Physical Sciences and Mathematics Commons^™

Tall Fescue Expressed Sequence Tag And Simple Sequence Repeats: Important Resources For Grass Species, Malay C. Saha, J. C. Zwonitzer, K. Chekhovskiy, M. A. R. Mian

IGC Proceedings (1993-2023)

Expressed sequence tag (EST) databases have been growing exponentially. The simple sequence repeat (SSR) has become one of the most useful molecular marker systems in plant breeding and is widely used in cultivar fingerprinting, genetic diversity assessment, molecular mapping and marker-assisted selection. ESTs are a potential source for SSRs. The EST-SSR markers are of high quality and have versatile applications in molecular breeding (Bughrara et al., 2003; Saha et al., 2004 a, b, c). Here, we present an overview of our efforts to develop SSRs from tall fescue ESTs and their application for the genetic improvement of forage …

A Core Aflp Map Of Aposporic Tetraploid Paspalum Notatum (Bahiagrass), J. P. A. Ortiz, J. Stein, E. J. Martínez, S. C. Pessino, C. L. Quarin

IGC Proceedings (1993-2023)

Paspalum notatum (Bahiagrass) is a perennial rhizomatous species that reproduces by aposporous apomixis. Tetraploid races (2n=4x=40) are widely distributed from Central to South America and constitute one of the most valuable natural forage grasses for the subtropical areas of Paraguay, southern Brazil and north-eastern Argentina. Apospory in the species is controlled by a single locus, which exhibits a distorted segregation ratio. The objectives of this work were to develop a core genetic linkage map of the species by using AFLP markers and characterize the genomic region related to apospory.

Repulsion-Phase Linkage Analysis Of Tetraploid Creeping Bentgrass (Agrostis Stolonifera L.), S. E. Warnke, N. Chakraborty, G. Jung

IGC Proceedings (1993-2023)

Creeping bentgrass is a cool-season grass species primarily used on golf course greens, tees, and fairways because of its tolerance of low mowing heights and recuperative ability. Creeping bentgrass is tetraploid and outcrossing and has been characterized as having bivalent chromosome pairing through cytogenetic analysis (Jones, 1956) and disomic inheritance based on the inheritance of isozyme markers (Warnke et al., 1998). The objective of this experiment was to evaluate the extent of repulsion-phase linkages of single dose AFLP type markers in a creeping bentgrass mapping population and to infer chromosome pairing behaviour based on the ratio of coupling to …

Towards A Genetic Map In Creeping Bentgrass Based On Ssrs, Aflps And Rflps, H. Zhao, S. Bughrara

IGC Proceedings (1993-2023)

Creeping bentgrass (Agrostis palustris) (2n=4x=28) is commonly used in golf course, putting green, tees and fairways. In spite of the importance of the species in turfgrass industry, the genetic study of the creeping bentgrass has received relatively little attention. Genetic mapping, as a new tool, helps traditional turfgrass breeding methods through the construction of linkage, identification of quantitative trait loci linked to traits of interest, and application of marker assisted selection program. Molecular markers such as AFLPs, SSRs and RFLPs have been used extensively for the preparation of linkage maps of a number of crop species. The objective …

Integration Of Perennial Ryegrass (L. Perenne) Genetic Maps Using Gene-Associated Snps, A. C. Vecchies, R. C. Ponting, M. C. Drayton, N. O. I. Cogan, K. F. Smith, G. C. Spangenberg, J. W. Forster

IGC Proceedings (1993-2023)

The reference genetic map of perennial ryegrass was developed by the International Lolium Genome Initiative (ILGI), using the p150/112 one-way pseudo-testcross population. A selection of public domain genetic markers including RFLPs, detected by wheat, barley, oat and rice cDNA probes, and AFLPs were mapped, allowing studies of comparative relationships between perennial ryegrass and other Poaceae species. The map was enhanced through the addition of unique perennial ryegrass genomic DNA-derived SSR (LPSSR) markers, providing the basis of framework genetic mapping in other populations. In addition, a small number of RFLP loci detected by candidate genes involved in herbage quality traits were …

Qtls For Morphogenetic Traits In Medicago Truncatula, B. Julier, T. Huguet, J. M. Prosperi, P. Barre, Christian Huyghe, G. Cardinet

IGC Proceedings (1993-2023)

