Current opinion in plant biology

Publications in this journal

• Article: The genetic control of flower-pollinator specificity.

  Yao-Wu Yuan, Kelsey Jrp Byers, Hd Bradshaw
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  ABSTRACT: The ca. 275,000 species of flowering plants are the result of a recent adaptive radiation driven largely by the coevolution between plants and their animal pollinators. Identification of genes and mutations responsible for floral trait variation underlying pollinator specificity is crucial to understanding how pollinator shifts occur between closely related species. Petunia, Mimulus, and Antirrhinum have provided a high standard of experimental evidence to establish causal links from genes to floral traits to pollinator responses. In all three systems, MYB transcription factors seem to play a prominent role in the diversification of pollinator-associated floral traits.
  Current opinion in plant biology 06/2013;
• Article: What's the 'buzz' about? The ecology and evolutionary significance of buzz-pollination.

  Paul A De Luca, Mario Vallejo-Marín
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  ABSTRACT: Many plant species have evolved floral characteristics that restrict pollen access. Some of these species are visited by insects, principally bees, which make use of vibrations to extract pollen from anthers. Buzz-pollination, as this phenomenon is generally known, is a widespread method of fertilization for thousands of species in both natural and agricultural systems. Despite its prevalence in pollination systems, the ecological and evolutionary conditions that favour the evolution of buzz-pollination are poorly known. We briefly summarize the biology of buzz-pollination and review recent studies on plant and pollinator characteristics that affect pollen removal. We suggest that buzz-pollination evolves as the result of an escalation in the competition between plants and pollen-consuming floral visitors (including pollen thieves and true pollinators) to control the rate of pollen removal from flowers.
  Current opinion in plant biology 06/2013;
• Article: Genes, communities & invasive species: understanding the ecological and evolutionary dynamics of host-pathogen interactions.

  Jj Burdon, Ph Thrall, L Ericson
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  ABSTRACT: Reciprocal interactions between hosts and pathogens drive ecological, epidemiological and co-evolutionary trajectories, resulting in complex patterns of diversity at population, species and community levels. Recent results confirm the importance of negative frequency-dependent rather than 'arms-race' processes in the evolution of individual host-pathogen associations. At the community level, complex relationships between species abundance and diversity dampen or alter pathogen impacts. Invasive pathogens challenge these controls reflecting the earliest stages of evolutionary associations (akin to arms-race) where disease effects may be so great that they overwhelm the host's and community's ability to respond. Viewing these different stabilization/destabilization phases as a continuum provides a valuable perspective to assessment of the role of genetics and ecology in the dynamics of both natural and invasive host-pathogen associations.
  Current opinion in plant biology 06/2013;
• Article: Physiology and metabolism: water for thought.

  Edward E Farmer, John Browse
  Current opinion in plant biology 05/2013;
• Article: Genome studies and molecular genetics: understanding the functional genome based on the rice model.

  Qifa Zhang, Rod Wing
  Current opinion in plant biology 05/2013;
• Article: Development of genomics-based genotyping platforms and their applications in rice breeding.

  Haodong Chen, Hang He, Fasong Zhou, Huihui Yu, Xing Wang Deng
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  ABSTRACT: Breeding by design has been an aspiration of researchers in the plant sciences for a decade. With the rapid development of genomics-based genotyping platforms and available of hundreds of functional genes/alleles in related to important traits, however, it may now be possible to turn this enduring ambition into a practical reality. Rice has a relatively simple genome comparing to other crops, and its genome composition and genetic behavior have been extensively investigated. Recently, rice has been taken as a model crop to perform breeding by design. The essential process of breeding by design is to integrate functional genes/alleles in an ideal genetic background, which requires high throughput genotyping platforms to screen for expected genotypes. With large amount of genome resequencing data and high-throughput genotyping technologies available, quite a number of genomics-based genotyping platforms have been developed. These platforms are widely used in genetic mapping, integration of target traits via marker-assisted backcrossing (MABC), pyramiding, recurrent selection (MARS) or genomic selection (GS). Here, we summarize and discuss recent exciting development of rice genomics-based genotyping platforms and their applications in molecular breeding.
  Current opinion in plant biology 05/2013;
• Article: Systems-integration of plant metabolism: means, motive and opportunity.

