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Silverleaf dogwood (Cornus alba L. ‘Argenteo-marginata’), forsythia (Forsythia × intermedia Zab. ‘Lynwood Gold’), and weigela (Weigela florida Bunge A.DC. ‘Red Prince’) were grown in #2 (6-L) containers filled with 100% bark or bark mixed with 20, 40 or 60% by volume each of raw paper mill sludge (RB group), Bio Soil compost containing 100% paper mill sludge (BCB group), Waterdown compost containing 40% paper sludge, 40% chicken manure and 20% sawdust (WCB group), and municipal compost consisting of leaf and yard waste (MCB group). A fifth substrate group (MCH) consisted of 100% hemp chips or hemp chips mixed with the same rates of municipal compost. The containers were trickle-irrigated and fertilized with a controlled-release fertilizer. Regression analysis indicated that growth among the barkamended groups was highest for dogwood and forsythia with WCB, increasing dramatically and peaking at about the 40% rate (68 and 94 g plant-1 aboveground dry weight, respectively). Growth of these species was intermediate with MCB and BCB and least with RB, increasing to rates ≥ 50% in these groups. There was no significant response of dogwood to RB. Growth of weigela increased equally with WCB and MCB substrates up to about 40% (117 g plant-1), but was not influenced by varying rates of RB and BCB. With the hemp-amended MCH group, growth of all three species increased to rates ≥ 50% (62, 93, and 116 g plant-1 for dogwood, forsythia and weigela, respectively). Growth of the three species over most rates of all substrate groups was similar to, or exceeded that in 80% bark: 15% peat: 5% topsoil, a proven nursery mix. Aboveground dry weight of all three species was positively correlated with soluble salts concentrations in the substrates sampled at planting and on other sampling dates during the season. Key words: Nursery, ornamentals, waste and compost utilization

There is little scientific information on substrates for pot-in-pot shade tree production. The objective of this research was to examine various organic-waste-derived substrates for growing shade trees in pot-in-pot systems. Seedling whips of green ash (Fraxinus pennsylvanica Marsh.), Japanese birch [Betula platyphylla var. japonica (Miq.) Hara], and silver maple (Acer saccharinum L.) were grown for two seasons in 76-L containers. The containers were trickle irrigated and fertilized with controlled-release fertilizers. Treatments included a control nursery mix (50% by volume of pine bark:15% compost:35% topsoil) and nine other mixes classified into three groups: Group I (25, 50 or 75% bark mixed with 50, 25, or 0% wood chips, and 25% paper mill sludge); Group II (25, 50 or 75% bark; 50, 25 or 0% wood chips; and 25% peat); and Group III (25, 50 or 75% peat; 50, 25 or 0% wood chips; and 25% paper mill sludge). In both years, trunk diameters of the three species were greatest with Group III substrates, intermediate with Group II, and least with Group I. Trunk growth was positively correlated with water retention porosity, which ranged from 42 to 57%, 38 to 42%, and 20 to 27% for Groups III, II, and I, respectively. Trunk diameters of Group II and III trees were equal to, or slightly exceeded (10–12%), those of the nursery mix. The nursery mix had a water retention porosity of 49% and generally the highest content of soluble salts. The high-peat (50 and 75%) substrates marginally but consistently produced trees with the largest trunk diameters, although with birch (not the other species) shorter trees resulted as the peat content increased. Key words: In-ground containers, nursery, ornamentals, waste utilization, container culture

Genetic information in eukaryotes is managed by strategic hierarchical organization of chromatin structure. Primary chromatin structure describes an unfolded nucleosomal array, often referred to as “beads on a string”. Chromatin is compacted by the nonlinear rearrangement of nucleosomes to form stable secondary chromatin structures. Chromatin conformational transitions between primary and secondary structures are mediated by both nucleosome-stacking interactions and the intervening linker DNA. Chromatin model system studies find that the topography of secondary structures is sensitive to the spacing of nucleosomes within an array. Understanding the relationship between nucleosome spacing and higher order chromatin structure will likely yield important insights into the dynamic nature of secondary chromatin structure as it occurs in vivo. Genome-wide nucleosome mapping studies find the distance between nucleosomes varies, and regions of uniformly spaced nucleosomes are often interrupted by regions of nonuniform spacing. This type of organization is found at a subset of actively transcribed genes in which a nucleosome-depleted region near the transcription start site is directly adjacent to uniformly spaced nucleosomes in the coding region. Here, we evaluate secondary chromatin structure and discuss the structural and functional implications of variable nucleosome distributions in different organisms and at gene regulatory junctions.

Williams syndrome transcription factor (WSTF) has emerged as an incredibly versatile nuclear protein. WSTF and the ATP-dependent chromatin remodeling complexes in which it exists, WINAC, WICH, and B-WICH, have been studied in a variety of organisms. This research has revealed roles for WSTF in a number of diverse molecular events. WSTF function includes chromatin assembly, RNA polymerase I and III gene regulation, vitamin D metabolism, and DNA repair. In addition to functioning as a subunit of several ATP-dependent chromatin remodeling complexes, WSTF binds specifically to acetylated histones and is itself a histone kinase as well as a target of phosphorylation. This review will describe the three known WSTF-containing complexes and discuss their various roles as well as mechanisms of regulating WSTF activity.

Linker histones are multifunctional proteins that are involved in a myriad of processes ranging from stabilizing the folding and condensation of chromatin to playing a direct role in regulating gene expression. However, how this class of enigmatic proteins binds in chromatin and accomplishes these functions remains unclear. Here we review data regarding the H1 structure and function in chromatin, with special emphasis on the C-terminal domain (CTD), which typically encompasses approximately half of the mass of the linker histone and includes a large excess of positively charged residues. Owing to its amino acid composition, the CTD was previously proposed to function in chromatin as an unstructured polycation. However, structural studies have shown that the CTD adopts detectable secondary structure when interacting with DNA and macromolecular crowding agents. We describe classic and recent experiments defining the function of this domain in chromatin folding and emerging data indicating that the function of this protein may be linked to intrinsic disorder.

Exploring and exploiting variety by environment (V × E) interaction is one of the major challenges facing plant breeders. In paper I of this series, we presented an approach to modelling V × E interaction in the analysis of complex multi-environment trials using factor analytic models. In this paper, we develop a range of statistical tools which explore V × E interaction in this context. These tools include graphical displays such as heat-maps of genetic correlation matrices as well as so-called E-scaled uniplots that are a more informative alternative to the classical biplot for large plant breeding multi-environment trials. We also present a new approach to prediction for multi-environment trials that include pedigree information. This approach allows meaningful selection indices to be formed either for potential new varieties or potential parents.

Molecular chaperones of the Hsp70 family have diverse functions in cells. They assist the folding of newly synthesized and stress-denatured proteins, as well as the import of proteins into organelles, and the dissociation of aggregated proteins. The well-conserved Hsp70 chaperones are ATP dependent: binding and hydrolysis of ATP regulates their interactions with unfolded polypeptide substrates, and ATPase cycling is necessary for their function. All cellular functions of Hsp70 chaperones use the same mechanism of ATP-driven polypeptide binding and release. The Hsp40 co-chaperones stimulate ATP hydrolysis by Hsp70 and the type 1 Hsp40 proteins are conserved from Escherichia coli to humans. Various nucleotide exchange factors also promote the Hsp70 ATPase cycle. Recent advances have added to our understanding of the Hsp70 mechanism at a molecular level.