Plant morphogenesis that includes growth, development and flowering date, drives a large number of agronomical important traits in both grain and forage crops. Quantitative trait locus (QTL) mapping is a way to locate zones of the genome that are involved in the variations observed in a segregating population. Co-location of QTLs and candidate genes is an indication of the involvement of the genes in the variation. The objective of this study was to analyse segregation of aerial morphogenetic traits in a mapping population of recombinant inbred lines of the model legume species M. truncatula , to locate QTLs and candidate …

Construction And Comparison Of Genetic Linkage Maps Of Four F1 Populations Of Italian Ryegrass (Lolium Multiflorum Lam.), M. Vandewalle

IGC Proceedings (1993-2023)

The objective of this work was to integrate genetic maps and QTL-positions within 4 two-way pseudo-testcross F1 populations (each 110 genotypes) of Italian ryegrass (Lolium multiflorum) To integrate genetic maps and QTL-positions within the 4 populations and to the ILGI reference map, the maps used for initial QTL-analysis and marker assisted selection for yield and for different quality traits were further evaluated.

A Comprehensive Analysis Of Gene Expression And Genomic Alterations In A Newly Formed Autotetraploid Of Paspalum Notatum, L. G. Martelotto, J. P. A. Ortiz, F. Espinoza, C. L. Quarin, S. C. Pessino

IGC Proceedings (1993-2023)

The proportion of angiosperms that have experienced one or more episodes of chromosome doubling is estimated to be of the order of 50-70%. This prominence of polyploidy probably implies some adaptive significance. The emergence of novel phenotypes could allow polyploids to enter new niches or enhance their chances of being selected for use in agriculture. Although the causes of novel variation in polyploids are not well understood, they could involve changes in gene expression through dosage-regulation, altered regulatory interactions and rapid genetic/epigenetic changes. The objective of this work was to carry out an extensive transcript profiling and genome analysis of …

Effects Of Sowing Date And Phosphorus Fertiliser Application On Winter Survival Of Lucerne Cv. Aohan In The Northern Semi-Arid Region Of China, Z. L. Wang, Q. Zh. Sun, Y. W. Wang, Zh. Y. Li, Sh. F. Zhao

IGC Proceedings (1993-2023)

In the northern semi-arid region of China, winter survival is always a limiting factor for lucerne production, because low temperatures and a dry climate in winter (Zhou et al., 1993; Ma, 2000; Sun & Gui, 2001; Sun et al., 2003). An experiment was conducted to find an appropriate sowing date and P application rate in order to improve lucerne winter survival.

Projected Long-Term Climate Trends Reveal The Critical Role Of Vapor Pressure Deficit For Soybean Yields In The Us Midwest, Wenguang Sun, David Fleisher, Dennis Timlin, Chittaranjan Ray, Zhuangji Wang, Sahila Beegum, Vangimalla Reddy

Nebraska Water Center: Faculty Publications

Extreme climate events including heat waves and droughts are projected to become more frequent under future climate change conditions. However, the mechanisms between soybean yields and climate factors, specifically involving variable rainfall and high heat episodes, are still unclear, particularly with respect to spatial trends in the United States (US) Midwest. A recently modified version of the model GLYCIM was used to evaluate rainfed soybean production across 12 states at a 10 km spatial resolution for three time periods (2011–2020, 2051–2060, 2091–2099) under Representative Concentration Pathway (RCP) scenarios 4.5 and 8.5. Results showed that except for the northernmost Midwest counties, …

Federated Learning Framework Integrating Refined Cnn And Deep Regression Forests, Daniel Nolte, Omid Bazgir, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Predictive learning from medical data incurs additional challenge due to concerns over privacy and security of personal data. Federated learning, intentionally structured to preserve high level of privacy, is emerging to be an attractive way to generate cross-silo predictions in medical scenarios. However, the impact of severe population-level heterogeneity on federated learners is not well explored. In this article, we propose a methodology to detect presence of population heterogeneity in federated settings and propose a solution to handle such heterogeneity by developing a federated version of Deep Regression Forests. Additionally, we demonstrate that the recently conceptualized REpresentation of Features as …

Federated Learning Framework Integrating Refined Cnn And Deep Regression Forests, Daniel Nolte, Omid Bazgir, Souparno Ghosh, Ranadip Pal

Department of Statistics: Faculty Publications

Predictive learning from medical data incurs additional challenge due to concerns over privacy and security of personal data. Federated learning, intentionally structured to preserve high level of privacy, is emerging to be an attractive way to generate cross-silo predictions in medical scenarios. However, the impact of severe population-level heterogeneity on federated learners is not well explored. In this article, we propose a methodology to detect presence of population heterogeneity in federated settings and propose a solution to handle such heterogeneity by developing a federated version of Deep Regression Forests. Additionally, we demonstrate that the recently conceptualized REpresentation of Features as …

