Polymorphic simple sequence repeat regions in chloroplast genomes: applications to the population genetics of pines.

Simple sequence repeats (SSRs), consisting of tandemly repeated multiple copies of mono-, di-, tri-, or tetranucleotide motifs, are ubiquitous in eukaryotic genomes and are frequently used as genetic markers, taking advantage of their length polymorphism. We have examined the polymorphism of such sequences in the chloroplast genomes of plants, by using a PCR-based assay. GenBank searches identified the presence of several (dA)n.(dT)n mononucleotide stretches in chloroplast genomes. A chloroplast (cp) SSR was identified in three pine species (Pinus contorta, Pinus sylvestris, and Pinus thunbergii) 312 bp upstream of the psbA gene. DNA amplification of this repeated region from 11 pine species identified nine length variants. The polymorphic amplified fragments were isolated and the DNA sequence was determined, confirming that the length polymorphism was caused by variation in the length of the repeated region. In the pines, the chloroplast genome is transmitted through pollen and this PCR assay may be used to monitor gene flow in this genus. Analysis of 305 individuals from seven populations of Pinus leucodermis Ant. revealed the presence of four variants with intrapopulational diversities ranging from 0.000 to 0.629 and an average of 0.320. Restriction fragment length polymorphism analysis of cpDNA on the same populations previously failed to detect any variation. Population subdivision based on cpSSR was higher (Gst = 0.22, where Gst is coefficient of gene differentiation) than that revealed in a previous isozyme study (Gst = 0.05). We anticipate that SSR loci within the chloroplast genome should provide a highly informative assay for the analysis of the genetic structure of plant populations.

The genetics, breeding and improvement of corn and cotton; a bibliography covering more than forty years work (1889-1929) in the breeding, improvement, and study of inheritance in corn and cotton (with many abstract references)

Cover title.

Maize genetics cooperation news letter.

Mode of access: Internet.

Altered fungal sensitivity to a plant antimicrobial peptide through over-expression of yeast cDNAs

A yeast cDNA expression library was screened to identify genes and cellular processes that influence fungal sensitivity to a plant antimicrobial peptide. A plasmid-based, GAL1 promoter-driven yeast cDNA expression library was introduced into a yeast genotype susceptible to the antimicrobial peptide MiAMP1 purified from Macadamia integrifolia. Following a screen of 20,000 cDNAs, three yeast cDNAs were identified that reproducibly provided transformants with galactose-dependent resistance to MiAMP1. These cDNAs encoded a protein of unknown function, a component (VMA11) of the vacuolar H+-ATPase and a component (cytochrome c oxidase subunit VIa) of the mitochondrial electron transport chain, respectively. To identify genes that increased sensitivity to MiAMP1, the yeast cDNA expression library was introduced into a yeast mutant with increased resistance to MiAMP1. From 11,000 cDNAs screened, two cDNA clones corresponding to a ser/thr kinase and a ser/thr phosphatase reproducibly increased MiAMP1 susceptibility in the mutant in a galactose-dependent manner. Deletion mutants were available for three of the five genes identified but showed no change in their sensitivity to MiAMP1, indicating that these genes could not be detected by screening of yeast deletion mutant libraries. Yeast cDNA expression library screening therefore provides an alternative approach to gene deletion libraries to identify genes that can influence the sensitivity of fungi to plant antimicrobial peptides.

Identification and molecular modeling of a novel, plant-like, human purple acid phosphatase

Purple acid phosphatases are a family of binuclear metallohydrolases that have been identified in plants, animals and fungi. Only one isoform of similar to 35 kDa has been isolated from animals, where it is associated with bone resorption and microbial killing through its phosphatase activity, and hydroxyl radical production, respectively. Using the sensitive PSI-BLAST search method, sequences representing new purple acid phosphatase-like proteins have been identified in mammals, insects and nematodes. These new putative isoforms are closely related to the similar to 55 kDa purple acid phosphatase characterized from plants. Secondary structure prediction of the new human isoform further confirms its similarity to a purple acid phosphatase from the red kidney bean. A structural model for the human enzyme was constructed based on the red kidney bean purple acid phosphatase structure. This model shows that the catalytic centre observed in other purple acid phosphatases is also present in this new isoform. These observations suggest that the sequences identified in this study represent a novel subfamily of plant-like purple acid phosphatases in animals and humans. (c) 2006 Elsevier B.V. All rights reserved.

