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Full-Text Articles in Life Sciences
An Integrative And Applicable Phylogenetic Footprinting Framework For Cis-Regulatory Motifs Identification In Prokaryotic Genomes, Bingqiang Liu, Hanyuan Zhang, Chaun Zhou, Guojaun Li, Anne Fennell, Guanghui Wang, Yu Kang, Qi Liu
An Integrative And Applicable Phylogenetic Footprinting Framework For Cis-Regulatory Motifs Identification In Prokaryotic Genomes, Bingqiang Liu, Hanyuan Zhang, Chaun Zhou, Guojaun Li, Anne Fennell, Guanghui Wang, Yu Kang, Qi Liu
Agronomy, Horticulture and Plant Science Faculty Publications
Background: Phylogenetic footprinting is an important computational technique for identifying cis-regulatory motifs in orthologous regulatory regions from multiple genomes, as motifs tend to evolve slower than their surrounding non-functional sequences. Its application, however, has several difficulties for optimizing the selection of orthologous data and reducing the false positives in motif prediction. Results: Here we present an integrative phylogenetic footprinting framework for accurate motif predictions in prokaryotic genomes (MP3 ). The framework includes a new orthologous data preparation procedure, an additional promoter scoring and pruning method and an integration of six existing motif finding algorithms as basic motif search engines. Specifically, …
Physiological And Molecular Characterisation Of Lucerne (Medicago Sativa L.) Germplasm With Improved Seedling Freezing Tolerance, M. Rokebul Anowar, Anne Fennell, Arvid Boe, Ivan W. Mott, Michael D. Peel, Yajun Wu
Physiological And Molecular Characterisation Of Lucerne (Medicago Sativa L.) Germplasm With Improved Seedling Freezing Tolerance, M. Rokebul Anowar, Anne Fennell, Arvid Boe, Ivan W. Mott, Michael D. Peel, Yajun Wu
Agronomy, Horticulture and Plant Science Faculty Publications
We conducted greenhouse experiments to compare 14 lucerne (alfalfa, Medicago sativa L.) germplasms for their survival following freezing. Some are collections adapted to the Grand River National Grasslands in South Dakota. We hypothesised that these collections might have developed a tolerance to survive the frigid growth conditions common there. Two of these collections, River side (RS) and Foster ranch (FR), showed greater freezing tolerance than the other germplasms tested, based on their consistent survival rates with or without cold acclimation. In multiple freezing studies, RS and FR had average survival rates of 74% and 79%, respectively, in contrast to the …
Maize, Switchgrass, And Ponderosa Pine Biochar Added To Soil Increased Herbicide Sorption And Decreased Herbicide Efficacy, Sharon A. Clay, Kaitlynn K. Krack, Stephanie A. Bruggeman, Sharon Papiernik, Thomas E. Schumacher
Maize, Switchgrass, And Ponderosa Pine Biochar Added To Soil Increased Herbicide Sorption And Decreased Herbicide Efficacy, Sharon A. Clay, Kaitlynn K. Krack, Stephanie A. Bruggeman, Sharon Papiernik, Thomas E. Schumacher
Agronomy, Horticulture and Plant Science Faculty Publications
Biochar, a by-product of pyrolysis made from a wide array of plant biomass when producing biofuels, is a proposed soil amendment to improve soil health. This study measured herbicide sorption and efficacy when soils were treated with low (1% w/w) or high (10% w/w) amounts of biochar manufactured from different feedstocks [maize (Zea mays) stover, switchgrass (Panicum vigatum), and ponderosa pine (Pinus ponderosa)], and treated with different post-processing techniques. Twenty-four hour batch equilibration measured sorption of 14C-labelled atrazine or 2,4-D to two soil types with and without biochar amendments. Herbicide efficacy was measured …
Next Generation Mapping Of Enological Traits In An F2 Interspecific Grapevine Hybrid Family, Shanshan Yang, Jonathan Fresnedo-Ramírez, Qi Sun, David C. Manns, Gavin L. Sacks, Anna Katherine Mansfield, James L. Luby, Jason Londo, Bruce I. Reisch, Lance Cadle-Davidson, Anne Y. Fennell
Next Generation Mapping Of Enological Traits In An F2 Interspecific Grapevine Hybrid Family, Shanshan Yang, Jonathan Fresnedo-Ramírez, Qi Sun, David C. Manns, Gavin L. Sacks, Anna Katherine Mansfield, James L. Luby, Jason Londo, Bruce I. Reisch, Lance Cadle-Davidson, Anne Y. Fennell
Agronomy, Horticulture and Plant Science Faculty Publications
In winegrapes (Vitis spp.), fruit quality traits such as berry color, total soluble solids content (SS), malic acid content (MA), and yeast assimilable nitrogen (YAN) affect fermentation or wine quality, and are important traits in selecting new hybrid winegrape cultivars. Given the high genetic diversity and heterozygosity of Vitis species and their tendency to exhibit inbreeding depression, linkage map construction and quantitative trait locus (QTL) mapping has relied on F1 families with the use of simple sequence repeat (SSR) and other markers. This study presents the construction of a genetic map by single nucleotide polymorphisms identified through genotyping-by-sequencing …