Baldcypress (Taxodium Distichum) And Their Growth And Development Under Abiotic Stressors Related To Restoration Efforts, George Washburn

LSU Doctoral Dissertations

Baldcypresss (Taxodium distichum (L.) Rich.) forests are crucial to the Southeast coastal region for the trees’ ecosystem services. Many organizations have been trying to restore the ghost and dead forests found throughout the Gulf region through restoration events. Baldcypress seedlings and saplings face several abiotic and biotic stressors, including but not limited to elevated levels of salinity, nutrients, temperature, and light intensity. These stressors can be the limiting factor in the success or failure of these massive planting efforts.

To assess which stressors were of most concern to the restoration efforts, we conducted common garden experiments with baldcypress seedlings …

An Advanced Deep Learning Models-Based Plant Disease Detection: A Review Of Recent Research, Muhammad Shoaib, Babar Shah, Shaker Ei-Sappagh, Akhtar Ali, Asad Ullah, Fayadh Alenezi, Tsanko Gechev, Tariq Hussain, Farman Ali

All Works

Plants play a crucial role in supplying food globally. Various environmental factors lead to plant diseases which results in significant production losses. However, manual detection of plant diseases is a time-consuming and error-prone process. It can be an unreliable method of identifying and preventing the spread of plant diseases. Adopting advanced technologies such as Machine Learning (ML) and Deep Learning (DL) can help to overcome these challenges by enabling early identification of plant diseases. In this paper, the recent advancements in the use of ML and DL techniques for the identification of plant diseases are explored. The research focuses on …

Prominent Size Effects Without A Depolarization Field Observed In Ultrathin Ferroelectric Oxide Membranes, Haoying Sun, Jiahui Gu, Yongqiang Li, Tula R. Paudel, Di Liu, Jierong Wang, Yipeng Zang, Chengyi Gu, Jiangfeng Yang, Wenjie Sun, Zhengbin Gu, Evgeny Y. Tsymbal, Junming Liu, Houbing Huang, Di Wu, Yuefeng Nie

Department of Physics and Astronomy: Faculty Publications

The increasing miniaturization of electronics requires a better understanding of material properties at the nanoscale. Many studies have shown that there is a ferroelectric size limit in oxides, below which the ferroelectricity will be strongly suppressed due to the depolarization field, and whether such a limit still exists in the absence of the depolarization field remains unclear. Here, by applying uniaxial strain, we obtain pure in-plane polarized ferroelectricity in ultrathin SrTiO₃ membranes, providing a clean system with high tunability to explore ferroelectric size effects especially the thickness-dependent ferroelectric instability with no depolarization field. Surprisingly, the domain size, ferroelectric transition …

Advancing An Agenda For Social Equity And Coastal Resilience Through A Multi-Sectoral, Multi-Disciplinary And Applied Research Lens, Wie Yusuf, Marina Saitgalina, Jennifer Whytlaw, Nicole Hutton, Tom Allen, Joshua Behr

Presentations, Lectures, Posters, Reports

No abstract provided.

Fuzzy Kc Clustering Imputation For Missing Not At Random Data, Markku A. Malmi Jr.

USF Tampa Graduate Theses and Dissertations

Research has a variety of difficulties, especially when involving human subjects, and one of the most prevalent is the issue of missing data. Missing data will always be present in research due to the fact there is no perfect method for collecting data and protecting against human error or mechanical failure. This requires researchers to be able to mitigate the problems that come along with missing data; reduction in power of an analysis and bias introduced by the missing pattern. This research investigated a non-parametric method using a nested approach of fuzzy K-Modes and fuzzy C-Means clustering to impute missing …

Movement, Behavior, And Trophic Ecology Of A Pelagic Predator Guild In The Eastern Tropical Pacific Ocean, Ryan Keith Logan

All HCAS Student Capstones, Theses, and Dissertations

Pelagic apex predators exert strong influences on ecological communities, and often support valuable commercial or recreational fisheries worldwide. Yet, due to their rarity and pelagic lifestyle, many species, such as billfishes, have proven particularly difficult to study at resolutions necessary to define dynamics of recovery from fishery interaction, physical interaction with environmental features and prey exploitation, and competitive interactions among other billfish predators. This leads to a paucity of knowledge on billfish ecology and habitat use, and hinders management efforts. With the ever-improving and miniaturization of technology and oceanographic datasets, the ability to define and quantify these interactions of fish …

On Characterization Of The Exponential Distribution Via Hypoexponential Distributions, George Yanev

School of Mathematical and Statistical Sciences Faculty Publications and Presentations

The sum of independent, but not necessary identically distributed, exponential random variables follows a hypoexponential distribution. We focus on a particular case when all but one rate parameters of the exponential variables are identical. This is known as exponentially modified Erlang distribution in molecular biology. We prove a characterization of the exponential distribution, which complements previous characterizations via hypoexponential distribution with all rates different from each other.

