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Articles 31 - 42 of 42
Full-Text Articles in Life Sciences
Application Of Machine Learning In Snp Discovery, Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curtis P. Van Tassell
Application Of Machine Learning In Snp Discovery, Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curtis P. Van Tassell
Department of Agronomy and Horticulture: Faculty Publications
Background: Single nucleotide polymorphisms (SNP) constitute more than 90% of the genetic variation, and hence can account for most trait differences among individuals in a given species. Polymorphism detection software PolyBayes and PolyPhred give high false positive SNP predictions even with stringent parameter values. We developed a machine learning (ML) method to augment PolyBayes to improve its prediction accuracy. ML methods have also been successfully applied to other bioinformatics problems in predicting genes, promoters, transcription factor binding sites and protein structures. Results: The ML program C4.5 was applied to a set of features in order to build a SNP classifier …
Snp-Phage – High Throughput Snp Discovery Pipeline, Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curt P. Van Tassell
Snp-Phage – High Throughput Snp Discovery Pipeline, Lakshmi K. Matukumalli, John J. Grefenstette, David L. Hyten, Ik-Young Choi, Perry B. Cregan, Curt P. Van Tassell
Department of Agronomy and Horticulture: Faculty Publications
Background: Single nucleotide polymorphisms (SNPs) as defined here are single base sequence changes or short insertion/deletions between or within individuals of a given species. As a result of their abundance and the availability of high throughput analysis technologies SNP markers have begun to replace other traditional markers such as restriction fragment length polymorphisms (RFLPs), amplified fragment length polymorphisms (AFLPs) and simple sequence repeats (SSRs or microsatellite) markers for fine mapping and association studies in several species. For SNP discovery from chromatogram data, several bioinformatics programs have to be combined to generate an analysis pipeline. Results have to be stored in …
Impacts Of Genetic Bottlenecks On Soybean Genome Diversity, D. L. Hyten, Qijian Song, Youlin Zhu, Ik-Young Choi, Randall L. Nelson, Jose M. Costa, James E. Specht, Randy C. Shoemaker, Perry B. Cregan
Impacts Of Genetic Bottlenecks On Soybean Genome Diversity, D. L. Hyten, Qijian Song, Youlin Zhu, Ik-Young Choi, Randall L. Nelson, Jose M. Costa, James E. Specht, Randy C. Shoemaker, Perry B. Cregan
Department of Agronomy and Horticulture: Faculty Publications
Soybean has undergone several genetic bottlenecks. These include domestication in Asia to produce numerous Asian landraces, introduction of relatively few landraces to North America, and then selective breeding over the past 75 years. It is presumed that these three human-mediated events have reduced genetic diversity. We sequenced 111 fragments from 102 genes in four soybean populations representing the populations before and after genetic bottlenecks. We show that soybean has lost many rare sequence variants and has undergone numerous allele frequency changes throughout its history. Although soybean genetic diversity has been eroded by human selection after domestication, it is notable that …
Soybean Cultivars Resulted From More Recombination Events Than Unselected Lines In The Same Population, T. R. Stefaniak, D. L. Hyten Jr., V. R. Pantalone, A. Klarer, T. W. Pfeiffer
Soybean Cultivars Resulted From More Recombination Events Than Unselected Lines In The Same Population, T. R. Stefaniak, D. L. Hyten Jr., V. R. Pantalone, A. Klarer, T. W. Pfeiffer
Department of Agronomy and Horticulture: Faculty Publications
The selection of superior adapted cultivars has contributed to the doubling of soybean [Glycine max (L.) Merr.] yields in the USA since 1930. Genetic variation was required for this selection to be effective. The objective of this study was to evaluate the importance of homologous chromosome meiotic recombination in the creation of soybean cultivars. A set of 10 adapted high-yielding cultivars selected from the cross ‘Williams’ × ‘Essex’ was com-pared with a set of 156 random recombinant inbred lines (RILs) from the same population. Crossover events were identified using 143 simple sequence repeat (SSR) markers span-ning all 20 soybean …
Ethylene Could Influence Ferric Reductase, Iron Transporter, And H+-Atpase Gene Expression By Affecting Fer (Or Fer-Like) Gene Activity, Carlos Lucera, Brian M. Waters, Francisco Javier Romera, María José García, María Morales, Esteban Alcántara, Rafael Pérez-Vicente
Ethylene Could Influence Ferric Reductase, Iron Transporter, And H+-Atpase Gene Expression By Affecting Fer (Or Fer-Like) Gene Activity, Carlos Lucera, Brian M. Waters, Francisco Javier Romera, María José García, María Morales, Esteban Alcántara, Rafael Pérez-Vicente
Department of Agronomy and Horticulture: Faculty Publications
In previous works, it has been shown, by using ethylene inhibitors and precursors, that ethylene could participate in the regulation of the enhanced ferric reductase activity of Fe-deficient Strategy I plants. However, it was not known whether ethylene regulates the ferric reductase gene expression or other aspects related to this activity. This paper is a study of the effects of ethylene inhibitors and precursors on the expression of the genes encoding the ferric reductases and iron transporters of Arabidopsis thaliana (FRO2 and IRT1) and Lycopersicon esculentum (= Solanum lycopersicum) (FRO1 and IRT1) plants. The effects …