More than 30 years of research on nuclear RNA polymerases (RNAP I, II, and III) has uncovered numerous factors that regulate the activity of these enzymes during the transcription reaction. However, very little is known about the machinery that regulates the fate of RNAPs before or after transcription. In particular, the mechanisms of biogenesis of the 3 nuclear RNAPs, which comprise both common and specific subunits, remains mostly uncharacterized and the proteins involved are yet to be discovered. Using protein affinity purification coupled to mass spectrometry (AP–MS), we recently unraveled a high-density interaction network formed by nuclear RNAP subunits from the soluble fraction of human cell extracts. Validation of the dataset using a machine learning approach trained to minimize the rate of false positives and false negatives yielded a high-confidence dataset and uncovered novel interactors that regulate the RNAP II transcription machinery, including a set of proteins we named the RNAP II-associated proteins (RPAPs). One of the RPAPs, RPAP3, is part of an 11-subunit complex we termed the RPAP3/R2TP/prefoldin-like complex. Here, we review the literature on the subunits of this complex, which points to a role in nuclear RNAP biogenesis.

The classic 18.5 kDa isoform of myelin basic protein (MBP) is central to maintaining the structural homeostasis of the myelin sheath of the central nervous system. It is an intrinsically disordered, promiscuous, multifunctional, peripheral membrane protein, whose conformation adapts to its particular environment. Its study requires the selective and complementary application of diverse approaches, of which solution and solid-state NMR spectroscopy are the most powerful to elucidate site-specific features. We review here several recent solution and solid-state NMR spectroscopic studies of 18.5 kDa MBP, and the induced partial disorder-to-order transitions that it has been demonstrated to undergo when complexed with calmodulin, actin, and phospholipid membranes.

The Rvb1 and Rvb2 proteins are 2 members of the AAA+ family, involved in roles as diverse as chromatin remodeling, transcription, small nucleolar RNA maturation, cellular transformation, signaling of apoptosis and mitosis. These proteins are capable of playing a role in such diverse cellular activities because they are components of different macromolecular assemblies. In the last few years, there has been a number of groups reporting on the structure of purified Rvbs. The reported results have been rather controversial, because there are significant differences observed among the published structures in spite of the high degree of homology among these proteins. Surprisingly, contradictions are observed not only between structures representing the Rvb proteins from different species, but also between protein structures from the same species. This review describes the available Rvb structures from different species and also makes a comparative analysis of them. Finally, we identify some aspects of these structural studies worth pursuing in additional investigations to ensure that the reported structures reflect physiologically relevant conformations of the Rvb1–Rvb2 complex.

Dyneins are microtubule motors, the core of which consists of a ring of AAA+ domains. ATP-driven conformational changes of the AAA+ ring are used to drive the movement of a mechanical element (termed the linker domain) that provides the motor’s powerstroke and to change the affinity of the motor for microtubules (strong binding during the power stroke and weak binding to allow stepping and recocking of the linker domain). Dynein’s microtubule-binding domain (MTBD) is located at the end of a 10 nm long anti-parallel coiled coil (the stalk) and conformational changes that alter the affinity for microtubules must propagate through this coiled coil. A recent crystal structure of dynein’s MTBD sheds new light on how this long-range communication along a coiled coil might occur.

Hsp104, a hexameric AAA+ ATPase found in yeast, transduces energy from cycles of ATP binding and hydrolysis to resolve disordered protein aggregates and cross-β amyloid conformers. These disaggregation activities are often co-ordinated by the Hsp70 chaperone system and confer considerable selective advantages. First, renaturation of aggregated conformers by Hsp104 is critical for yeast survival after various environmental stresses. Second, amyloid remodeling by Hsp104 enables yeast to exploit multifarious prions as a reservoir of beneficial and heritable phenotypic variation. Curiously, although highly conserved in plants, fungi and bacteria, Hsp104 orthologues are absent from metazoa. Indeed, metazoan proteostasis seems devoid of a system that couples protein disaggregation to renaturation. Here, we review recent endeavors to enhance metazoan proteostasis by applying Hsp104 to the specific protein-misfolding events that underpin two deadly neurodegenerative amyloidoses. Hsp104 potently inhibits Aβ42 amyloidogenesis, which is connected with Alzheimer’s disease, but appears unable to disaggregate preformed Aβ42 fibers. By contrast, Hsp104 inhibits and reverses the formation of α-synuclein oligomers and fibers, which are connected to Parkinson’s disease. Importantly, Hsp104 antagonizes the degeneration of dopaminergic neurons induced by α-synuclein misfolding in the rat substantia nigra. These studies raise hopes for developing Hsp104 as a therapeutic agent.

Telomeres, the natural ends of linear chromosomes, must be protected and completely replicated to guarantee genomic stability in eukaryotic cells. However, the protected state of telomeres is not compatible with recruitment of telomerase, an enzyme responsible for extending telomeric G-rich repeats during S-phase; thus, telomeres must undergo switches from a protected state to an accessible state during the cell cycle. In this minireview, we will summarize recent advances in our understanding of proteins involved in the protection and replication of telomeres, and the way these factors are dynamically recruited to telomeres during the cell cycle. We will focus mainly on recent results from fission yeast Schizosaccharomyces pombe , and compare them with results from budding yeast Saccharomyces cerevisiae and mammalian cell studies. In addition, a model for the way in which fission yeast cells replicate telomeres will be presented.

The yellow seed characteristic in Brassica napus L. is desirable because of its association with higher oil content and better quality of oil-extracted meal. YN01-429 is a yellow-seeded canola-quality germplasm developed in Canada arising from several years of research. Seed-coat pigmentation is due to oxidized proanthocyanidins (PA; condensed tannins) derived from phenylpropanoids and malonyl CoA. We found PA accumulation to be most robust in young seed coats (20 d post anthesis; dpa) of a related black-seeded line N89-53 and only very little PA in YN01-429, which also contained much less extractable phenolics. The flavonol content, however, did not show as great a difference between these two lines. Furthermore, sinapine, a product of the general phenylpropanoid metabolism, was present at comparable levels in the embryos of both lines. Dihydroflavonol reductase (DFR) activity that commits phenolics to PA synthesis was lower in YN01-429 seed coats. The results of Southern blot and in silico analyses were indicative of two copies of the DFR gene in B. napus. Both copies were functional in YN01-429, ruling out homeoallelic repression or silencing, but together they showed very low expression levels (17-fold fewer transcripts) relative to DFR activity in N89-53 seed coats. These results collectively suggest that YN01-429 differs in regulatory circuits that impact the PA synthesis branch much more than the flavonol synthesis branch in the seed coats and such circuits do not impinge upon general phenylpropanoid metabolism in the embryos.

