Toby Hodgkin

Bio: Toby Hodgkin is an academic researcher. The author has contributed to research in topics: Biodiversity & Agricultural biodiversity. The author has an hindex of 1, co-authored 1 publications receiving 379 citations.

Genetic diversity and conservation and utilization of plant genetic resources

Abstract: Biodiversity refers to variation within the living world, while genetic diversity represents the heritable variation within and between populations of organisms, and in the context of this paper, among plant species. This pool of genetic variation within an inter-mating population is the basis for selection as well as for plant improvement. Thus, conservation of this plant genetic diversity is essential for present and future human well-being. During recent years, there has been increasing awareness of the importance of adopting a holistic view of biodiversity, including agricultural biodiversity, conservation for sustainable utilization and development. These principles have been enshrined in the Convention on Biological Diversity and the Global Plan of Action of the Food and Agriculture Organization of the United Nations. The emphasis is now to understand the distribution and extent of genetic diversity available to humans in plant species, so that the genetic diversity can be safely conserved and efficiently used. It is generally recognized that plant genetic diversity changes in time and space. The extent and distribution of genetic diversity in a plant species depends on its evolution and breeding system, ecological and geographical factors, past bottlenecks, and often by many human factors. Much of the large amount of diversity of a species may be found within individual populations, or partitioned among a number of different populations. A better understanding of genetic diversity and its distribution is essential for its conservation and use. It will help us in determining what to conserve as well as where to conserve, and will improve our understanding of the taxonomy and origin and evolution of plant species of interest. Knowledge of both these topics is essential for collecting and use of any plant species and its wild relatives. In order to mange conserved germplasm better, there is also a need to understand the genetic diversity that is present in collections. This will help us to rationalize collections and develop and adopt better protocols for regeneration of germplasm seed. Through improved characterization and development of core collections based on genetic diversity information, it will be possible to exploit the available resources in more valuable ways.

Population genomic and genome-wide association studies of agroclimatic traits in sorghum

Abstract: Accelerating crop improvement in sorghum, a staple food for people in semiarid regions across the developing world, is key to ensuring global food security in the context of climate change. To facilitate gene discovery and molecular breeding in sorghum, we have characterized ∼265,000 single nucleotide polymorphisms (SNPs) in 971 worldwide accessions that have adapted to diverse agroclimatic conditions. Using this genome-wide SNP map, we have characterized population structure with respect to geographic origin and morphological type and identified patterns of ancient crop diffusion to diverse agroclimatic regions across Africa and Asia. To better understand the genomic patterns of diversification in sorghum, we quantified variation in nucleotide diversity, linkage disequilibrium, and recombination rates across the genome. Analyzing nucleotide diversity in landraces, we find evidence of selective sweeps around starch metabolism genes, whereas in landrace-derived introgression lines, we find introgressions around known height and maturity loci. To identify additional loci underlying variation in major agroclimatic traits, we performed genome-wide association studies (GWAS) on plant height components and inflorescence architecture. GWAS maps several classical loci for plant height, candidate genes for inflorescence architecture. Finally, we trace the independent spread of multiple haplotypes carrying alleles for short stature or long inflorescence branches. This genome-wide map of SNP variation in sorghum provides a basis for crop improvement through marker-assisted breeding and genomic selection.

Conservation in vitro of threatened plants - progress in the past decade

Abstract: In vitro techniques have found increasing use in the conservation of threatened plants in recent years and this trend is likely to continue as more species face risk of extinction. The Micropropagation Unit at Royal Botanic Gardens, Kew, UK (RBG Kew) has an extensive collection of in vitro plants including many threatened species from throughout the world. The long history of the unit and the range of plants cultured have enabled considerable expertise to be amassed in identifying the problems and developing experimental strategies for propagation and conservation of threatened plants. While a large body of knowledge is available on the in vitro culture of plants, there are limited publications relating to threatened plant conservation. This review highlights the progress in in vitro culture and conservation of threatened plants in the past decade (1995–2005) and suggests future research directions. Works on non-threatened plants are also included wherever methods have applications in rare plant conservation. Recalcitrant plant materials collected from the wild or ex situ collections are difficult to grow in culture. Different methods of sterilization and other treatments to establish clean material for culture initiation are reviewed. Application of different culture methods for multiplication, and use of unconventional materials for rooting and transplantation are reviewed. As the available plant material for culture initiation is scarce and in many cases associated with inherent problems such as low viability and endogenous contamination, reliable protocols on multiplication, rooting, and storage methods are very important. In this context, photoautotrophic micropropagation has the potential for development as a routine method for the in vitro conservation of endangered plants. Long-term storage of material in culture is challenging and the potential applications of cryopreservation are significant in this area. Future conservation biotechnology research and its applications must be aimed at conserving highly threatened, mainly endemic, plants from conservation hotspots.