  Mark Stitt
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  ABSTRACT: System integration of metabolism is considered in analogy to the investigation of corporate misdemeanour. Motive, or goal-oriented explanation, provides hypotheses that can guide the investigation of network structure. Opportunity can be established by correlative analysis using large-scale omics resources. However, correlative approaches on their own remain inconclusive and seldom identify all the links in a network. Establishment of means, or the ability to act on other network components and contribute to a phenotype, is therefore crucial. This requires functional information. Integration of quantitative data in the context of pathway models provides a powerful approach to establish 'means'. This is illustrated by discussing: first, how protein abundance is regulated by a network including transcript abundance, translation and protein degradation and second, how a combination of experimentation and modelling provides information about pathway flux, an emergent network property that integrates changes in proteins and metabolites and determines composition and biomass.
  Current opinion in plant biology 05/2013;
• Article: Phytochemical genomics-a new trend.

  Kazuki Saito
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  ABSTRACT: Phytochemical genomics is a recently emerging field, which investigates the genomic basis of the synthesis and function of phytochemicals (plant metabolites), particularly based on advanced metabolomics. The chemical diversity of the model plant Arabidopsis thaliana is larger than previously expected, and the gene-to-metabolite correlations have been elucidated mostly by an integrated analysis of transcriptomes and metabolomes. For example, most genes involved in the biosynthesis of flavonoids in Arabidopsis have been characterized by this method. A similar approach has been applied to the functional genomics for production of phytochemicals in crops and medicinal plants. Great promise is seen in metabolic quantitative loci analysis in major crops such as rice and tomato, and identification of novel genes involved in the biosynthesis of bioactive specialized metabolites in medicinal plants.
  Current opinion in plant biology 04/2013;
• Article: Root responses to flooding.

  Margret Sauter
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  ABSTRACT: Soil water-logging and submergence pose a severe threat to plants. Roots are most prone to flooding and the first to suffer from oxygen shortage. Roots are vital for plant function, however, and maintenance of a functional root system upon flooding is essential. Flooding-resistant plants possess a number of adaptations that help maintain oxygen supply to the root. Plants are also capable of initiating organogenesis to replace their original root system with adventitious roots if oxygen supply becomes impossible. This review summarizes current findings on root development and de novo root genesis in response to flooding.
  Current opinion in plant biology 04/2013;
• Article: Rice breaks ground for cadmium-free cereals.

  Shimpei Uraguchi, Toru Fujiwara
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  ABSTRACT: It is important to reduce the risk of long-term cadmium (Cd) exposure through ingestion. Cd in plant-derived foods (especially rice grain in Japan) is a major source of human Cd intake. In rice, Cd uptake and xylem loading in roots, remobilization from leaf blades and intervascular transfer in nodes to redirect Cd transport are crucial for grain Cd accumulation. Different metal transporters mediate these processes with cell-type specific expressions. In this review, we summarize and discuss the recent rapid advance in molecular understanding of Cd transport in rice. The achievements and perspectives in developing 'low-Cd rice' by the use of various alleles of Cd transporter genes are also discussed.
  Current opinion in plant biology 04/2013;
• Article: Heterosis in elite hybrid rice: speculation on the genetic and biochemical mechanisms.

  Stephen A Goff, Qifa Zhang
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  ABSTRACT: Because of the tremendous advances in functional genomics and the current availability of a large number of superior hybrids, rice is an excellent model crop system for heterosis research. Genetic dissection of yield and yield component traits of an elite rice hybrid using an ultra-high density linkage map identified overdominance as the principal genetic basis of heterosis in this hybrid. This is not an expected finding based on the reported effects of single genes. Here we propose a gene expression and protein quality control hypothesis as one possible explanation for the overdominance in hybrids bred for yield. Future studies will be directed toward the identification of the genetic and biochemical mechanisms underlying the biology of hybrid vigor.
  Current opinion in plant biology 04/2013;
• Article: Evolution of flexible non-photochemical quenching mechanisms that regulate light harvesting in oxygenic photosynthesis.