Ecological genetics of Melaleuca quinquenervia (Myrtaceae): Population variation in Florida and its influence on performance of the biological control agent Oxyops vitiosa (Coleoptera: Curculionidae)

Melaleuca quinquenervia (Cav.) Blake (Myrtaceae) was imported into Florida from Australia over a century ago as a landscape plant. A favorable climate and periodic wildfires helped M. quinquenervia thrive; it now occupies about 200,000 hectares in southern Florida. A biological control (i.e., biocontrol) program against M. quinquenervia has been initiated, but not all biocontrol releases are successful. Some scientists have argued that poor biocontrol agent success may relate to genetic differences among populations of invasive weeds. I tested this premise by determining (1) the number and origins of M. quinquenervia introductions into Florida, (2) whether multiple introduction events resulted in the partitioning of Florida's M. quinquenervia populations into discrete biotypes, and (3) whether Oxyops vitiosa, an Australia snout beetle imported to control this weed, might discriminate among putative M. quinquenervia biotypes. Careful scrutiny of early horticultural catalogs and USDA plant introduction records suggested at least six distinct introduction events. Allozyme analyses indicated that the pattern of these introductions, and the subsequent redistribution of progeny, has resulted in geographic structuring of the populations in southern Florida. For example, trees on Florida's Gulf Coast had a greater effective number of alleles and exhibited greater heterozygosity than trees on the Atlantic Coast. Essential oil yields from M. quinquenervia leaves followed a similar trend; Gulf Coast trees yielded nearly twice as much oil as Atlantic Coast trees when both were grown in a common garden. These differences were partially explained by the predominance of a chemical phenotype (chemotype) very rich in the sesquiterpene (E)-nerolidol in M. quinquenervia trees from the Gulf Coast, but rich in a mixture of the monoterpene 1,8-cineole and the sesquiterpene viridiflorol in trees from the Atlantic Coast. Performance of O. vitiosa differed dramatically in laboratory studies depending on the chemotype of the foliage they were fed. Larval survivorship was four-fold greater on the (E)-nerolidol chemotype. Growth was also greater, with adult O. vitiosa gaining nearly 50% more biomass on the (E)-nerolidol plants than on the second chemotype. The results of this study thus confirmed the premise that plant genotype can affect the population dynamics of insects released as weed biocontrols. ^

Landscape genetics of Phaedranassa herb. (Amaryllidaceae) in Ecuador

Speciation can be understood as a continuum occurring at different levels, from population to species. The recent molecular revolution in population genetics has opened a pathway towards understanding species evolution. At the same time, speciation patterns can be better explained by incorporating a geographic context, through the use of geographic information systems (GIS). Phaedranassa (Amaryllidaceae) is a genus restricted to one of the world’s most biodiverse hotspots, the Northern Andes. I studied seven Phaedranassa species from Ecuador. Six of these species are endemic to the country. The topographic complexity of the Andes, which creates local microhabitats ranging from moist slopes to dry valleys, might explain the patterns of Phaedranassa species differentiation. With a Bayesian individual assignment approach, I assessed the genetic structure of the genus throughout Ecuador using twelve microsatellite loci. I also used bioclimatic variables and species geographic coordinates under a Maximum Entropy algorithm to generate distribution models of the species. My results show that Phaedranassa species are genetically well-differentiated. Furthermore, with the exception of two species, all Phaedranassa showed non-overlapping distributions. Phaedranassa viridiflora and P. glauciflora were the only species in which the model predicted a broad species distribution, but genetic evidence indicates that these findings are likely an artifact of species delimitation issues. Both genetic differentiation and nonoverlapping geographic distribution suggest that allopatric divergence could be the general model of genetic differentiation. Evidence of sympatric speciation was found in two geographically and genetically distinct groups of P. viridiflora. Additionally, I report the first register of natural hybridization for the genus. The findings of this research show that the genetic differentiation of species in an intricate landscape as the Andes does not necessarily show a unique trend. Although allopatric speciation is the most common form of speciation, I found evidence of sympatric speciation and hybridization. These results show that the processes of speciation in the Andes have followed several pathways. The mixture of these processes contributes to the high biodiversity of the region.