Characterisation Of Perennial Ryegrass Parental Inbred Lines For Generating Recombinant Inbred Lines For Fine Mapping And Gene Cloning, U. C. M. Anhalt, S. Barth, T. Schwarzacher, J. S. Heslop-Harrison

IGC Proceedings (1993-2023)

Intermated recombinant inbred lines (IRIs) are a powerful tool for fine mapping and cloning of genes. Such population structures have been particularly helpful for cloning of genes in the model genetic plant Arabidopsis thaliana. IRIs or recombinant inbred lines (RILs) would be valuable for perennial ryegrass (Lolium perenne), but its allogamous character means that the construction of RILs is a difficult task. The international Lolium community would benefit from the development of such lines. The aims of the projects are to characterise the parental lines and initial generations at the (1) phenotypic, (2) molecular and (3) molecular …

A High-Density Ssr Linkage Map Of Red Clover And Its Transferability To Other Legumes, S. Isobe, S. Sato, E. Asamizu, I. Klimenko, N. N. Kozlov, K. Okumura, S. Tabata

IGC Proceedings (1993-2023)

A high-density linkage map of red clover was constructed based on SSR and RFLP markers. In order to construct a linkage map with user (breeder) friendly markers; i.e. informative and easy detection, two policies were adopted for marker development. One was that the markers should be derived from cDNA or gene-rich regions, and the other was that the SSR markers should be detected polymorphisms on agarose gels. We also discuss the transferability of the markers on the map to other red clover germplasm and legumes. Such highly transferable markers could be used to screen anchor markers for both on a …

Development Of Est And Aflp Markers Linked To A Gene For Resistance To Ryegrass Blast (Pyricularia Sp.) In Italian Ryegrass (Lolium Multiflorum Lam.), Y. Miura, C. Ding, R. Ozaki, M. Hirata, M. Fujimori, H. Cai, K. Mizuno

IGC Proceedings (1993-2023)

Ryegrass blast, caused by the fungus Pyricularia sp. is one of the most serious diseases of Italian ryegrass (Lolium multiflorum Lam.). However, in Italian ryegrass, except for a new cultivar ‘Sachiaoba’, no resistant cultivars were found in Japan (Mizuno et al., 2003). For these reasons, improving the disease resistance of Italian ryegrass is one of the most important goals in the breeding programs. The aim of this study was to identify genes for resistance to ryegrass blast and to develop EST and AFLP markers linked tightly to the resistance genes.

Qtl Analysis And Trait Dissection In Ryegrass (Lolium Spp.), T. Yamada, J. W. Forster

IGC Proceedings (1993-2023)

Key points

1. Molecular marker-based genetic analysis permits the dissection of complex phenotypes through resolution of the locations of pleiotropic and interacting genetic factors.
2. Several QTLs for agronomically important characters such as flowering time, winter hardiness and forage quality have been identified in perennial ryegrass by molecular marker-based map analysis.
3. Some QTLs were putatively orthologous to those for equivalent traits in cereals.
4. The identification of co-location between QTLs and functionally-associated genetic markers is critical for the future implementation of marker-assisted selection programs.

Construction And Exploitation Of A Bacterial Artificial Chromosome (Bac) Library For Lolium Perenne (Perennial Ryegrass), K. Farrar, A. M. Thomas, M. O. Humphreys, I. S. Donnison

IGC Proceedings (1993-2023)

BAC libraries are an important tool in genomics, enabling physical maps, genome sequencing, marker development and map based cloning strategies. A BAC library has therefore been generated for the temperate grass species Lolium perenne (perennial ryegrass) which compliments an existing BAC library of the closely related species, Festuca pratensis also generated by IGER. Moreover the L. perenne BAC library will provide a useful tool for grass comparative genomics to compliment the existing BAC libraries of cereal crops including rice, wheat, barley, Sorghum and maize. In particular it will allow a comparison of micro-synteny between this large genome forage crop species …