  Krishna K Niyogi, Thuy B Truong
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  ABSTRACT: All photosynthetic organisms need to regulate light harvesting for photoprotection. Three types of flexible non-photochemical quenching (NPQ) mechanisms have been characterized in oxygenic photosynthetic cyanobacteria, algae, and plants: OCP-, LHCSR-, and PSBS-dependent NPQ. OCP-dependent NPQ likely evolved first, to quench excess excitation in the phycobilisome (PB) antenna of cyanobacteria. During evolution of eukaryotic algae, PBs were lost in the green and secondary red plastid lineages, while three-helix light-harvesting complex (LHC) antenna proteins diversified, including LHCSR proteins that function in dissipating excess energy rather than light harvesting. PSBS, an independently evolved member of the LHC protein superfamily, seems to have appeared exclusively in the green lineage, acquired a function as a pH sensor that turns on NPQ, and eventually replaced LHCSR in vascular plants.
  Current opinion in plant biology 04/2013;
• Article: Functional genomics based understanding of rice endosperm development.

  Shi-Rong Zhou, Lin-Lin Yin, Hong-Wei Xue
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  ABSTRACT: Seed development, especially the relevant regulatory mechanism and genetic network are of fundamental scientific interest. Seed development consists of the development of embryo and endosperm; and endosperm development of rice (model species of monocots) is closely related to grain yield and quality. Recent genetic studies, together with other approaches, including transcriptome and proteomics analysis, high-throughput sequencing (RNA-seq, ChIP-seq), revealed the crucial roles of genetic and epigenetic controls in rice endosperm development. Here we summarize and update the genetic networks involved in the regulation of endosperm initiation, cell cycle regulation, aleurone layer specification, starch synthesis, storage protein accumulation and endosperm size, and the interactions between embryo and endosperm.
  Current opinion in plant biology 04/2013;
• Article: Plant phenomics and high-throughput phenotyping: accelerating rice functional genomics using multidisciplinary technologies.

  Wanneng Yang, Lingfeng Duan, Guoxing Chen, Lizhong Xiong, Qian Liu
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  ABSTRACT: The functional analysis of the rice genome has entered into a high-throughput stage, and a project named RICE2020 has been proposed to determine the function of every gene in the rice genome by the year 2020. However, as compared with the robustness of genetic techniques, the evaluation of rice phenotypic traits is still performed manually, and the process is subjective, inefficient, destructive and error-prone. To overcome these limitations and help rice phenomics more closely parallel rice genomics, reliable, automatic, multifunctional, and high-throughput phenotyping platforms should be developed. In this article, we discuss the key plant phenotyping technologies, particularly photonics-based technologies, and then introduce their current applications in rice (wheat or barley) phenomics. We also note the major challenges in rice phenomics and are confident that these reliable high-throughput phenotyping tools will give plant scientists new perspectives on the information encoded in the rice genome.
  Current opinion in plant biology 04/2013;
• Article: Rice breeding in the post-genomics era: from concept to practice.

