased resource (water and nutrient) inputs. Plant symbiotic relationships with mycorrhizal fungi alter root aquaporin gene expression and greatly increase the surface area over which plant root systems take up water and nutrients. Soil bacteria on the root surface alter root phytohormone status thereby increasing growth, and can make nutrients more available to the plant. Combining different classes of soil organism within one inoculant can potentially take advantage of multiple plant growth-promoting mechanisms, but biological interactions between inoculant constituents and the plant are difficult to predict. Whether the yield benefits of such inocula allow modified nutrient and water management continues to challenge crop biotechnologists.     

中国东部南北样带森林优势植物叶片的水分利用效率和氮素利用效率

通过测定中国东部南北样带主要森林生态系统中10种优势植物(兴安落叶松、蒙古栎、水曲柳、紫椴、色木槭、红松、杉木、木荷、马尾松、锥栗)叶片的碳氮含量(Cmass、Nmass)、同位素丰度(δ13C、δ15N)以及光合响应曲线,分析了不同优势植物叶片的水分利用效率和氮素利用效率之间的差异及其相互关系.结果表明： 不同生活型植物叶片的Nmass和δ15N差异显著,表现为阔叶植物>针叶植物,落叶植物>常绿植物;最大光合速率(Pn max)表现为针叶植物>阔叶植物,落叶植物>常绿植物;植物叶片的瞬时水分利用效率(WUEi)和长期水分利用效率(WUE)均表现为阔叶植物>针叶植物,常绿植物>落叶植物;植物叶片的瞬时氮素利用效率(NUEi)和长期氮素利用效率(NUE)则表现出相反的规律,且常绿植物和落叶植物叶片的NUE差异显著;WUEi和WUE之间相关性不显著,而NUEi和NUE之间呈显著正相关.植物叶片的水分利用效率与氮素利用效率显著负相关.两种资源利用效率均受植物生活型的影响,并且存在一定的制约关系.     

The plant genome's methylation status and response to stress: implications for plant improvement

Plant improvement depends on generating phenotypic variation and selecting for characteristics that are heritable. Classical genetics and early molecular genetics studies on single genes showed that differences in chromatin structure, especially cytosine methylation, can contribute to heritable phenotypic variation. Recent molecular genetic and genomic studies have revealed a new importance of cytosine methylation for gene regulation and have identified RNA interference (RNAi)-related proteins that are necessary for methylation. Methylation differences among plants can be caused by cis- or trans-acting DNA polymorphisms or by epigenetic phenomena. Although regulatory proteins might be important in creating this variation, recent examples highlight the central role of transposable elements and DNA repeats in generating both genetic and epigenetic methylation polymorphisms. The plant genome's response to environmental and genetic stress generates both novel genetic and epigenetic methylation polymorphisms. Novel, stress-induced genotypes may contribute to phenotypic diversity and plant improvement.     

An approach to the genetics of nitrogen use efficiency in maize

To study the genetic variability and the genetic basis of nitrogen (N) use efficiency in maize, a set of recombinant inbred lines crossed with a tester was studied at low input (N-) and high input (N+) for grain yield and its components, grain protein content, and post-anthesis nitrogen uptake and remobilization. Other physiological traits, such as nitrate content, nitrate reductase, glutamine synthetase (GS), and glutamate dehydrogenase activities were studied at the level of the lines. Genotypexnitrogen (GxN) interaction was significant for yield and explained by variation in kernel number. In N-, N-uptake, the nitrogen nutrition index, and GS activity in the vegetative stage were positively correlated with grain yield, whereas leaf senescence was negatively correlated. Whatever N-input, post-anthesis N-uptake was highly negatively related to N-remobilization. As a whole, genetic variability was expressed differently in N+ and N-. This was confirmed by the detection of QTLs. More QTLs were detected in N+ than in N- for traits of vegetative development, N-uptake, and grain yield and its components, whereas it was the reverse for grain protein content and N-utilization efficiency. Several coincidences between genes encoding for enzymes of N metabolism and QTLs for the traits studied were observed. In particular, coincidences in three chromosome regions of QTLs for yield and N-remobilization, QTLs for GS activity and a gene encoding cytosolic GS were observed. This may have a physiological meaning. The GS locus on chromosome 5 appears to be a good candidate gene which can, at least partially, explain the variation in nitrogen use efficiency.     