Understanding the quantitative and qualitative changes in skeletal muscle that control changes in function is crucial in the development of countermeasures to the loss of skeletal muscle function observed with real and simulated microgravity exposure (i.e., unloading) and with aging in humans. Qualitative changes that could influence the force and power producing properties of skeletal muscle are changes in the distribution of the 3 isoforms of the main motor protein myosin heavy chain (MHC), as well as the abundance of MHC, actin (the other main contractile protein), and the force distributing the connective tissue network. Numerous studies have examined quantitative and qualitative changes in skeletal muscle, from the whole muscle to the single myofiber from individuals undergoing real and simulated space flight for a few weeks to several months, as well as from aging men and women. When considering the relative content of the main functional and structural elements (i.e., myosin, actin, collagen), it appears that human muscle appropriately scales changes in size of 10%–40% induced over a relatively short time period (1–3 months) and over the lifespan (in humans 20 to 90+ years old). The main qualitative change with unloading and aging is a redistribution of the 3 MHC isoforms, which have vastly different contractile characteristics. It is now known that the response of skeletal muscle to unloading is muscle and gender specific. In summary, changes in muscle mass (quantity) combined with the alterations in MHC distribution (quality) are the primary determinants of changes in muscle function with unloading and aging. These parameters are the key components of muscle that should be targeted with countermeasures for conditions related to muscle loss, along with considerations for muscle- and gender-specific responses.

Endurance exercise promotes skeletal muscle adaptation, and exercise-induced peroxisome proliferator-activated receptor γ coactivator-1α (Pgc-1α) gene expression may play a pivotal role in the adaptive processes. Recent applications of mouse genetic models and in vivo imaging in exercise studies have started to delineate the signaling-transcription pathways that are involved in the regulation of the Pgc-1α gene. These studies revealed the importance of p38 mitogen-activated protein kinase/activating transcription factor 2 and protein kinase D/histone deacetylase 5 signaling transcription axes in exercise-induced Pgc-1α transcription and metabolic adaptation in skeletal muscle. The signaling-transcription network that is responsible for exercise-induced skeletal muscle adaption remains to be fully elucidated.

Energy metabolism is at the crossroad of cell function and dysfunction. Cardiac and skeletal muscle cells, the energy metabolism of which is high, fluctuating, and adaptable to the special needs of the body, have developed sophisticated strategies for synthesizing, transferring, and utilizing energy in accordance with the needs of the body. Adaptation to endurance training mainly involves energetic remodelling in skeletal muscles, but less is known for the cardiac muscle. Alterations in energy metabolism participate in many pathophysiological processes, among which is heart failure. Because endurance training improves symptoms and quality of life and decreases mortality rate and hospitalization, it is increasingly recognized as a beneficial practice for heart failure patients. The mechanisms involved in the beneficial effects of exercise training are far from being understood. Proper evaluation of these mechanisms is thus a major health issue for populations living in industrialized countries. This review mainly focuses on oxidative metabolism and intracellular energy transfer in muscles and the heart, their alterations in heart failure, and the effects of endurance exercise training.

The tribe Triticeae Dumortier in the grass family (Poaceae) includes the most important cereal crops (e.g., wheat, barley, and rye) and some economically important forage grasses. Elymus L. is the largest and most complex genus in the Triticeae tribe with approximately 150 species occurring worldwide. The genomic constitutions of ~40% of Elymus species are unknown and some have unverified genomic combinations. Of those known for genome constitutions, Elymus species have a genomic formula of StH, StP, StY, StStY, StHY, StPY, or StWY. However, the origin of the Y genome is unknown because no diploid species have been identified as the Y genome donor. A putative Y genome specific random amplified polymorphic DNA (RAPD) marker was converted to a sequence tagged site (STS) marker. The reliability of this STS marker for confirming the presence of the Y genome was demonstrated using 42 accessions of Elymus. The STS-PCR for the Y genome marker was then assayed on 43 accessions of diploid Pseudoroegneria (Nevski) A. Löve species having the St genome to identify possible donors of the Y genome. A rare accession of Pseudoroegneria spicata (Pursh) A. Löve was found to possess sequences that most closely related to those from the tetraploid Elymus longearistatus (Boiss.) Tzvelev (StStYY), making P. spicata the most likely donor of the Y genome, although Pseudoroegneria libanotica (Heck.) D.R. Dewey or other Pseudoroegneria species could not be excluded. Our findings support the hypothesis that the Y genome in some Elymus species shares a progenitor genome (designated StY) with the St genome of Pseudoroegneria.

Mutations in methyl DNA binding protein 2 (MeCP2) cause the neurodevelopmental disorder Rett syndrome (RTT). The mechanism(s) by which the native MeCP2 protein operates in the cell are not well understood. Historically, MeCP2 has been characterized as a proximal gene silencer with 2 functional domains: a methyl DNA binding domain and a transcription repression domain. However, several lines of new data indicate that MeCP2 structure and function relationships are more complex. In this review, we first discuss recent studies that have advanced understanding of the basic structural biochemistry of MeCP2. This is followed by an analysis of cell-based experiments suggesting MeCP2 is a regulator, rather than a strict silencer, of transcription. The new data establish MeCP2 as a multifunctional nuclear protein, with potentially important roles in chromatin architecture, regulation of RNA splicing, and active transcription. We conclude by discussing clinical correlations between domain-specific mutations and RTT pathology to stress that all structural domains of MeCP2 are required to properly mediate cellular function of the intact protein.

The dynamic interaction between nuclear proteins and chromatin leads to the functional plasticity necessary to mount adequate responses to regulatory signals. Here, we review the factors regulating the chromatin interactions of the high mobility group proteins (HMGs), an abundant and ubiquitous superfamily of chromatin-binding proteins in living cells. HMGs are highly mobile and interact with the chromatin fiber in a highly dynamic fashion, as part of a protein network. The major factors that affect the binding of HMGs to chromatin are operative at the level of the single nucleosome. These factors include structural features of the HMGs, competition with other chromatin-binding proteins for nucleosome binding sites, complex formation with protein partners, and post-translational modifications in the protein or in the chromatin-binding sites. The versatile modulation of the interaction between HMG proteins and chromatin plays a role in processes that establish the cellular phenotype.

The fourth chromosome of Drosophila melanogaster has a number of unique properties that make it a convenient model for the study of chromatin structure. Only 4.2 Mb overall, the 1.2 Mb distal arm of chromosome 4 seen in polytene chromosomes combines characteristics of heterochromatin and euchromatin. This domain has a repeat density of ~35%, comparable to some pericentric chromosome regions, while maintaining a gene density similar to that of the other euchromatic chromosome arms. Studies of position-effect variegation have revealed that heterochromatic and euchromatic domains are interspersed on chromosome 4, and both cytological and biochemical studies have demonstrated that chromosome 4 is associated with heterochromatic marks, such as heterochromatin protein 1 and histone 3 lysine 9 methylation. Chromosome 4 is also marked by POF (painting-of-fourth), a chromosome 4-specific chromosomal protein, and utilizes a dedicated histone methyltransferase, EGG. Studies of chromosome 4 have helped to shape our understanding of heterochromatin domains and their establishment and maintenance. In this review, we provide a synthesis of the work to date and an outlook to the future.