  Zhi-Kang Li, Fan Zhang
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  ABSTRACT: Future world food security requires continued and sustainable increase in rice production. Much of this increase has to come from new high yielding cultivars with resistances to multiple stresses. While future rice breeding in the post-genomics era has to build upon the progress in rice functional genomics research, great challenges remain in understanding the genetic/molecular systems underlying complex traits and linking the tremendous genome sequence diversity in the rice germplasm collections to the phenotypic variation of important traits. To meet the challenges in future rice improvement, a molecular breeding (MB) strategy has been practiced in China with significant progress in establishing the MB material and information platforms in the process of breeding, and in developing new varieties through two novel MB schemes. However, full implementation of this strategy requires tremendous investment to build capacities in high-throughput genotyping, reliable/precision phenotyping and in developing and adopting new genomics/genetic information-based analytic/application breeding tools, which are not in place in most of the public rice breeding institutions. Nevertheless, future advances and developments in these areas are expected to generate enormous knowledge of rice traits and application tools that enable breeders to deploy more efficient and effective breeding strategies to maximize rice productivity and resource use efficiencies in various ecosystems.
  Current opinion in plant biology 04/2013;
• Article: Promise and issues of genetically modified crops.

  Hao Chen, Yongjun Lin
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  ABSTRACT: The growing area of genetically modified (GM) crops has substantially expanded since they were first commercialized in 1996. Correspondingly, the adoption of GM crops has brought huge economic and environmental benefits. All these achievements have been primarily supported by two simple traits of herbicide tolerance and insect resistance in the past 17 years. However, this situation will change soon. Recently, the advance of new products, technologies and safety assessment approaches has provided new opportunities for development of GM crops. In this review, we focus on the developmental trend in various aspects of GM crops including new products, technical innovation and risk assessment approaches, as well as potential challenges that GM crops are currently encountering.
  Current opinion in plant biology 04/2013;
• Article: Genomic resources for functional analyses of the rice genome.

  Ying Yang, Yan Li, Changyin Wu
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  ABSTRACT: With the availability of the rice genome sequence, rice research communities are entering a new era of plant functional genomics. The last decade has seen rapid worldwide progress on establishing platforms for rice functional genomic research. These platforms offer practical toolkits and genomic resources for high-throughput identification of genes and pathways. In this review, we summarize available genomic resources for functional analyses of the rice genome. These genomic resources include high-quality bacterial artificial chromosome libraries, large-scale expression sequence tags, full-length cDNA collections, large amounts of data on global expression profiles, various mutant libraries and integrated bioinformatics databases. We not only present the current status of genomic resources but also discuss their usage in elucidating gene functions of the rice genome.
  Current opinion in plant biology 04/2013;
• Article: Improvement of phosphorus efficiency in rice on the basis of understanding phosphate signaling and homeostasis.

  Ping Wu, Huixia Shou, Guohua Xu, Xinming Lian
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  ABSTRACT: Rice is one of the most important cereal crops feeding a large segment of the world's population. Inefficient utilization of phosphate (Pi) fertilizer by the plant in rice production increases cost and pollution. Developing cultivars with improved Pi use efficiency is essential for the sustainability of agriculture. Pi uptake, translocation and remobilization are regulated by complex molecular mechanisms through the functions of Pi transporters (PTs) and other downstream Pi Starvation Induced (PSI) genes. Expressions of these PSI genes are regulated by the Pi Starvation Response Regulator (OsPHR2)-mediated transcriptional control and/or PHO2-mediated ubiquitination. SPX-domain containing proteins and the type I H(+)-PPase AVP1 involved in the maintenance and utilization of the internal phosphate. The potential application of posttranscriptional regulation of PT1 through OsPHF1 for Pi efficiency is proposed.
  Current opinion in plant biology 04/2013;
• Article: Sequencing-based genome-wide association study in rice.

  Bin Han, Xuehui Huang
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  ABSTRACT: Rice, which has a modest genome size, is a wonderful model crop that has been comprehensively studied in functional genomics. With vast germplasm resources and reduced sequencing cost, genome-wide association study (GWAS) has been feasible to explore the allelic variation underlying agronomic traits in rice. In this review, we firstly summarize the work on constructing GWAS platforms in human genetics and in Arabidopsis and maize, from which we have a lot to learn. We then discuss the sequencing strategies and experimental designs for GWAS of agronomic traits in rice, and the perspective and challenges coupled with GWAS work are further addressed.
  Current opinion in plant biology 04/2013;