Recent advances in the application of in vitro systems to plant improvement

The horticultural industry was instrumental in the early development and exploitation of genetic techniques over a century ago. This review will describe recent advances in a range of in vitro methods and their application to plant breeding, with especial emphasis on horticultural crops. These methods include improvements in the efficiency of haploid breeding techniques in many fruit and vegetable species using either microspore-derived or ovule-derived plants. Significant molecular information is now available to supplement these essentially empirical approaches and this may enable the more predictable application of these technologies in previously intransigent crops. Similarly there are now improved techniques for isolation of somatic hybrids, by application of either in vitro fertilisation or the culture of excised ovules from interspecific crosses. In addition to examples taken from the traditional scientific literature, emphasis will also be given to the use of patent databases as a valuable source of information on recent novel technologies developed in the commercial world.

Transcriptome analysis and crop improvement (a review)

The identification and characterization of differential gene expression from tissues subjected to stress has gained much attention in plant research. The recognition of elements involved in the response to a particular stress enhances the possibility of promoting crop improvement through direct genetic modification. However, the performance of some of the 'first generation' of transgenic plants with the incorporation of a single gene has not always been as expected. These results have stimulated the development of new transgenic constructions introducing more than one gene and capable of modifying complex pathways. Several techniques are available to conduct the analysis of gene regulation, with such information providing the basis for novel constructs specifically designed to modify metabolism. This review deals with techniques that allow the identification and characterization of differentially-expressed genes and the use of molecular pathway information to produce transgenic plants.

Electrochemical determination of plant-derived leuco-indigo after chemical reduction by glucose

Electrochemical determination of redox active dye species is demonstrated in indigo samples contaminated with high levels of organic and inorganic impurities. The use of a hydrodynamic electrode system based on a vibrating probe (250 Hz, 200 mu m lateral amplitude) allows time-independent diffusion controlled signals to be enhanced and reliable concentration data to be obtained under steady state conditions at relatively fast scan rates up to 4 V s-1In this work the indigo content of a complex plant-derived indigo sample (dye content typically 30%) is determined after indigo is reduced by addition of glucose in aqueous 0.2 M NaOH. The soluble leuco-indigo is measured by its oxidation response at a vibrating electrode. The vibrating electrode, which consisted of a laterally vibrating 500 mu m diameter gold disc, is calibrated with Fe(CN)(6) 3-/4- in 0.1 M KCl and employed for indigo determination at 55, 65, and 75 C in 0.2 M NaOH. Determinations of the indigo content of 25 different samples of plant-derived indigo are compared with those obtained by conventional spectrophotometry. This comparison suggests a significant improvement by the electrochemical method, which appears to be less sensitive to impurities.

Farmers' management of rice varietal diversity in the mid-hills of Nepal: implications for on-farm conservation and crop improvement

Season-long monitoring of on-farm rice (Oryza sativa, L.) plots in Nepal explored farmers' decision-making process on the deployment of varieties to agroecosystems, application of production inputs to varieties, agronomic practices and relationship between economic return and area planted per variety. Farmers deploy varieties [landraces (LRs) and modern varieties (MVs)] to agroecosystems based on their understanding of characteristics of varieties and agroecosystems, and the interaction between them. In marginal growing conditions, LRs can compete with MVs. Within an agroecosystem, economic return and area planted to varieties have positive relationship, but this is not so between agroecosystems. LRs are very diverse on agronomic and economic traits; therefore, they cannot be rejected a priori as inferior materials without proper evaluation. LRs have to be evaluated for useful traits and utilized in breeding programmes to generate farmer-preferred materials for marginal environments and for their conservation on-farm.

Regulatory hotspots are associated with plant gene expression under varying soil phosphorus supply in Brassica rapa

Gene expression is a quantitative trait that can be mapped genetically in structured populations to identify expression quantitative trait loci (eQTL). Genes and regulatory networks underlying complex traits can subsequently be inferred. Using a recently released genome sequence, we have defined cis- and trans-eQTL and their environmental response to low phosphorus (P) availability within a complex plant genome and found hotspots of trans-eQTL within the genome. Interval mapping, using P supply as a covariate, revealed 18,876 eQTL. trans-eQTL hotspots occurred on chromosomes A06 and A01 within Brassica rapa; these were enriched with P metabolism-related Gene Ontology terms (A06) as well as chloroplast-and photosynthesis-related terms (A01). We have also attributed heritability components to measures of gene expression across environments, allowing the identification of novel gene expression markers and gene expression changes associated with low P availability. Informative gene expression markers were used to map eQTL and P use efficiency-related QTL. Genes responsive to P supply had large environmental and heritable variance components. Regulatory loci and genes associated with P use efficiency identified through eQTL analysis are potential targets for further characterization and may have potential for crop improvement.

Participatory crop improvement: the challenges of and opportunities for institutionalisation in the Indian public research sector

This thesis considers Participatory Crop Improvement (PCI) methodologies and examines the reasons behind their continued contestation and limited mainstreaming in conventional modes of crop improvement research within National Agricultural Research Systems (NARS). In particular, it traces the experiences of a long-established research network with over 20 years of experience in developing and implementing PCI methods across South Asia, and specifically considers its engagement with the Indian NARS and associated state-level agricultural research systems. In order to address the issues surrounding PCI institutionalisation processes, a novel conceptual framework was derived from a synthesis of the literatures on Strategic Niche Management (SNM) and Learning-based Development Approaches (LBDA) to analyse the socio-technical processes and structures which constitute the PCI ‘niche’ and NARS ‘regime’. In examining the niche and regime according to their socio-technical characteristics, the framework provides explanatory power for understanding the nature of their interactions and the opportunities and barriers that exist with respect to the translation of lessons and ideas between niche and regime organisations. The research shows that in trying to institutionalise PCI methods and principles within NARS in the Indian context, PCI proponents have encountered a number of constraints related to the rigid and hierarchical structure of the regime organisations; the contractual mode of most conventional research, which inhibits collaboration with a wider group of stakeholders; and the time-limited nature of PCI projects themselves, which limits investment and hinders scaling up of the innovations. It also reveals that while the niche projects may be able to induce a ‘weak’ form of PCI institutionalisation within the Indian NARS by helping to alter their institutional culture to be more supportive of participatory plant breeding approaches and future collaboration with PCI researchers, a ‘strong’ form of PCI institutionalisation, in which NARS organisations adopt participatory methodologies to address all their crop improvement agenda, is likely to remain outside of the capacity of PCI development projects to deliver.