Development and application of SSR markers for measuring gene flow in Douglas-fir

Gene flow is a major evolutionary force and an important factor in the breeding and conservation of forest trees. I studied the applicability of SSR markers for measuring pollen-mediated gene flow (i.e., pollen flow) in Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). I developed SSR markers, tested alternative approaches for measuring pollen flow using SSR markers, then measured pollen contamination and characterized within-block mating patterns in one block of a seed orchard complex. Useful markers were developed from 4.1% of the SSR sequences screened. The 22 markers obtained are among the most informative genetic markers available for Douglas-fir. The observed heterozygosity and the number of alleles per marker averaged 0.855 (SE=0.020) and 23 (SE=1.6), respectively. Mistyping (i.e., false identification of genotypes) results in overestimating pollen flow. Requiring multiple mismatches for paternity exclusion, while assuring that the probability of detecting immigrant genotypes is high, results in accurate estimates of pollen flow. I developed and made available the Pollen Flow (PFL) computer program, which performs paternity exclusion and measures pollen flow based on multiple fatheroffspring mismatches. Pollen contamination was consistently high in all three years in which seed crops were sampled from the orchard block (mean = 35.3%). Levels of pollen contamination varied substantially among clones, and were significantly higher in clones with early female receptivity (mean = 55.5%) than in those with intermediate (mean = 36.4%) or late (mean = 28.3%) female receptivity. Seeds resulting from self-fertilization were rare (mean = 1.8%). Differences in the relative paternal contributions of the clones in the block were greater than ten-fold, and there was preferential mating among parents with similar floral phenology. Information from analyses of SSR data can be used to minimize pollen contamination and improve within-orchard mating patterns. Furthermore, SSRs can be used to advance knowledge of gene flow in natural populations. The availability of large sets of highly variable SSRs makes it possible to perform landscape-scale studies of gene flow and better understand the interactions between gene flow and adaptation. These studies will ultimately provide a basis for decisions in breeding and conservation programs

Advances in the genetic dissection of plant cell walls: tools and resources available in Miscanthus

Tropical C(4) grasses from the genus Miscanthus are believed to have great potential as biomass crops. However, Miscanthus species are essentially undomesticated, and genetic, molecular and bioinformatics tools are in very early stages of development. Furthermore, similar to other crops targeted as lignocellulosic feedstocks, the efficient utilization of biomass is hampered by our limited knowledge of the structural organization of the plant cell wall and the underlying genetic components that control this organization. The Institute of Biological, Environmental and Rural Sciences (IBERS) has assembled an extensive collection of germplasm for several species of Miscanthus. In addition, an integrated, multidisciplinary research programme at IBERS aims to inform accelerated breeding for biomass productivity and composition, while also generating fundamental knowledge. Here we review recent advances with respect to the genetic characterization of the cell wall in Miscanthus. First, we present a summary of recent and on-going biochemical studies, including prospects and limitations for the development of powerful phenotyping approaches. Second, we review current knowledge about genetic variation for cell wall characteristics of Miscanthus and illustrate how phenotypic data, combined with high-density arrays of single-nucleotide polymorphisms, are being used in genome-wide association studies to generate testable hypotheses and guide biological discovery. Finally, we provide an overview of the current knowledge about the molecular biology of cell wall biosynthesis in Miscanthus and closely related grasses, discuss the key conceptual and technological bottlenecks, and outline the short-term prospects for progress in this field

Mechanisms of cadmium toxicity and tolerance in Populus

Abstract ID#: 26642
Background and Methods:

Cadmium (Cd), ranked the 7th most hazardous substance, is one of the most widespread pollutants of soil and water in industrialized nations. Its increased movement in soil-plant systems is posing a serious threat to human health. Cd, without any known functions in plants, was found to be toxic even at minute concentrations, leading to the development of symptoms such as leaf roll, chlorosis and root and shoot growth reduction. Phytoremediation is an emerging cost-effective and environment friendly technology that utilizes high biomass producing plants including Populus plants to remove, transform or stabilize contaminants in soils. The objectives of our study were to record phenotypic variation in a Populus pedigree to Cd exposure, to identify Cd tolerant and susceptible genotypes of Populus, to map QTLs (Quantitative Trait Loci - genomic regions responsible) for Cd tolerance and accumulation in Populus and to predict a mechanism for Cd toxicity and tolerance in susceptible and tolerant Populus genotypes.