Proteomic analysis of the GlnR-mediated response to nitrogen limitation in Streptomyces coelicolor M145

GlnR is the global regulator of nitrogen assimilation in Streptomyces coelicolor M145 and other actinobacteria. Two-dimensional polyacrylamide gel electrophoresis analyses were performed to identify new GlnR target genes by proteomic comparison of wild-type S. coelicolor M145 and a ΔglnR mutant. Fifty proteins were found to be differentially regulated between S. coelicolor M145 and the ΔglnR mutant. These spots were identified by nanoHPLC–ESI-MS/MS and classified according to their cellular role. Most of the identified proteins are involved in amino acid biosynthesis and in carbon metabolism, demonstrating that the role of GlnR is not restricted to nitrogen metabolism. Thus, GlnR is supposed to play an important role in the global metabolic control of S. coelicolor M145.     

Apomixis for crop improvement

Summary Apomixis is a genetically controlled reproductive process by which embryos and seeds develop in the ovule without female meiosis and egg cell fertilization. Apomixis produces seed progeny that are exact replicas of the mother plant. The major advantage of apomixis over sexual reproduction is the possibility to select individuals with desirable gene combinations and to propagate them as clones. In contrast to clonal propagation through somatic embryogenesis or in vitro shoot multiplication, apomixis avoids the need for costly processes, such as the production of artificial seeds and tissue culture. It simplifies the processes of commercial hybrid and cultivar production and enables a large-scale seed production economically in both seed- and vegetatively propagated crops. In vegetatively reproduced plants (e.g., potato), the main applications of apomixis are the avoidance of phytosanitary threats and the spanning of unfavorable seasons. Because of its potential for crop improvement and global agricultural production, apomixis is now receiving increasing attention from both scientific and industrial sectors. Harnessing apomixis is a major goal in applied plant genetic engineering. In this regard, efforts are focused on genetic and breeding strategies in various plant species, combined with molecular methods to analyze apomictic and sexual modes of reproduction and to identify key regulatory genes and mechanisms underlying these processes. Also, investigations on the components of apomixis, i.e., apomeiosis, parthenogenesis, and endosperm development without fertilization, genetic screens for apomictic mutants and transgenic approaches to modify sexual reproduction by using various regulatory genes are receiving a major effort. These can open new avenues for the transfer of the apomixis trait to important crop species and will have far-reaching potentials in crop improvement regarding agricultural production and the quality of the products.     

Domestication effects on nitrogen allocation,internal recycling and nitrogen use efficiency in the perennial new crop Silphium integrifolium (Asteraceae)

Improvements in seed yield during domestication and breeding are frequently achieved moving plants from the conservative syndrome of the plant economic spectrum towards the more acquisitive side, changing how plants acquire, allocate, use and store C and nutrients in relation to their wild relatives. The aims were to evaluate if domestication changed the N allocation, the internal plant N recycling (N resorption efficiency and proficiency, and N storage) and N-use-efficiency, in the perennial new crop Silphium integrifolium. We compared in a field experiment repeated in two locations (Kansas and Patagonia), a Wild (W) and two improved accessions, with high- (HYI) and low-seed yield improved (LYI) accessions. HYI accessions produced more than twice the biomass and acquired twofold more N than LYI and Wild accessions. Changes in proportional N allocation were similar in both improved accessions (HYI and LYI) and locations: higher allocation to leaves and lower to the crown at pre-anthesis (growth-storage trade-off) and higher allocation to seeds and lower to the crown at maturity (reproduction-storage trade-off). HYI and LYI allocated 50% more N to seeds in average, reducing a 31% the N allocated to the crown in relation to the Wild. Nitrogen use efficiency (NUE) and mean residence time (MRT) of N were reduced in both improved accessions. In HYI, the lower MRT was related to the lower storage of N in the crown and N removal through seed production, and in LYI was the result of the N lost through leaf senescence. HYI produced litter with lower N concentration (more proficient) that the wild accession. These could decrease the net N mineralization rate and soil N availability at long term. HYI plants should require higher external N inputs to the soil to sustain their N uptake requirements. LYI and Wild accessions, had lower resorption efficiency, but N recycled was allocated to the crown for future remobilization and uses (better internal cycling). The leaf litter type of these accessions with higher N content should sustain faster N-cycles rates and N release to the soil. If the focus is on the ecosystem services, HYI accessions could help achieve a reduction in nitrate leaching by maximizing N uptake, N resorption and N removal through seed (i.e. nitrate catch crop), and also produce crop residues that slow down biogeochemical cycling and soil nutrient retention.