Introgression Mapping In The Grasses, I. P. King, J. King, I. P. Armstead, J. A. Harper, L. A. Roberts, H. Thomas, H. J. Ougham, R. N. Jones, A. Thomas, B. J. Moore, L. Huang, I. S. Donnison

IGC Proceedings (1993-2023)

Key points

1. Lolium perenne/Festuca pratensis hybrids and their derivatives provide an ideal system for intergeneric introgression.
2. The Lolium perenne/Festuca pratensis system is being exploited to elucidate genome organisation in the grasses, determination of the genetic control of target traits and the isolation of markers for MAS in breeding programmes.
3. The potential of the system as an aid to contig the Lolium and Festuca genomes and for gene isolation is discussed.

Application Of Molecular Technologies In Forage Plant Breeding, K. F. Smith, J. W. Forster, M. P. Dobrowolski, N. O. I. Cogan, N. R. Bannan, E. Van Zijll De Jong, M Emmerling, G. C. Spangenberg

IGC Proceedings (1993-2023)

Key points

1. A range of molecular breeding technologies have been developed for forage plant species including both transgenic and non-transgenic methodologies.
2. The application of these technologies has the potential to greatly increase the range of genetic variation that is available for incorporation into breeding programs and subsequent delivery to producers in the form of improved germplasm.
3. Further developments in detailing the phenotypic effect of genes and alleles both through research in target species and through inference from results from model species will further refine the delivery of new forage cultivars.

Application Of Molecular Markers In Genetic Resources Management Of Perennial Ryegrass, R. Van Treuren

IGC Proceedings (1993-2023)

Key points

1. Molecular markers are effective tools to support traditional approaches in plant genetic resources management.
2. Genetic diversity assessed for perennial ryegrass by AFLP analysis revealed differentiation of populations occurring in traditional Dutch grasslands from commercial varieties, but not from populations occurring in Dutch nature reserves.
3. No specific conservation measures were recommended to maintain the genetic diversity of perennial ryegrass occurring in traditional Dutch grasslands.
4. Pollination rates estimated by microsatellite analysis for a rejuvenated population of a perennial ryegrass genebank accession were very well described by an inverse quadratic function of inter-plant distance between potential mating pairs, while recorded flowering …

A Computational Pipeline For The Development Of Comparative Anchor Tagged Sequence (Cats) Markers, J. Schauser, J. Fredslund, L. Heegaard Madsen, Niels Sandal, Jens Stougaard

IGC Proceedings (1993-2023)

Key points:

1. Molecular markers that allow the transfer of map information from one species to another are vital in comparative genetics.
2. To identify potential anchor marker sequences more efficiently, we have established a bioinformatic pipeline that combines multi-species EST- and genome- sequence data.
3. Taking advantage of information from a few related species, comparative EST sequence analysis identifies evolutionary conserved sequences in less well-characterised species in the same family.
4. Alignment of evolutionary conserved EST sequences with corresponding genomic sequences defines sets of PCR primer sites flanking introns.
5. Markers identified by this procedure will be readily transferable to other species since they …

Leaves Of High Yielding Perennial Ryegrass Contain Less Aggregated Rubisco Than S23, A. Kingston-Smith, P. W. Wilkins

IGC Proceedings (1993-2023)

Breeding diploid perennial ryegrass for improved dry matter yield under nitrogen-limiting conditions has reduced the nitrogen (N) concentration of the herbage (Wilkins et al., 2003). Reduced N concentration in the ruminant diet is one potential way to reduce losses of N to the environment by reducing the amount of N that animals excrete. The underlying physiological basis of this increased N-use efficiency in ryegrass was investigated.

Variability In Quantity And Composition Of Water Soluble Carbohydrates Among Irish Accessions And European Varieties Of Perennial Ryegrass, S. Mcgrath, S. Barth, A. Frohlich, M. Francioso, S. A. Lamorte, T. R. Hodkinson

IGC Proceedings (1993-2023)

The objective of this study was to identify perennial ryegrass accessions displaying high fructose and glucose contents and an improved ratio between fructose and glucose fractions across different time points throughout the year. Fructose and glucose are the main constituents of the water soluble carbohydrate (WSC) fraction in perennial ryegrass. For animal nutrition the amount of WSC is crucial as it is the primary energy source available to metabolise the intake of plant protein. The ratio between fructose and glucose fractions is important since fructosan chains, which are an excellent energy source for ruminants, are built from fructose. Furthermore the …