Epigenetic control is required to maintain competency for the activation and suppression of genes during cell division. The association between regulatory proteins and target gene loci during mitosis is a parameter of the epigenetic control that sustains the transcriptional regulatory machinery that perpetuates gene-expression signatures in progeny cells. The mitotic retention of phenotypic regulatory factors with cell cycle, cell fate, and tissue-specific genes supports the coordinated control that governs the proliferation and differentiation of cell fate and lineage commitment.

Defining human protein interaction networks has become essential to develop an overall, systems-based understanding of the molecular events that sustain cell growth in normal and disease conditions. To characterize protein interaction networks from human cells, we have undertaken the development of a systematic, unbiased technology pipeline that couples experimental and computational approaches. This discovery engine is central to the Human Proteotheque Initiative (HuPI), a multidisciplinary project aimed at building a repertoire of comprehensive maps of human protein interaction networks, the Human Proteotheque. The information contained in the Proteotheque is made publicly available through an interactive web site that can be consulted to visualize some of the fundamental molecular connections formed in human cells and to determine putative functions of previously uncharacterized proteins based on guilt by association. The process governing the evolution of HuPI towards becoming a repository of accurate and complete protein interaction maps is described.

Mineral and petroleum exploration in the Cariboo-Chilcotin region of British Columbia is hampered by widespread and extensive cover of Pleistocene glacial deposits and Tertiary volcanic successions. Seeing through this geological cover is critical to reducing exploration risk and enhancing exploration activity. Also critical to exploration is effective community engagement, hopefully resulting in endorsement and support for exploration initiatives. The forests in the Cariboo-Chilcotin region have been extensively destroyed by an infestation of the mountain pine beetle, Dendroctonus ponderosae , disrupting established communities and greatly affecting economic activity in the region. Governments of all levels recognized that geological exploration activity could provide a ready and appreciable stimulus to economic activity, but only if local communities endorsed such programs. Relatively little oil and gas exploration and research has taken place in the region, and its effects have been poorly understood locally. Consequently, an extended effort was undertaken to establish an integrated geoscience program for the Cariboo-Chilcotin region, focused on mineral and petroleum exploration-related research and coupled with engagement with local communities to inform them of exploration benefits and risks. This Introduction to the “Mountain Pine Beetle” Special Issue of Canadian Journal of Earth Sciences provides a brief overview of the scientific papers included in the issue and also a review of the community engagement process that was undertaken to establish working relationships with First Nations and other communities in the region.

The south-central Intermontane belt of British Columbia has a complex architecture comprising late Paleozoic to Mesozoic volcanic and plutonic arc magmatic suites, marine and nonmarine clastic basins, high-grade metamorphic complexes, and accretionary rocks. Jurassic and Cretaceous clastic basins within this framework contain stratigraphy with hydrocarbon potential. The geology is complicated by Cretaceous to Eocene deformation, dismemberment, and dislocation. The Eocene to Neogene history of the southern Intermontane belt is dominated by non-arc volcanism, followed by Pleistocene to Recent glaciation. The volcanic and glacial cover makes this a difficult region to explore for resources. Much recent work has involved re-evaluating the challenges that the overlying volcanic cover has historically presented to geophysical imaging of the sedimentary rocks in this region in light of technological advances in geophysical data collection and analysis. This paper summarizes the lithological and stratigraphic framework of the region, with emphasis on description of the sedimentary units that have been the targets of hydrocarbon exploration.

In the Archean Blake River Group, mafic to intermediate fragmental units have controversially been proposed to have formed during the collapse of a giant submarine caldera. This paper describes and interprets these rocks, summarizing their physical characteristics, inferred origins, age relationships, and geochemical signatures. The widespread Stadacona member, south of Rouyn-Noranda, consists of several hundred metres of bedded volcaniclastic rocks interpreted to have been mostly deposited from aqueous density currents fed directly by explosive eruptions. The magmas involved in these eruptions were plagioclase-phyric, tholeiitic to transitional basalts. The similarly widespread D’Alembert tuff, in the northern part of the Blake River Group, shares many physical characteristics with the Stadacona member and is thought to have a similar origin. However, the D’Alembert tuff is approximately six million years younger than the Stadacona member. It is composed mostly of transitional to calc-alkaline andesites and basaltic andesites with very distinct trace element profiles. Volcaniclastic rocks from other areas, such as Tannahill Township in Ontario and the Monsabrais area in Quebec, are interpreted to represent mostly in situ to remobilized hyaloclastite, with no explosive eruptions involved in their genesis. Our observations and interpretations are not compatible with models in which the volcaniclastic units are emplaced during a catastrophic event in relation with the collapse of a giant caldera. Instead, the fragmental rocks were produced by various mechanisms at many distinct times during the evolution of the Blake River Group.

A field experiment was designed to assess the effects on tree nutrition of surface application of municipal biosolids and shredded paper mulch, which have previously been reported to improve the performance of high-density apples despite wide differences in nutrient content. The experiment involved four treatments which included two levels (with or without) of two organic amendments, shredded paper mulch and Greater Vancouver Regional District (GVRD) municipal biosolids. Treatments were established over a 2 m wide strip centred on the tree row in a high-density (3700 trees ha-1) Golden Delicious (Malus × domestica Borkh.) orchard in the year of planting (1997) and maintained until 2004. GVRD-biosolids was applied at 40 t ha-1 (DW) in 1997 and 20.3 t ha-1 (DW) in 2001 potentially supplying larger amounts of all plant nutrients (N, P, K, Mg, Zn, Cu and Mn) except Ca than the paper mulch. All trees received standard commercial treatments of drip fertigation of 30 g N tree-1 yr-1 and 20 g P tree-1 in the establishment year. Leaf N concentration was unaffected by biosolids application and decreased, but not to inadequate concentrations, in 3 of 6 yr for trees grown in the high C:N ratio shredded paper mulch. This response indicates the effectiveness of drip fertigated N. Leaf K declined to inadequate concentrations by the end of the experiment, regardless of treatment, but trees in the paper mulch treatment were able to sustain higher leaf K, were more vigourous, had higher yield the first three fruiting seasons and cumulatively after 8 yr despite the low N and K content of the paper. Improved K uptake was attributed to better distribution of soil moisture beneath the mulch but for long-term sustainable production, K fertigation would have been desirable. Biosolids application often raised leaf Zn, Cu and Mn concentration but increases were modest, with concentrations of Zn insufficient to change standard commercial recommendations for annual dormant Zn applications. Key words: Leaf N, K, Zn, Cu and Mn, nutrient additions, organic amendments, vigour, yield

Intentional contamination of drinking water with anthrax spores is a concern to water utilities. The spores may become embedded in the distribution pipe corrosion and biofilm, where they will be protected from residual disinfectants. This paper compares the disinfection effectiveness of chlorine and chlorine dioxide on Bacillus globigii , a surrogate for B. anthracis . Batch experiments were performed using both disinfectants. Data was analyzed using the delayed Chick-Watson model to determine the corresponding CTlag (CT = concentration × time) values and Watson plots, which indicate the dominant factors affecting disinfection kinetics. Chlorine dioxide had CTlag values almost one tenth of those observed for chlorine. However, Watson plots showed that exposure time and disinfectant concentrations have equal weights on the inactivation rate of both disinfectants.