Evolutionary response of landraces to climate change in centers of crop diversity

Abstract: Landraces cultivated in centers of crop diversity result from past and contemporary patterns of natural and farmer-mediated evolutionary forces. Successful in situ conservation of crop genetic resources depends on continuity of these evolutionary processes. Climate change is projected to affect agricultural production, yet analyses of impacts on in situ conservation of crop genetic diversity and farmers who conserve it have been absent. How will crop landraces respond to alterations in climate? We review the roles that phenotypic plasticity, evolution, and gene flow might play in sustaining production, although we might expect erosion of genetic diversity if landrace populations or entire races lose productivity. For example, highland maize landraces in southern Mexico do not express the plasticity necessary to sustain productivity under climate change, but may evolve in response to altered conditions. The outcome for any given crop in a given region will depend on the distribution of genetic variation that affects fitness and patterns of climate change. Understanding patterns of neutral and adaptive diversity from the population to the landscape scale is essential to clarify how landraces conserved in situ will continue to evolve and how to minimize genetic erosion of this essential natural resource.

Patterns of molecular variation in a species-wide germplasm set of Brassica napus

Abstract: Rapeseed (Brassica napus L.) is the leading European oilseed crop serving as source for edible oil and renewable energy. The objectives of our study were to (i) examine the population structure of a large and diverse set of B. napus inbred lines, (ii) investigate patterns of genetic diversity within and among different germplasm types, (iii) compare the two genomes of B. napus with regard to genetic diversity, and (iv) assess the extent of linkage disequilibrium (LD) between simple sequence repeat (SSR) markers. Our study was based on 509 B. napus inbred lines genotyped with 89 genome-specific SSR primer combinations. Both a principal coordinate analysis and software STRUCTURE revealed that winter types, spring types, and swedes were assigned to three major clusters. The genetic diversity of winter oilseed rape was lower than the diversity found in other germplasm types. Within winter oilseed rape types, a decay of genetic diversity with more recent release dates and reduced levels of erucic acid and glucosinolates was observed. The percentage of linked SSR loci pairs in significant (r2 > Q95 unlinked loci pairs) LD was 6.29% for the entire germplasm set. Furthermore, LD decayed rapidly with distance, which will allow a relatively high mapping resolution in genome-wide association studies using our germplasm set, but, on the other hand, will require a high number of markers.

Assessment of genetic diversity in crop plants - an overview

Abstract: Crop plant evolution either natural or human-directed, is primarily based on existing genetic diversity in the population. Diversity can be described as the degree of differentiation between or within species. Existing intraand inter-specific differences are at the base of all crop improvement programmes. If all the individuals within the species would have been similar, then possibly there could not have been any scope for improvement in plant performances for different traits. Since the beginning of systematic plant breeding, natural variability and divergence between crops have been extensively identified and used in improvement of crop species. However, with the progress of time, natural variability got depleted due to (i) lopsided breeding practices focusing on improvement of only few traits (like yield and its component traits), (ii) frequent use of few selected genotypes as parents in varietal development programme and (iii) introduction of few outstanding lines to many countries thereby leading to increased genetic similarity between modern crop cultivars. Reduced genetic variability and diversity among crop plant species has raised serious concern among agricultural workers. With reduced genetic diversity, further improvement in crop varieties will be an arduous task. Breaking yield barriers will become difficult and plant breeders will be unable to meet the requirements arising out of ever-increasing demand on account of exploding population. Genetic diversity becomes more important in context of climatic change and associated unforeseen events as it may serve as the reservoir of many novel traits conferring tolerance to different biotic and abiotic stresses. Genetic diversity is the underlying cause of many important agriculturally important phenomena like heterosis and transgressive segregation. Diverse lines are needed for defect correction of commercial varieties and development of novel varieties. Hence, identification of diverse lines (if available), creation of diversity (if not available or limited) and its subsequent utilization are the major goals of any crop improvement programmes. In this context, knowledge on all aspects of genetic diversity viz., factors affecting genetic diversity, different methods of diversity analysis, their measurement and the softwares for carrying statistical analysis becomes imperative in order to utilize them prudently. Many reviews have been written focusing on vital issues like changes in genetic diversity under plant breeding,1 genetic vulnerability of modern crop cultivars,2 conservation and utilization of genetic resources3,4 assessment of genetic diversity using molecular markers5 and measurement of genetic diversity using statistical tools.6–8 In the present review, an attempt is being made for comprehensive compilation of overall concepts in the area of genetic diversity, which could be of immense significance for extending knowledge and meaningful research.