QTL mapping was accomplished by conducting a greenhouse hydroponic study in which 252 genotypes of a Populus pseudo-backcross progeny were grown for 40 days and treated with 25 µM Cd. Phenotypic variation in total dry weight was recorded on these genotypes and was used for identifying QTL for Cd tolerance. We identified genotypes with contrasting responses to the Cd treatment and conducted a microarray study to identify potential Cd tolerance mechanisms based on gene expression patterns.

 

Results/Conclusions:

Significant variation was observed among genotypes in response to Cd treatment based on changes in total dry weight. Cd tolerant and susceptible genotypes were identified based on the least square mean differences (Control-Cd treated for each genotype) among all the genotypes. Three QTLs were identified for Cd tolerance and they accounted for approximately 25% of the phenotypic variation in Cd tolerance measured as total dry weights.

In the microarray study, the Cd-susceptible genotype had higher expression of Fe-transporters compared to the tolerant genotypes, and Cd and Fe levels were significantly different in foliage. Even the susceptible genotype controls had higher, though not significant, Fe levels than tolerant genotype controls. We therefore hypothesize that part of the mechanism for Cd tolerance is determined by the differences in the activity of Fe transporters in genotypes with differential Fe homeostasis

Contrasting patterns of evolution following whole genome versus tandem duplication events in Populus

Comparative analysis of multiple angiosperm genomes has implicated gene duplication in the expansion and diversification of many gene families. However, empirical data and theory suggest that whole-genome and small-scale duplication events differ with respect to the types of genes preserved as duplicate pairs. We compared gene duplicates resulting from a recent whole genome duplication to a set of tandemly duplicated genes in the model forest tree Populus trichocarpa. We used a combination of microarray expression analyses of a diverse set of tissues and functional annotation to assess factors related to the preservation of duplicate genes of both types. Whole genome duplicates are 700 bp longer and are expressed in 20% more tissues than tandem duplicates. Furthermore, certain functional categories are over-represented in each class of duplicates. In particular, disease resistance genes and receptor-like kinases commonly occur in tandem but are significantly under-retained following whole genome duplication, while whole genome duplicate pairs are enriched for members of signal transduction cascades and transcription factors. The shape of the distribution of expression divergence for duplicated pairs suggests that nearly half of the whole genome duplicates have diverged in expression by a random degeneration process. The remaining pairs have more conserved gene expression than expected by chance, consistent with a role for selection under the constraints of gene balance. We hypothesize that duplicate gene preservation in Populus is driven by a combination of subfunctionalization of duplicate pairs and purifying selection favoring retention of genes encoding proteins with large numbers of interactions

Novel insights into chromosome evolution in birds, archosaurs, and reptiles

Homologous synteny blocks (HSBs) and evolutionary breakpoint regions (EBRs) in mammalian chromosomes are enriched for distinct DNA features, contributing to distinct phenotypes. To reveal HSB and EBR roles in avian evolution, we performed a sequence-based comparison of 21 avian and 5 outgroup species using recently sequenced genomes across the avian family tree and a newly-developed algorithm. We identified EBRs and HSBs in ancestral bird, archosaurian (bird, crocodile, and dinosaur), and reptile chromosomes. Genes involved in the regulation of gene expression and biosynthetic processes were preferably located in HSBs, including for example, avian-specific HSBs enriched for genes involved in limb development. Within birds, some lineage-specific EBRs rearranged genes were related to distinct phenotypes, such as forebrain development in parrots. Our findings provide novel evolutionary insights into genome evolution in birds, particularly on how chromosome rearrangements likely contributed to the formation of novel phenotypes