Water Stress Vulnerability Of Four Banksia Species In Contrasting Ecohydrological Habitats On The Gnangara Mound, Western Australia, Caroline Canham
Water Stress Vulnerability Of Four Banksia Species In Contrasting Ecohydrological Habitats On The Gnangara Mound, Western Australia, Caroline Canham
Theses : Honours
The distribution of obligate and facultative phreatophytic vegetation reflects the gradient of ecohydrological habitats in a landscape. Preliminary investigations of Banksia vulnerability to xylem embolism have reported that obligate phreatophytes are more susceptible to water stress than facultative phreatophytes (Froend & Drake 2006). A quantitative measure of plant susceptibility to water stress is vital when establishing environmental water requirements. This study investigated interspecific differences in vulnerability to water stress for two facultative phreatophytes (B. attenuata and B. menziesii) and two obligate pln·eatophytes (B. ilicifolia and B. littoralis) at the same position along an ecohydrological gradient on the Gnangara Groundwater Mound, …
The Effects Of Light Reduction Treatments On Mobile Epifaunain An Amphibolis Griffithii (Black) Den Hartog Seagrass Ecosystem, Helen Barwick
The Effects Of Light Reduction Treatments On Mobile Epifaunain An Amphibolis Griffithii (Black) Den Hartog Seagrass Ecosystem, Helen Barwick
Theses : Honours
One of the main anthropogenic disturbances to seagrass meadows in Australia is reduction in light availability, through nutrient enrichment or suspended sediments. Dredging can create suspended sediment plumes from the expulsion of particulates into the water column and in tum reduces light penetration to seagrass ecosystems. Preliminary investigations have demonstrated that light reduction for different intensities and durations results in reduced seagrass and epiphytic algae biomass. The main aim of this study was to determine the effects of different intensities and durations of light reduction on epifaunal assemblages in Amphibolis griffithii seagrass meadows in Jurien Bay, Western Australia. This was …
Evaluation Of Water-Retention Ability Of Eastern Arkansas Prairie And Agricultural Soil, Maria L. Barrenechea, Kristofor R. Brye
Evaluation Of Water-Retention Ability Of Eastern Arkansas Prairie And Agricultural Soil, Maria L. Barrenechea, Kristofor R. Brye
Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences
Agricultural land use affects soil physical properties, such as bulk density, water content, organic matter content, and soil structure; all of which in turn affect ecosystem productivity. The objective of this study was to evaluate the effects of: 1) time since aboveground biomass has been removed by haying (i.e., 0 vs. 23 years), and 2) land use (i.e., undisturbed tallgrass prairie vs. cultivated agriculture) on water-retention characteristics in a silt-loam soil of the Grand Prairie region of eastern Arkansas. Soil samples were collected from the 0- to 10-cm depth and were wetted with varying amounts of distillated water to create …
Adventitious Shoot Propagation And Cultural Inputs In Nursery Production Of A Primocane-Fruiting Blackberry Selection, Kimberley Dennis, John R. Clark, James A. Robbins
Adventitious Shoot Propagation And Cultural Inputs In Nursery Production Of A Primocane-Fruiting Blackberry Selection, Kimberley Dennis, John R. Clark, James A. Robbins
Discovery, The Student Journal of Dale Bumpers College of Agricultural, Food and Life Sciences
Studies were conducted from January to October 2005 to determine the effect of root-cutting length on adventitious shoot yield and the management practices necessary to produce nurseryquality primocane-fruiting blackberry plants. The first portion of the study measured the average number of shoots produced from 7.6 cm- and 15.2 cm-long root cuttings of APF-44 blackberry—a primocane-fruiting genotype from the University of Arkansas breeding program. Cuttings were forced in a shallow bin containing a soilless potting medium. The average number of shoots per root cutting from 7.6 cm- and 15.2 cm- long root cuttings averaged 1.6 and 2.7 shoots per root cutting, …
A Guide For Skeleton Weed Management And Control, Department Of Agriculture And Food, Western Australia
A Guide For Skeleton Weed Management And Control, Department Of Agriculture And Food, Western Australia
Bulletins 4000 -
Assisting Western Australian landholders to eradicate skeleton weed and to prevent its further spread within the State
Cellular And Organ Level Localization Of Maltose In Maltose-Excess Arabidopsis Mutants, Yan Lu, Jon Steichen, Sean Weise, Thomas Sharkey
Cellular And Organ Level Localization Of Maltose In Maltose-Excess Arabidopsis Mutants, Yan Lu, Jon Steichen, Sean Weise, Thomas Sharkey
Yan Lu
No abstract provided.
The Role Of Cytosolic A-Glucan Phosphorylase In Maltose Metabolism And The Comparison Of Amylomaltose In Arabidopsis And E. Coli, Yan Lu, Jon Steichen, Jian Yao, Thomas Sharkey
The Role Of Cytosolic A-Glucan Phosphorylase In Maltose Metabolism And The Comparison Of Amylomaltose In Arabidopsis And E. Coli, Yan Lu, Jon Steichen, Jian Yao, Thomas Sharkey
Yan Lu
No abstract provided.