A Next-Generation Marker Genotyping Platform (Ampseq) In Heterozygous Crops: A Case Study For Marker-Assisted Selection In Grapevine, Shanshan Yang, Jonathan Fresnedo-Ramírez, Minghui Wang, Linda Cote, Peter Schweitzer, Paola Barba, Elizabeth M. Takacs, Matthew Clark, James Luby, David C. Manns, Gavin Sacks, Anna Katharine Mansfield, Jason Londo, Anne Fennell Dr, David Gadoury, Bruce Reisch, Lance Cadle-Davidson, Qi Sun
A Next-Generation Marker Genotyping Platform (Ampseq) In Heterozygous Crops: A Case Study For Marker-Assisted Selection In Grapevine, Shanshan Yang, Jonathan Fresnedo-Ramírez, Minghui Wang, Linda Cote, Peter Schweitzer, Paola Barba, Elizabeth M. Takacs, Matthew Clark, James Luby, David C. Manns, Gavin Sacks, Anna Katharine Mansfield, Jason Londo, Anne Fennell Dr, David Gadoury, Bruce Reisch, Lance Cadle-Davidson, Qi Sun
Agronomy, Horticulture and Plant Science Faculty Publications
Marker-assisted selection (MAS) is often employed in crop breeding programs to accelerate and enhance cultivar development, via selection during the juvenile phase and parental selection prior to crossing. Next-generation sequencing and its derivative technologies have been used for genome-wide molecular marker discovery. To bridge the gap between marker development and MAS implementation, this study developed a novel practical strategy with a semi-automated pipeline that incorporates traitassociated single nucleotide polymorphism marker discovery, low-cost genotyping through amplicon sequencing (AmpSeq) and decision making. The results document the development of a MAS package derived from genotyping-by-sequencing using three traits (flower sex, disease resistance and …
Biochar Reduced Nitrous Oxide And Carbon Dioxide Emissions From Soil With Different Water And Temperature Cycles, Jiyul Chang, David E. Clay, Sharon A. Clay, Rajesh Chintala, Janet M. Miller, Thomas Schumacher
Biochar Reduced Nitrous Oxide And Carbon Dioxide Emissions From Soil With Different Water And Temperature Cycles, Jiyul Chang, David E. Clay, Sharon A. Clay, Rajesh Chintala, Janet M. Miller, Thomas Schumacher
Agronomy, Horticulture and Plant Science Faculty Publications
Interactions among biochar, respiration, nitrification, and soils can result in biochar increasing, decreasing, or not impacting greenhouse gas (GHG) emissions. This experiment determined the impact of water-filled porosity (WFP) and corn (Zea mays L.) stover biochar on CO2 and N2O emissions in May (spring) and August (summer). The May experiment contained two N rates [0 and 224 kg Ca(NO3)2–N ha–1], whereas the August had three N rates [0, 224 kg Ca(NO3)2–N ha–1, and 224 kg (NH4)2SO4–N ha–1 …
Toward The Elucidation Of Cytoplasmic Diversity In North American Grape Breeding Programs, Jonathan Fresnedo-Ramirez, Qi Sun, Chin-Feng Hwang, Craig A. Ledbetter, David W. Ramming, Anne Fennell, M. Andrew Walker, James J. Luby, Matthew D. Clark, Jason P. Londo, Lance Cadle-Davidson, Gan-Yuan Zhong
Toward The Elucidation Of Cytoplasmic Diversity In North American Grape Breeding Programs, Jonathan Fresnedo-Ramirez, Qi Sun, Chin-Feng Hwang, Craig A. Ledbetter, David W. Ramming, Anne Fennell, M. Andrew Walker, James J. Luby, Matthew D. Clark, Jason P. Londo, Lance Cadle-Davidson, Gan-Yuan Zhong
Agronomy, Horticulture and Plant Science Faculty Publications
Plants have an intriguing tripartite genetic system: Nuclear genome 9 Mitochondria 9 Plastids and their interactions may impact germplasm breeding. In grapevine, the study of cytoplasmic genomes has been limited, and their role with respect to grapevine germplasm diversity has yet to be elucidated. In the present study, the results of an analysis of the cytoplasmic diversity among 6073 individuals (comprising cultivars, interspecific hybrids and segregating progenies) are presented. Genotyping by sequencing (GBS) was used to elucidate plastid and mitochondrial DNA sequences, and results were analyzed using multivariate techniques. Single nucleotide polymorphism (SNP) effects were annotated in reference to plastid …
Towards An Open Grapevine Information System, A-F Adam-Blondon, M. Alaux, C. Pommier, D. Cantu, Z-M Cheng, Gr Cramer, C. Davies, S. Delrot, L. Deluc, G. Di Gaspero, J. Grimplet, A. Fennell Dr, Et. Al
Towards An Open Grapevine Information System, A-F Adam-Blondon, M. Alaux, C. Pommier, D. Cantu, Z-M Cheng, Gr Cramer, C. Davies, S. Delrot, L. Deluc, G. Di Gaspero, J. Grimplet, A. Fennell Dr, Et. Al
Agronomy, Horticulture and Plant Science Faculty Publications
Viticulture, like other fields of agriculture, is currently facing important challenges that will be addressed only through sustained, dedicated and coordinated research. Although the methods used in biology have evolved tremendously in recent years and now involve the routine production of large data sets of varied nature, in many domains of study, including grapevine research, there is a need to improve the findability, accessibility, interoperability and reusability (FAIR-ness) of these data. Considering the heterogeneous nature of the data produced, the transnational nature of the scientific community and the experience gained elsewhere, we have formed an open working group, in the …