New Model for Moving Forward with Marker-based Selection

Increasing the frequency of favorable alleles in populations is the goal of tree breeding based on an additive genetic model. Conceptually, marker based selection (MBS) combined with accelerated breeding offers a more efficient means to this end by reducing the generation interval and increasing genetic gain per generation. Yet, while DNA markers for qualitative and quantitative traits have been identified and reported, neither these nor other genetic markers have been widely accepted in southern pine breeding programs. Some of the reasons for not using MBS include the following: marker development and genotyping costs are too high, QTL effects appear too small and have not been demonstrated in independent families, and the requirement of multiple populations, traits and environment complicate matters such that there is no clear path forward. To address these theoretical and operational issues we are proposing two general strategies for MBS-accelerated southern pine breeding. One strategy applies QTL detection and marker selection to established breeding resources, while the other generates breeding populations structured to make optimal use of DNA marker information in an operational breeding context. Both strategies depend on performing multiple generations of selection prior to progeny testing. This is in contrast to the normal mode of operation in which selections are progeny tested each generation. We suggest that these strategies offer much flexibility with respect to moving selections to production populations and therefore should offer additional genetic gain at intermediate time points. Options for population structure and family sizes and for phenotypic and genotypic data requirements of each strategy will be discussed. Half-sib family designs are utilized in both strategies to capture linkage-disequilibrium of the constructed populations and to infer linkage phase relationships of marker and QTL alleles in individual families. Selective genotyping using highly informative DNA markers are required to reduce genotyping costs, while BLUP analyses are proposed to improve phenotypic data quality. Accelerated breeding options include top grafting or the use of a short generation pine species, such as Virginia pine, as a model species.Papers and abstracts from the 27th Southern Forest Tree Improvement Conference held at Oklahoma State University in Stillwater, Oklahoma on June 24-27, 2003

Ultra-low energy scattering of a He atom off a He dimer

We present a new, mathematically rigorous, method suitable for bound state and scattering processes calculations for various three atomic or molecular systems where the underlying forces are of a hard-core nature. We employed this method to calculate the binding energies and the ultra-low energy scattering phase shifts below as well as above the break-up threshold for the three He-atom system. The method is proved to be highly successful and suitable for solving the three-body bound state and scattering problem in configuration space and thus it paves the way to study various three-atomic systems, and to calculate important quantities such as the cross-sections, recombination rates etc.Comment: LaTeX, RevTeX and amssymb styles, 7 pages (25 Kb), 3 table

Polytetrahedral Clusters

By studying the structures of clusters bound by a model potential that favours polytetrahedral order, we find a previously unknown series of `magic numbers' (i.e. sizes of special stability) whose polytetrahedral structures are characterized by disclination networks that are analogous to hydrocarbons.Comment: 4 pages, 4 figure

New Tetrahedral Global Minimum for the 98-atom Lennard-Jones Cluster

A new atomic cluster structure corresponding to the global minimum of the 98-atom Lennard-Jones cluster has been found using a variant of the basin-hopping global optimization algorithm. The new structure has an unusual tetrahedral symmetry with an energy of -543.665361, which is 0.022404 lower than the previous putative global minimum. The new LJ_98 structure is of particular interest because its tetrahedral symmetry establishes it as one of only three types of exceptions to the general pattern of icosahedral structural motifs for optimal LJ microclusters. Similar to the other exceptions the global minimum is difficult to find because it is at the bottom of a narrow funnel which only becomes thermodynamically most stable at low temperature.Comment: 3 pages, 2 figures, revte

An annotated genetic map of loblolly pine based on microsatellite and cDNA markers

BACKGROUND: Previous loblolly pine (Pinus taeda L.) genetic linkage maps have been based on a variety of DNA polymorphisms, such as AFLPs, RAPDs, RFLPs, and ESTPs, but only a few SSRs (simple sequence repeats), also known as simple tandem repeats or microsatellites, have been mapped in P. taeda. The objective of this study was to integrate a large set of SSR markers from a variety of sources and published cDNA markers into a composite P. taeda genetic map constructed from two reference mapping pedigrees. A dense genetic map that incorporates SSR loci will benefit complete pine genome sequencing, pine population genetics studies, and pine breeding programs. Careful marker annotation using a variety of references further enhances the utility of the integrated SSR map. RESULTS: The updated P. taeda genetic map, with an estimated genome coverage of 1,515 cM((Kosambi)) across 12 linkage groups, incorporated 170 new SSR markers and 290 previously reported SSR, RFLP, and ESTP markers. The average marker interval was 3.1 cM. Of 233 mapped SSR loci, 84 were from cDNA-derived sequences (EST-SSRs) and 149 were from non-transcribed genomic sequences (genomic-SSRs). Of all 311 mapped cDNA-derived markers, 77% were associated with NCBI Pta UniGene clusters, 67% with RefSeq proteins, and 62% with functional Gene Ontology (GO) terms. Duplicate (i.e., redundant accessory) and paralogous markers were tentatively identified by evaluating marker sequences by their UniGene cluster IDs, clone IDs, and relative map positions. The average gene diversity, H(e), among polymorphic SSR loci, including those that were not mapped, was 0.43 for 94 EST-SSRs and 0.72 for 83 genomic-SSRs. The genetic map can be viewed and queried at http://www.conifergdb.org/pinemap. CONCLUSIONS: Many polymorphic and genetically mapped SSR markers are now available for use in P. taeda population genetics, studies of adaptive traits, and various germplasm management applications. Annotating mapped genes with UniGene clusters and GO terms allowed assessment of redundant and paralogous EST markers and further improved the quality and utility of the genetic map for P. taeda