The Roles of Phenotypic Plasticity and Plant-Microbe Interactions in the Evolution of Complex Traits in Boechera stricta

<p>All organisms live in complex habitats that shape the course of their evolution by altering the phenotype expressed by a given genotype (a phenomenon known as phenotypic plasticity) and simultaneously by determining the evolutionary fitness of that phenotype. In some cases, phenotypic evolution may alter the environment experienced by future generations. This dissertation describes how genetic and environmental variation act synergistically to affect the evolution of glucosinolate defensive chemistry and flowering time in Boechera stricta, a wild perennial herb. I focus particularly on plant-associated microbes as a part of the plant’s environment that may alter trait evolution and in turn be affected by the evolution of those traits. In the first chapter I measure glucosinolate production and reproductive fitness of over 1,500 plants grown in common gardens in four diverse natural habitats, to describe how patterns of plasticity and natural selection intersect and may influence glucosinolate evolution. I detected extensive genetic variation for glucosinolate plasticity and determined that plasticity may aid colonization of new habitats by moving phenotypes in the same direction as natural selection. In the second chapter I conduct a greenhouse experiment to test whether naturally-occurring soil microbial communities contributed to the differences in phenotype and selection that I observed in the field experiment. I found that soil microbes cause plasticity of flowering time but not glucosinolate production, and that they may contribute to natural selection on both traits; thus, non-pathogenic plant-associated microbes are an environmental feature that could shape plant evolution. In the third chapter, I combine a multi-year, multi-habitat field experiment with high-throughput amplicon sequencing to determine whether B. stricta-associated microbial communities are shaped by plant genetic variation. I found that plant genotype predicts the diversity and composition of leaf-dwelling bacterial communities, but not root-associated bacterial communities. Furthermore, patterns of host genetic control over associated bacteria were largely site-dependent, indicating an important role for genotype-by-environment interactions in microbiome assembly. Together, my results suggest that soil microbes influence the evolution of plant functional traits and, because they are sensitive to plant genetic variation, this trait evolution may alter the microbial neighborhood of future B. stricta generations. Complex patterns of plasticity, selection, and symbiosis in natural habitats may impact the evolution of glucosinolate profiles in Boechera stricta.</p>

Estimating production costs and profitability of strawberry genotypes in southeast Queensland using plant traits

In Queensland the subtropical strawberry (Fragaria ×ananassa) breeding program aims to combine traits into new genotypes that increase production efficiency. The contribution of individual plant traits to cost and income under subtropical Queensland conditions has been investigated. The study adapted knowledge of traits and the production and marketing system to assess the economic impact (gross margin) of new cultivars on the system, with the overall goal of improving the profitability of the industry through the release of new strawberry cultivars. Genotypes varied widely in their effect on gross margin, from 48% above to 10% below the base value. The advantage of a new genotype was also affected by the proportion of total area allocated to the new genotype. The largest difference in gross margin between that at optimum allocation (8% increase in gross margin) and an all of industry allocation (20% decrease in gross margin) of area to the genotype was 28%. While in other cases the all of industry allocation was also the optimum allocation, with one genotype giving a 48% benefit in gross margin.