The kinetics of the spontaneous, proton- and AlIII-catalysed hydrolyses of the C1—O4′ bond in 1,5-anhydrocellobiitol have been measured at elevated temperatures (125.0–220.0 °C). Data for the first two processes extrapolate to the expression k = (8.6 ± 2.1 × 10–16) + (1.4 ± 0.2 × 10–9-pH) s–1 at 25 °C. These room-temperature figures were used to model cellulose depolymerization by the af Ekenstam equation. The spontaneous process is too slow to contribute to loss of paper strength on aging, and even the acid-catalysed process is significant only below ~pH 4.0. However, the spontaneous hydrolysis readily accounts for the reduction of cellulose degree of polymerization (DP) during alkaline (e.g., kraft) pulping of cellulose fibres. Efficient electrophilic catalysis by AlIII was observed at 150.0 °C in 0.1 mol/L succinate buffers of room temperature pH 3.05 and 3.35 (k2 = 8.1 ± 0.4 × 10–3 and 4.2 ± 0.2 × 10–3 (mol/L) –1 s–1, respectively). The apparent activation energy of the AlIII-catalysed process was 31 ± 4 kJ mol-1, lower than that of the proton-catalysed path, suggesting the electrophilic catalysis increases in importance as the temperature approaches ambient. Consequently, it appears that the culprit in the impermanence of “rosin-alum” -sized paper is AlIII, directly acting as a Lewis acid, not the AlIII hydration sphere as a Brønsted acid. Conservation measures should either address this or be generic (e.g., low-temperature storage). Key words: cellulose, hydrolysis, kraft pulping, paper conservation, rosin-alum sizing.

The Penobscot arc system of the northeastern Appalachians is an Early Cambrian to early Tremadocian (ca. 514- 485 Ma) ensialic to ensimatic arc-back-arc complex that developed along the margin of the peri-Gondwanan microcontinent Ganderia. Remnants of this Paleozoic arc system are best preserved in the Exploits Subzone of central Newfoundland. Cor- relative rocks in southern New Brunswick are thought to occur in the ca. 514 Ma Mosquito Lake Road Formation of the Ellsworth Group and ca. 497-493 Ma Annidale Group; however in the past, the work that has been conducted on the latter has been of a preliminary nature. New data bearing on the age and tectonic setting of the Annidale Group provides more conclusive evidence for this correlation. The Annidale Group contains subalkaline, tholeiitic to transitional, basalts to basal- tic andesites, picritic tuffs and calc-alkaline to tholeiitic felsic dome complexes that have geochemical signatures consistent with suprasubduction zone magmatism that was likely generated in a back-arc basin. New U-Pb ages establish that the Late Cambrian to Early Tremadocian Annidale Group and adjacent ca. 541 Ma volcanic rocks of the Belleisle Bay Group in the New River belt were affected by a period of younger magmatism ranging in age from ca. 479-467 Ma. This provides im- portant constraints on the timing of tectonism in the area. A ca. 479 Ma age for the Stewarton Gabbro that stitches the faulted contact between the Annidale and Belleisle Bay groups, demonstrates that structural interleaving and juxtaposition occurred during early Tremadocian time, which closely coincides with the timing of obduction of Penobscottian back-arc ophiolites onto the Ganderian margin in Newfoundland. Resume : Le systeme d'arc Penobscot du nord-est des Appalaches est un complexe d'arc-d'arriere-arc ensialique a ensima- tique datant du Cambrien precoce au Tremadocien precoce (~514-485 Ma) qui s'est developpe le long de la bordure peri- gondwannienne du microcontinent Ganderia. Des lambeaux de ce systeme d'arc paleozoique sont le mieux conserves dans la sous-zone Exploits du centre de Terre-Neuve. Des roches correlatives dans le sud du Nouveau-Brunswick seraient presen- tes dans la Formation de Mosquito Lake Road (~514 Ma) du Groupe d'Ellsworth et dans le Groupe d'Annidale (~497-493 Ma); toutefois, par le passe, le travail effectue sur ce dernier groupe n'a ete que preliminaire. De nouvelles donnees sur l'âge et l'environnement tectonique du Groupe d'Annidale fournissent des evidences plus concluantes de cette correlation. Le Groupe d'Annidale contient des basaltes a des andesites basaltiques, subalcalins, tholeiitiques a intermediaires, des tufs picritiques et des complexes de domes felsiques, calco-alcalins a tholeiitiques, possedant des signatures geochimiques qui concordent avec un magmatisme de zone de suprasubduction probablement generee dans un bassin d'arriere-arc. De nou- veaux âges U-Pb ont etabli que le Groupe d'Annidale, Cambrien tardif a Tremadocien precoce, et les roches volcaniques ad- jacentes du Groupe de Belleisle Bay (~541 Ma) dans la ceinture de New River ont ete affectes par une periode de magmatisme plus jeune, datant d'environ 479 a 467 Ma. Ces donnees fournissent des contraintes importantes sur le moment du tectonisme dans la region. Un âge d'environ 479 Ma pour le gabbro de Stewarton, qui reunit le contact de faille entre les groupes d'Annidale et de Belleisle Bay, demontre que l'imbrication et la juxtaposition structurales ont eu lieu au debut du Tremadocien, ce qui coincide de pres avec le moment de l'obduction des ophiolites d'arriere-arc de Penobscot par-dessus la bordure de Ganderia a Terre-Neuve. (Traduit par la Redaction)

This study demonstrates how ice-flow history, geochronology, geology, and geophysics may be integrated to enhance the effectiveness of boulder tracing in glaciated regions affected by multiple ice-flow events. Mineralized felsic granitoid boulders (erratics) were discovered 18 years ago on a claim block located 10 km northwest of Little Fort, in the Bonaparte Lake map area (NTS 092P), in south-central British Columbia. Although the boulders have yielded significant gold concentrations (up to 4.15 g/t), their bedrock source is not known. The till near the boulders contains up to 1382 gold grains per 15 kg of bulk material with 75% of the grains having pristine morphology, suggesting a short distance of glacial transport. A U–Pb zircon crystallization age of 198.1 ± 0.5 Ma on one mineralized boulder indicates derivation from an Early Jurassic intrusion. Using a vector addition model based on regional ice-flow patterns, the most recent and detailed bedrock geology map, and recently acquired airborne radiometrics and magnetic data, the northeast sector of the Thuya Batholith (195–205 Ma) is interpreted as the most likely bedrock source of the mineralized boulders.

