Oil palm (Elaeis guineensis) produces over five times more oil/year/hectare than oil seed rape and accounted for 33% of world vegetable oil production in 2011. Being a cross-pollinated perennial tree crop with long breeding cycles (typically 12 years) and a large planting area requirement (usually 143 palms/hectare), utilization of molecular technology could greatly improve the efficiency of oil palm breeding. In the present study, various approaches were used to develop molecular markers for genetic linkage mapping and QTL analysis, with the ultimate goal of marker-assisted selection in oil palm. Firstly, Representational Difference Analysis (RDA) and Amplified Fragment Length Polymorphism (AFLP) were coupled with Bulked Segregant Analysis (BSA) to try to identify marker(s) closely linked to the important shell-thickness gene. A novel combination of RDA with Roche 454 pyrosequencing enabled a more comprehensive study of the enrichment profiles compared to Sanger sequencing. Identification of >35% redundant sequences, repetitive sequences and organelle DNA suggested that subtractive hybridization and target enrichment of RDA were inefficient here, with the lack of elimination of common sequences masking the real difference products. The use of the AFLP method identified 29 primer pairs that yielded 49 putative shell-thickness related-polymorphic bands. A detailed analysis will need to be carried out to fully evaluate and validate these markers. The use of the relatively new Diversity Array Technology “Genotyping-By-Sequencing” (DArTSeq) platform through genotyping of two closely-related tenera self-pollinated F2 populations, 768 (n=44) and 769 (n=57), generated a total of 11,675 DArTSeq polymorphic markers of good quality. These markers were used in the construction of the first reported DArTSeq based high-density linkage maps for oil palm. Both genetic maps consist of 16 major independent linkage groups (total map length of 1874.8 and 1720.6 cM, with an average marker density of one marker every 1.33 and 1.62 cM, respectively), corresponding well with the 16 homologous chromosome pairs of oil palm (2n = 2x = 32; 14/16 chromosomes were confirmed by known location SSR markers). Preliminary quantitative trait loci (QTL) mapping of the yield and vegetative growth traits detected four significant and 34 putative as well as two significant and 30 putative QTLs for these small 768 and 769 populations, respectively. No common significant QTL were detected between the two closely-related controlled crosses which could have allowed combination of QTL across the two populations. Saturation of the shell-thickness (Sh) region with all available DArTSeq markers, as well as map integration around the Sh regions for both populations, identified 32 Single Nucleotide Polymorphism (SNP) and DArT markers mapped within a 5 cM flanking region of the Sh gene. Homology search of the DArTSeq marker sequence tag (64 bp) against the recently published oil palm genome assembly confirmed that 23 out of the 32 (72%) DArTSeq markers were located on the p5_sc00060 scaffold in which the SHELL gene was identified. The identified shell-thickness markers could be useful as molecular screening tools. This study demonstrated the potential and feasibility of using genomic resources available for genetic improvement of oil palm breeding programmes.

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Shawn M. Verbout. / Also issued as Thesis (M.S.)--Massachusetts Institute of Technology, Dept. of Electrical Engineering and Computer Science, 1994. / Includes bibliographical references (p. 81-84). / Supported by the Staff Associate Program at MIT Lincoln Laboratory.

The Bromeliaceae is one of the largest and most ecologically diverse angiosperm families in the Neotropics. In recent years, this family has begun to emerge as a model system for the study of plant evolutionary ecology and physiology, and major advances have been made in understanding the factors involved in episodes of rapid diversification and adaptive radiation in specific bromeliad lineages. However, despite a long tradition of ecophysiological research on the Bromeliaceae, an integrative, evolutionarily-contextualised synthesis of the links between anatomical) physiological, and ecological aspects of bromeliad biology has hitherto been lacking. The overarching aim of this research project was therefore to use new quantitative data representing a wide range of bromeliad taxonomic and functional groups to elucidate how variation in leaf traits connected by structure-function relationships influences ecological differentiation among bromeliad taxa. Special emphasis was placed on hydraulic and water relations traits because of fast-paced contemporary developments in these fields. The methodologies employed included an assessment of the diversity of bromeliad hydrological habitat occupancy, quantification of key anatomical and physiological traits and their correlations, investigation of the links between vascular and extra-xylary anatomy and hydraulic efficiency and vulnerability, quantification of stomatal sensitivity to leaf-air vapour pressure deficit and stomatal kinetics, and a case study of trait-mediated niche segregation among congeneric epiphytic bromeliad species on the Caribbean island of Trinidad. The results highlight how divergences in a range of continuous and categorical anatomical traits underpin differences in physiological capacities and sensitivities, which in turn determine environmental relations and ecological distinctiveness. This research project therefore provides critical insights into the mechanistic basis of evolutionary diversification in a highly ecologically important family. It also represents the most comprehensive analysis of the significance of trait variation for ecological differentiation across any major radiation of herbaceous angiosperms.

In the context of increasing food insecurity, new integrated and more sustainable crop protection methods need to be developed. The phyllosphere, i.e. the leaf habitat, hosts a considerable number of microorganisms. However, only a limited number of these are pathogenic and the roles of the vast majority still remain unknown. Managing the leaf-associated microbial communities is emerging as a potential integrated crop protection strategy. This thesis reports the characterisation of the phyllosphere of barley, an economically important crop in Scotland, with the purpose of developing tools to manipulate it. Field experiments were carried out to determine the composition of the culturable bacterial phyllosphere. The leaf-associated populations were demonstrated to be dominated by bacteria belonging to the Pseudomonas genus. Two bacterial isolates, Pseudomonas syringae and Pectobacterium atrosepticum, hindered the growth of Rhynchosporium commune, the causal agent of the leaf scald, but promoted the development of powdery mildew symptoms, caused by Blumeria graminis f.sp. hordei. However, using a molecular fingerprinting technique, namely T-RFLP, the global community was shown to be significantly richer and more diverse than indicated by the culture-based methods, thus increasing the complexity of interactions taking place in the phyllosphere. Various factors were found to affect the structure of the phyllobacteria significantly. Under controlled conditions, a root-associated symbiont, Piriformospora indica, was shown to increase the plant fitness and shift the abundance of the most common bacteria. In the field, both agro-chemical treatments tested, conventional fungicide and an elicitor mixture, increased the bacterial diversity, but fungicide application resulted in a higher yield and better protection against diseases. Finally, the plant genotype also affected the phyllosphere structure. Mutations in the leaf epicuticular waxes led to significant changes in the bacterial diversity and differentially affected disease in the field. A negative correlation between bacterial diversity and scald infection was also observed.