The Bin Area Method: A Computationally Efficient Technique for Analysis of Ventricular and Atrial Intracardiac Electrograms

Peer Reviewedhttp://deepblue.lib.umich.edu/bitstream/2027.42/74901/1/j.1540-8159.1990.tb02028.x.pd

Infuence of the year and HMW glutenin subunits on end-use quality predictors if bread wheat waxy lines

The effects of environment and the high molecular weight glutenins on some quality properties (sedimentation volume, % protein content, and starch pasting viscosity) of bread wheat mutant waxy lines were evaluated. Thirty-eight 100% amylose-free F 2 derived F 6 and F 7 lines were used. The results indicated that the environment did not influence sedimentation volume, mixograph parameters and starch viscosity parameters of waxy flour. Variation in the % protein content was determined mainly by the environment. The sedimentation volume and the mixograph peak development time were influenced by the variation at over expression of Bx7 and the mixograph peak development time was influenced by the Glu-D1 locus. One starch viscosity parameter, time to peak viscosity, was influenced by variation at the Glu-A1 locus. This parameter is significantly lower in the waxy lines than the parent line, which shows the influence of the waxy loci. No significant correlation was observed for sedimentation volume, mixograph parameters, protein content and viscosity parameters of waxy line

Characterization of variable EST SSR markers for Norway spruce (Picea abies L.)

<p>Abstract</p> <p>Background</p> <p>Norway spruce is widely distributed across Europe and the predominant tree of the Alpine region. Fast growth and the fact that timber can be harvested cost-effectively in relatively young populations define its status as one of the economically most important tree species of Northern Europe. In this study, EST derived simple sequence repeat (SSR) markers were developed for the assessment of putative functional diversity in Austrian Norway spruce stands.</p> <p>Results</p> <p>SSR sequences were identified by analyzing 14,022 publicly available EST sequences. Tri-nucleotide repeat motifs were most abundant in the data set followed by penta- and hexa-nucleotide repeats. Specific primer pairs were designed for sixty loci. Among these, 27 displayed polymorphism in a testing population of 16 <it>P. abies </it>individuals sampled across Austria and in an additional screening population of 96 <it>P. abies </it>individuals from two geographically distinct Austrian populations. Allele numbers per locus ranged from two to 17 with observed heterozygosity ranging from 0.075 to 0.99.</p> <p>Conclusions</p> <p>We have characterized variable EST SSR markers for Norway spruce detected in expressed genes. Due to their moderate to high degree of variability in the two tested screening populations, these newly developed SSR markers are well suited for the analysis of stress related functional variation present in Norway spruce populations.</p

Sentinel node procedure in Ib cervical cancer: a preliminary series

The aim of this study was to determine the diagnostic accuracy and feasibility of sentinel lymph node (SLN) detection using a gamma probe in patients with Figo IB cervical cancer. Between January 1999 and September 2000, 14 patients with cervical cancer, planned for radical hysterectomy were eligible for the study. The day before radical hysterectomy we injected technetium99m-labelled nanocolloid in each quadrant of the cervix. Dynamic and static images were recorded using a gamma camera. SLNs were identified intraoperatively using a handheld gamma-detection probe. After resection of SLNs a standard radical hysterectomy with pelvic lymph node dissection was performed. Patients and tumour characteristics were compared with sentinel node detection and with final histopathological and immunohistochemical results. Scintigraphy showed focal uptake in 13 of the 14 patients. Intraoperatively we detected 26 sentinel nodes by gamma probe. In 8 of 13 patients, one or more sentinel nodes were identified unilaterally, in 5 women bilaterally. Histologically positive SLNs were found in only 1 patient. We did not find any false-negative SLN in our series. In conclusion identification of sentinel nodes in cervical cancer is feasible with preoperatively administered technetium99m-labelled nanocolloid. A larger series will be required to establish sentinel node detection in cervical cancer for further therapy concepts and planning. © 2001 Cancer Research Campaignhttp://www.bjcancer.co