The structure and stratigraphy of the southeast Nechako Basin, which are poorly understood primarily because of substantial volcanic cover, are investigated in an analysis of seismic reflection, well, and potential field data. Formation and development of the SE Nechako Basin resulted in sub-basins containing Cretaceous and Eocene rocks. Interpretation reveals that dextral transtension in the Early to Middle Eocene created NNW-trending, en echelon, strike-slip faults linked by pull-apart basins, which locally contain a thickness of Eocene volcaniclastic rocks of >3 km. This structural pattern is consistent with regional observations that suggest the transfer of slip from the Yalakom fault to the north via a series of en echelon strike-slip faults. In the Middle to Late Eocene, faults associated with a change in the direction of stress, echoed by the north-trending right-lateral Fraser fault, reactivated and cut earlier structures. A simple model agrees with local observations, that northeast-directed compression was subparallel to the relic Cretaceous grain. Cretaceous rocks are discontinuous throughout the basin and may be remnants of a broader basin, or a number of contemporaneous basins, formed in a regional transpressional tectonic setting that caused northeast-directed thrusting along the eastern side of the Coast Plutonic Complex. Results suggest that thrusting affected most of the SE Nechako Basin, as observed across the Intermontane Belt to the northwest and southeast. The pattern of deposition of Neogene volcanic rocks of the Chilcotin Group was in part controlled by the Eocene structural grain, but we find no evidence of Neogene deformation.

Lower to Middle Jurassic clastic sequences are widespread within the interior of the Canadian Cordillera. These successions cap waning Jurassic volcanism in many Cordilleran arc terranes and are succeeded by clastic sequences of the Intermontane basins. Fine-grained, carbonaceous lithologies, which locally contain elevated levels of organic carbon, characterize these clastic successions. These include sections of the Spatsizi Formation (Abou Member) and Smithers Formation in northern and western Bowser basin, respectively, Ashcroft Formation and equivalent strata in central Quesnellia, and Last Creek Formation and Junction Creek rocks below the Tyaughton–Methow basin. These rocks locally contain metre-thick sections with total organic carbon (TOC) levels >5 wt.% and others have thicknesses approaching 100 m with TOC between 3 and 5 wt.%. Thermal maturation levels are high in many sections, suggesting original organic contents were greater and that these rocks may have been excellent source beds. Associated bitumen in these successions, together with Mesozoic oil in some overlying Intermontane clastic rocks, also suggests these sequences may have been effective oil source rocks. TOC levels, thermal maturity, and thickness of some sections are comparable with shale gas sequences being exploited elsewhere in North America. TOC concentrations within these rocks, together with other elemental abundances, indicate anoxic conditions during deposition. The age of these clastic rocks brackets the global Toarcian anoxic event and that of other organic-rich sequences in North America. Elemental abundances suggest predominantly volcanic-arc complexes as source terranes, although continental signatures are suggested by rocks in western Quesnellia.

The ability of airborne sensors to image the magnetic signatures of prospective Quesnel terrane rocks through ubiquitous Quaternary glacial sedimentary cover in central British Columbia helps target new areas for mineral exploration. Newly acquired high-resolution data provide new perspectives on the nature and probable areal distribution of many geological units, revealing detail and information unattainable by conventional geological mapping. In combination with gravity data, these magnetic data indicate the presence of a granitic intrusion and a development of Nicola Group volcanic rocks, both potential hosts for porphyry- and (or) vein-type mineralization, under younger Tertiary volcanic cover. At a finer scale, magnetic patterns and fabrics permit discrimination between volcanic rocks of the Tertiary Chilcotin and Kamloops groups, and detection of subtle compositional and (or) structural variations within the groups. Contacts between volcanic cover and basement rocks and between basement units are more accurately defined, significantly reducing locally the areal extent of volcanic cover and opening up more ground for exploration. The high resolution of features in images of magnetic vertical derivatives reveals the Naver pluton to be more complex than currently mapped, comprising several integral elements, one of which may be a large roof pendant. Internal subdivisions of the Thuya batholith are defined, and annular marginal phases are proposed within two large granodioritic intrusions. Several new intrusions are proposed within the extensive, mainly sedimentary Devonian–Triassic terrain northeast of Kamloops, internal composition variation is suggested for some larger mapped intrusions, and areas underlain by some intrusions are enlarged.

In the BATHOLITHSonland seismic project, a refraction – wide-angle reflection survey was shot in 2009 across the Coast Mountains and Interior Plateau of central British Columbia. Part of the seismic profile crossed the Nechako Basin, a Jurassic–Cretaceous basin with potential for hydrocarbons within sedimentary strata that underlies widespread volcanic rocks. Along this 205 km-long line segment, eight large explosive shots were fired into 980 seismometers. Forward and inverse modelling of the traveltime data were conducted with two independent methods: ray-tracing based modelling of first and secondary arrivals, and a higher resolution wavefront-based first-arrival seismic tomography. Material with velocities less than 5.0 km/s is interpreted as sedimentary rocks of the Nechako Basin, while velocities from 5.0–6.0 km/s may correspond to interlayered sedimentary and volcanic rocks. The greatest thickness of sedimentary rocks in the basin is found in the central 110 km of the profile. Two sub-basins were identified in this region, with widths of 20–50 km and maximum sedimentary depths of 2.5 and 3.3 km. Such features are well-defined in the velocity model, since resolution tests indicate that features with widths greater than ∼13 km are reliable. Beneath the sedimentary rocks, seismic velocities increase more slowly with depth — from 6.0 km/s just below the basin to 6.3 km/s at ∼17 km in depth, and then to 6.8–7.0 km/s at the base of the crust. The Moho is found at a depth of 33.5–35 km beneath the profile, and mantle velocities are high at 8.05–8.10 km/s.

The Nechako Basin in British Columbia, Canada is suspected to have hydrocarbon potential. However, it has been a difficult basin to explore because of the presence of Tertiary volcanic outcrop. The volcanic outcrop makes the use of conventional seismic exploration methods difficult owing to a strong velocity inversion at its base. An alternative is the passive source method known as ambient noise surface wave tomography. The method, which examines the high-frequency surface wave field that is obtained from noise analysis, is sensitive to large-scale crustal structure and has been successfully applied to measuring the depths of sedimentary basins. Station-to-station Green’s functions within the basin were estimated by cross-correlating the vertical components of the seismic noise data recorded by 12 POLARIS (Portable Observatories for Lithosphere Analysis and Research Investigating Seismicity) and CNSN (Canadian National Seismgraph Network) seismic stations between September 2006 and November 2007. The resulting Green’s functions were dominated by Rayleigh waves. The dispersion characteristics of the Rayleigh waveforms were measured within the microseismic band. Inversion of the dispersion curves produced 1-D and 2-D thickness models and 2-D group velocity models for the Nechako Basin and its surrounding region. The velocity models indicate two low group velocity structures within the basin that might represent sedimentary packages, and some pockets of high-velocity zones that show the presence of volcanic rocks within and on the basin. The thickness models indicated the presence of about six different velocity layers, in which the average thickness of the basin and the crust are ∼4.8 and 30–34 km, respectively.