Investigating the origins and evolution of a glyphosate-resistant weed invasion in South America

The global invasion, and subsequent spread and evolution of weeds provides unique opportunities to address fundamental questions in evolutionary and invasion ecology. Amaranthus palmeri is a widespread glyphosate-resistant (GR) weed in the USA. Since 2015, GR populations of A. palmeri have been confirmed in South America, raising questions about introduction pathways and the importance of pre- vs. post-invasion evolution of GR traits. We used RAD-sequencing genotyping to characterize genetic structure of populations from Brazil, Argentina, Uruguay and the USA. We also quantified gene copy number of the glyphosate target, 5-enolpyruvyl-3-shikimate phosphate synthase (EPSPS), and the presence of an extrachromosomal circular DNA (eccDNA) replicon known to confer glyphosate resistance in USA populations. Populations in Brazil, Argentina and Uruguay were only weakly differentiated (pairwise FST ≤0.043) in comparison to USA populations (mean pairwise FST =0.161, range =0.068–0.258), suggesting a single major invasion event. However, elevated EPSPS copy number and the EPSPS replicon were identified in all populations from Brazil and Uruguay, but only in a single Argentinean population. These observations are consistent with independent in situ evolution of glyphosate resistance in Argentina, followed by some limited recent migration of the eccDNA-based mechanism from Brazil to Argentina. Taken together, our results are consistent with an initial introduction of A. palmeri into South America sometime before the 1980s, and local evolution of GR in Argentina, followed by a secondary invasion of GR A. palmeri with the unique eccDNA-based mechanism from the USA into Brazil and Uruguay during the 2010s.Fil: Gaines, Todd A. State University of Colorado - Fort Collins; Estados UnidosFil: Slavov, Gancho. No especifíca;Fil: Hughes, David. No especifíca;Fil: Kupper, Anita. State University of Colorado - Fort Collins; Estados UnidosFil: Sparks, Crystal. State University of Colorado - Fort Collins; Estados UnidosFil: Oliva, Julian. Universidad Católica de Córdoba; ArgentinaFil: Vila Aiub, Martin Miguel. Consejo Nacional de Investigaciones Científicas y Técnicas. Oficina de Coordinación Administrativa Parque Centenario. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura. Universidad de Buenos Aires. Facultad de Agronomía. Instituto de Investigaciones Fisiológicas y Ecológicas Vinculadas a la Agricultura; ArgentinaFil: García, Alejandro Marcelo. Instituto Nacional de Tecnología Agropecuaria; ArgentinaFil: Merotto, Aldo. Universidade Federal do Rio Grande do Sul; BrasilFil: Neve, Paul. No especifíca

Genetic diversity and phylogenetic analysis of the native mountain ponies of Britain and Ireland reveal a novel rare population

The conservation of unique populations of animals is critical in order to preserve valuable genetic diversity and, where populations are free-living, maintain their irreplaceable influence upon habitat ecology. An accurate assessment of genetic diversity and structure within and between populations is crucial in order to design and implement conservation strategies in natural and domesticated species. Moreover, where it is possible to identify relic populations that are related to a structured breed an ideal opportunity presents itself to model processes that reveal historical factors that have shaped genetic diversity. The origins of native UK mountain and moorland ponies are uncertain, but they may have directly descended from prehistoric populations and potentially harbour specific adaptations to the uplands of Britain and Ireland. To date, there have been no studies of population structure and genetic diversity present within a free-living group of ponies in the Carneddau mountain range of North Wales. Herein, we describe the use of microsatellites and SNPs together with analysis of the mitochondrial control region to quantify the extent and magnitude of genetic diversity present in the feral Carneddau pony and relate this to several recognised British and Irish pony breeds. Our results establish that the feral Carneddau ponies represent a unique and distinctive population that merits recognition as a defined population and conservation priority. We discuss the implications for conservation of this population as a unique pool of genetic diversity adapted to the British uplands and potentially of particular value in maintaining the biodiversity of these habitats