The Lower Cretaceous Jackass Mountain Group of southwestern British Columbia records a complex history of deltaic and proximal marine sedimentation in a tectonically active area of the Canadian Cordillera. Two Jackass Mountain Group successions, exposed in the Camelsfoot Range and Chilko Lake regions and separated by ∼125 km across the northwest–southeast-trending Yalakom fault, provide details of stratigraphy, sedimentology, petrography, and geochemistry of the group. Restoring dextral movement across the Yalakom fault indicates that these locales were adjacent to one another during deposition; data presented herein support this reconstruction. In addition, detailed sedimentological investigations reveal widespread shallow-marine and deltaic features, indicating that deposition occurred predominantly within a large, shallow-water deltaic system. This interpretation is crucial to the understanding of regional facies patterns and for predicting hydrocarbon potential in adjacent subsurface rocks. New porosity, permeability, and thermal maturity data augment information collected from Jackass Mountain Group strata in the subsurface and indicate that some units represent potential hydrocarbon source rocks.

Two-dimensional (2-D) models of audio and broadband magnetotelluric (MT) data collected throughout the southern Nechako basin in south–central British Columbia, Canada, provide electrical resistivity images of the Cretaceous to Oligocene volcanic and sedimentary packages and underlying crustal-scale features. Analysis of distortion effects and structural dimensionality indicate that the MT responses are primarily one-dimensional (1-D) at periods less than 0.1 s. Departures from a 1-D response occur with maximum phase differences occurring between 0.1 and 10 s. The upper crustal resistivity models reveal a low resistivity layer at near surface depths, interpreted as Chilcotin basalts, that blankets portions of the region to depths less than 50 m, but locally thicken up to 200 m. Cretaceous sedimentary units (those showing the highest potential for hydrocarbons) are characterized by moderately low resistivities that are laterally variable. More uniform, lower resistivities appear to be associated with the Eocene volcaniclastic groups, suggesting that the MT method can distinguish between these units and may be useful in targeting areas that are more prospective for hydrocarbon exploration. In general midcrustal resistivity values are high, consistent with values of typical volcanic terranes; however, a low-resistivity zone is identified at 8–10 km depth that correlates closely with the location of seismic reflectors as well as recent microseismic activity. This low-resistivity zone is interpreted as a midcrustal reservoir of magma, the top of which marks the upper limit of fluids migrating from lower crust depths. Additionally, several crustal-scale faults are imaged.

The architecture of the Brassica napus genome is marked by its evolutionary origins. The genome of B. napus was formed from the hybridization of two closely related diploid Brassica species, both of which evolved from an hexaploid ancestor. The extensive whole genome duplication events in its near and distant past result in the allotetraploid genome of B. napus maintaining multiple copies of most genes, which predicts a highly complex and redundant transcriptome that can confound any expression analyses. A stringent assembly of 142 399 B. napus expressed sequence tags allowed the development of a well-differentiated set of reference transcripts, which were used as a foundation to assess the efficacy of available tools for identifying and distinguishing transcripts in B. napus ; including microarray hybridization and 3′ anchored sequence tag capture. Microarray platforms cannot distinguish transcripts derived from the two progenitors or close homologues, although observed differential expression appeared to be biased towards unique transcripts. The use of 3′ capture enhanced the ability to unambiguously identify homologues within the B. napus transcriptome but was limited by tag length. The ability to comprehensively catalogue gene expression in polyploid species could be transformed by the application of cost-efficient next generation sequencing technologies that will capture millions of long sequence tags.

Few association mapping studies have simultaneously accounted for population structure, genotype by environment interaction (GEI), and spatial variation. In this sugarcane association mapping study we tested models accounting for these factors and identified the impact that each model component had on the list of markers declared as being significantly associated with traits. About 480 genotypes were evaluated for cane yield and sugar content at three sites and scored with DArT markers. A mixed model was applied in analysis of the data to simultaneously account for the impacts of population structure, GEI, and spatial variation within a trial. Two forms of the DArT marker data were used in the analysis: the standard discrete data (0, 1) and a continuous DArT score, which is related to the marker dosage. A large number of markers were significantly associated with cane yield and sugar content. However, failure to account for population structure, GEI, and (or) spatial variation produced both type I and type II errors, which on the one hand substantially inflated the number of significant markers identified (especially true for failing to account for GEI) and on the other hand resulted in failure to detect markers that could be associated with cane yield or sugar content (especially when failing to account for population structure). We concluded that association mapping based on trials from one site or analysis that failed to account for GEI would produce many trial-specific associated markers that would have low value in breeding programs.

A Brassica rapa collection of 239 accessions, based on two core collections representing different morphotypes from different geographical origins, is presented and its use for association mapping is illustrated for flowering time. We analyzed phenotypic variation of leaf and seed pod traits, plant architecture, and flowering time using data collected from three field experiments and evaluated the genetic diversity with a set of SSR markers. The Wageningen University and Research Centre (WUR) and the Vavilov Research Institute of Plant Industry (VIR) core collections had similar representations of most morphotypes, as illustrated by the phenotypic and genetic variation within these groups. The analysis of population structure revealed five subgroups in the collection, whereas previous studies of the WUR core collection indicated four subgroups; the fifth group identified consisted mainly of oil accessions from the VIR core collection, winter oils from Pakistan, and a number of other types. A very small group of summer oils is described, that is not related to other oil accessions. A candidate gene approach was chosen for association mapping of flowering time with a BrFLC1 biallelic CAPS marker and a BrFLC2 multiallelic SSR marker. The two markers were significantly associated with flowering time, but their effects were confined to certain morphotypes and (or) alleles. Based on these results, we discuss the optimal design for an association mapping population and the need to fix the heterogeneous accessions to facilitate phenotyping and genotyping.

Results from genome-wide association studies in livestock, and humans, has lead to the conclusion that the effect of individual quantitative trait loci (QTL) on complex traits, such as yield, are likely to be small; therefore, a large number of QTL are necessary to explain genetic variation in these traits. Given this genetic architecture, gains from marker-assisted selection (MAS) programs using only a small number of DNA markers to trace a limited number of QTL is likely to be small. This has lead to the development of alternative technology for using the available dense single nucleotide polymorphism (SNP) information, called genomic selection. Genomic selection uses a genome-wide panel of dense markers so that all QTL are likely to be in linkage disequilibrium with at least one SNP. The genomic breeding values are predicted to be the sum of the effect of these SNPs across the entire genome. In dairy cattle breeding, the accuracy of genomic estimated breeding values (GEBV) that can be achieved and the fact that these are available early in life have lead to rapid adoption of the technology. Here, we discuss the design of experiments necessary to achieve accurate prediction of GEBV in future generations in terms of the number of markers necessary and the size of the reference population where marker effects are estimated. We also present a simple method for implementing genomic selection using a genomic relationship matrix. Future challenges discussed include using whole genome sequence data to improve the accuracy of genomic selection and management of inbreeding through genomic relationships.

We constructed a high-density Brassica rapa integrated linkage map by combining a reference genetic map of 78 doubled haploid lines derived from Chiifu-401-42 × Kenshin (CKDH) and a new map of 190 F2lines derived from Chiifu-401-42 × rapid cycling B. rapa (CRF2). The integrated map contains 1017 markers and covers 1262.0 cM of the B. rapa genome, with an average interlocus distance of 1.24 cM. High similarity of marker order and position was observed among the linkage groups of the maps with few short-distance inversions. In total, 155 simple sequence repeat (SSR) markers, anchored to 102 new bacterial artificial chromosomes (BACs) and 146 intron polymorphic (IP) markers were mapped in the integrated map, which would be helpful to align the sequenced BACs in the ongoing multinational Brassica rapa Genome Sequencing Project (BrGSP). Further, comparison of the B. rapa consensus map with the 10 B. juncea A-genome linkage groups by using 98 common IP markers showed high-degree colinearity between the A-genome linkage groups, except for few markers showing inversion or translocation. Suggesting that chromosomes are highly conserved between these Brassica species, although they evolved independently after divergence. The sequence information coming out of BrGSP would be useful for B. juncea breeding. and the identified Arabidopsis chromosomal blocks and known quantitative trait loci (QTL) information of B. juncea could be applied to improve other Brassica crops including B. rapa.

Oilseed rape ( Brassica napus ) is an allotetraploid species consisting of two genomes, derived from B. rapa (A genome) and B. oleracea (C genome). The presence of these two genomes makes single nucleotide polymorphism (SNP) marker identification and SNP analysis more challenging than in diploid species, as for a given locus usually two versions of a DNA sequence (based on the two ancestral genomes) have to be analyzed simultaneously during SNP identification and analysis. One hundred amplicons derived from expressed sequence tag (ESTs) were analyzed to identify SNPs in a panel of oilseed rape varieties and within two sister species representing the ancestral genomes. A total of 604 SNPs were identified, averaging one SNP in every 42 bp. It was possible to clearly discriminate SNPs that are polymorphic between different plant varieties from SNPs differentiating the two ancestral genomes. To validate the identified SNPs for their use in genetic analysis, we have developed Illumina GoldenGate assays for some of the identified SNPs. Through the analysis of a number of oilseed rape varieties and mapping populations with GoldenGate assays, we were able to identify a number of different segregation patterns in allotetraploid oilseed rape. The majority of the identified SNP markers can be readily used for genetic mapping, showing that amplicon sequencing and Illumina GoldenGate assays can be used to reliably identify SNP markers in tetraploid oilseed rape and to convert them into successful SNP assays that can be used for genetic analysis.

Most breeding programs develop elite genotypes that are well adapted to the normal range of environmental conditions in the target production region. These elite lines have similar essential alleles for desirable end use characteristics, agronomics, disease resistance, and adaptation in the target region. The genetic makeup of these elite lines is complex. Intermating among the elite lines will often produce new variability through recombination with minimal risk of introducing new undesirable features, and is the source of most new cultivars. Eventually, this variation will be exhausted and new alleles must be introduced into the elite breeding population. Introducing desirable alleles from exotic germplasm may “pollute” the elite gene pool with undesirable alleles. Exotic germplasm may also disrupt essential allele combinations for adaptation, quality, and agronomic performance. New desirable alleles from exotic germplasm can be introgressed into an elite population in a systematic way through limited backcrossing with a minimal disturbance to the finely tuned elite background. Combining recurrent selection within elite germplasm with a systematic introgression from exotic germplasm in the recurrent introgressive population enrichment (RIPE) system has created an open-ended, continually improving, and sustainable elite population breeding system, which is simple, effective, and a regular source of new cultivars.

Aluminium (Al3+) toxicity restricts productivity and profitability of wheat ( Triticum aestivum L.) crops grown on acid soils worldwide. Continued gains will be obtained by identifying superior alleles and novel Al3+resistance loci that can be incorporated into breeding programs. We used association mapping to identify genomic regions associated with Al3+resistance using 1055 accessions of common wheat from different geographic regions of the world and 178 polymorphic diversity arrays technology (DArT) markers. Bayesian analyses based on genetic distance matrices classified these accessions into 12 subgroups. Genome-wide association analyses detected markers that were significantly associated with Al3+resistance on chromosomes 1A, 1B, 2A, 2B, 2D, 3A, 3B, 4A, 4B, 4D, 5B, 6A, 6B, 7A, and 7B. Some of these genomic regions correspond to previously identified loci for Al3+resistance, whereas others appear to be novel. Among the markers targeting TaALMT1 (the major Al3+-resistance gene located on chromosome 4D), those that detected alleles in the promoter explained most of the phenotypic variance for Al3+resistance, which is consistent with this region controlling the level of TaALMT1 expression. These results demonstrate that genome-wide association mapping cannot only confirm known Al3+-resistance loci, such as those on chromsomes 4D and 4B, but they also highlight the utility of this technique in identifying novel resistance loci.

This study describes the use of regional association analyses to delineate a sequenced region of a Brassica napus chromosome with a significant effect on antinutritive seed meal compounds in oilseed rape. A major quantitative trait locus (QTL) influencing seed colour, fibre content, and phenolic compounds was mapped to the same position on B. napus chromosome A9 in biparental mapping populations from two different yellow-seeded × black-seeded B. napus crosses. Sequences of markers spanning the QTL region identified synteny to a sequence contig from the corresponding chromosome A9 in Brassica rapa . Remapping of sequence-derived markers originating from the B. rapa sequence contig confirmed their position within the QTL. One of these markers also mapped to a seed colour and fibre QTL on the same chromosome in a black-seeded × black-seeded B. napus cross. Consequently, regional association analysis was performed in a genetically diverse panel of dark-seeded, winter-type oilseed rape accessions. For this we used closely spaced simple sequence repeat (SSR) markers spanning the sequence contig covering the QTL region. Correction for population structure was performed using a set of genome-wide SSR markers. The identification of QTL-derived markers with significant associations to seed colour, fibre content, and phenolic compounds in the association panel enabled the identification of positional and functional candidate genes for B. napus seed meal quality within a small segment of the B. rapa genome sequence.

Genotyping technology now allows the rapid and affordable generation of million-SNP profiles for humans, leading to considerable activity in association mapping. Similar activity is anticipated for many plant species, including Brassica . These plant association mapping activities will require the same care in quality control and quality assurance as for humans. The subsequent analyses may draw upon the same body of theory that is described here in the language of quantitative genetics.

This review addresses the mechanisms by which epigenetic variation modulates plant gene regulation and phenotype. In particular we explore the scope for harnessing such processes within the context of crop genetic improvement. We focus on the role of DNA methylation as an epigenetic mark that contributes to epiallelic diversity and modulation of gene regulation. We outline the prevalence and distribution of epigenetic marks in relation to eukaryote developmental processes, and in particular identify where this may be relevant to crop traits both in terms of specific developmental stages and in relation to physiological responses to environmental change. Recent whole genome surveys have identified specific characteristics of the distribution of DNA methylation within plant genomes. Together with greater understanding of the mode of action of different maintenance and de novo methyltransferases, this provides an opportunity to modulate DNA methylation status at specific loci as an intervention strategy in crop genetic improvement. We discuss alternative approaches that may be suitable for harnessing such induced epiallelic variation. Most of the discussion is associated with Brassica crops, which demonstrate considerable morphological plasticity, segmental chromosomal duplication, and polyploidy.

We have previously shown that linkage disequilibrium (LD) in the elite cultivated barley ( Hordeum vulgare ) gene pool extends, on average, for