Agronomy and Crop Sciences Commons^™

Graph Convolutional Network Using Adaptive Neighborhood Laplacian Matrix For Hyperspectral Images With Application To Rice Seed Image Classification, Jairo Orozco, Vidya Manian, Estefania Alfaro, Harkamal Walia, Balpreet K. Dhatt

Department of Agronomy and Horticulture: Faculty Publications

Graph convolutional neural network architectures combine feature extraction and convolutional layers for hyperspectral image classification. An adaptive neighborhood aggregation method based on statistical variance integrating the spatial information along with the spectral signature of the pixels is proposed for improving graph convolutional network classification of hyperspectral images. The spatial-spectral information is integrated into the adjacency matrix and processed by a single-layer graph convolutional network. The algorithm employs an adaptive neighborhood selection criteria conditioned by the class it belongs to. Compared to fixed window-based feature extraction, this method proves effective in capturing the spectral and spatial features with variable pixel neighborhood …

Harvest Aids Did Not Advance Maturity Of Non-Shatter Pennycress, Julija A. Cubins, Samantha Wells, Russ W. Gesch, Gregg A. Johnson, Maninder K. Walia, Ratan Chopra, M. David Marks, Rebecca D. Swenson, Katherine Anna Frels

Department of Agronomy and Horticulture: Faculty Publications

Reliance on summer annual crops in the Upper Midwest results in fallow land from late fall through early spring, providing opportunities to integrate winter crops, such as pennycress (Thlapsi arvense L.), onto the landscape. Pennycress agronomics have primarily been studied using unimproved wild-type lines prone to seed shatter, resulting in significant yield loss if not harvested early. However, high plant and seed moisture complicates harvest and seed storage. A new breeding line with a reducedshatter mutation made it possible to use harvest aids to reduce plant moisture without the risk of seed loss. The objectives of this study were …

Pollen-Mediated Gene Flow From Genetically Modified Herbicide Resistant Creeping Bentgrass, L. S. Watrud, E. H. Lee, A. Fairbrother, C. Burdick, J. R. Reichman, M. Bollman, M. Storm, G. King, P. K. Van De Water

IGC Proceedings (1977-2023)

Approximately 162 ha of multiple experimental fields of creeping bentgrass (Agrostis stolonifera L.) genetically modified for resistance to Roundup ®herbicide, were planted in central Oregon in 2002. When the fields flowered for the first time in the summer of 2003, a unique opportunity was presented to evaluate methods to monitor potential pollen-mediated gene flow from the experimental GM crop fields to compatible sentinel and resident plants that were located in surrounding, primarily non-agronomic areas.

Assessing The Risk Posed By Transgenic Virus-Resistant Trifolium Repens To Native Grasslands In Southeast Australia, R. C. Godfree, P. W. G. Chu, A. G. Young

IGC Proceedings (1977-2023)

In Australia, comprehensive environmental risk assessments must be performed on transgenic plants (GMOs) prior to their commercial release. A key element is the determination of whether the release of a particular GMO poses any weediness threat to the environment or other agricultural systems, which can occur by means of direct invasion or by introgression of transgenes into wild populations of the same or closely related species. For transgenic pasture plants this question could be of added importance because many of these species have been selected for traits encouraging long-term persistence and competitiveness in complex plant communities (Godfree et al., …

Belowground Meristem Populations As Regulators Of Grassland Dynamics, Harmony J. Dalgleish, D. C. Hartnett

IGC Proceedings (1977-2023)

Studies of plant populations are critical for linking organism to ecosystem-level phenomena and for understanding mechanisms driving responses to global change. In perennial grasslands, the below-ground population of meristems (the bud bank) plays a fundamental role in local plant population recruitment, persistence and dynamics. We explore two aspects of the bud bank in North American grasslands. It has been hypothesized that low variability in arid biomes is explained by meristem limitation, which constrains responses to pulses of high resource availability. Our research tests this hypothesis by comparing bud-bank populations across six sites in the United States that vary 3-fold in …

The Impact Of Vegetation Structure And Spatial Heterogeneity On Invertebrate Biodiversity Within Upland Landscapes, L. Cole, M. L. Pollock, D. Robertson, J. P. Holland, D. I. Mccraken

IGC Proceedings (1977-2023)

Livestock grazing influences vegetation structure and composition at both the patch and wider landscape scale (Milne et al., 1998), and this may have effects on upland invertebrate communities, which in turn influence bird abundance and distribution (Fuller & Gough, 1999; Cole et al., 2002). Of particular importance are open grasslands and wet flushes where invertebrates are abundant and more accessible to birds. However, there have been few studies of invertebrates associated with upland habitats, and most of these have focused on heather moorland, blanket bog, or very fine-scaled structure within grasslands (Dennis et al. 1997; 1998; 2001). This …

Lanza® Tedera Is Strongly Suppressed By Competition From Lolium Multiflorum And Is Best Adapted To Light-Textured Soils, Jesús Fernández-Habas, D. Real, Tom Vanwalleghem, Pilar Fernández-Rebollo

Grain and Other Field Crops Research Articles

Bituminaria bituminosa var. albomarginata, known as Tedera, is a promising forage for Mediterranean climates. An improved variety named LANZA® has been developed. Previous research suggests that soil water saturation in heavy-textured soils might affect its initial development. Competition from grasses could also compromise its successful establishment and persistence. We investigated the effects of soils with contrasting textures (loamy sand vs. clay) with a high soil water content and the competition from Lolium multiflorum on the development of LANZA® in a pot experiment. Dry mass (DM) production of LANZA® was strongly reduced (86%) when grown with L. multiflorum. LANZA® …

A Role For Heritable Transcriptomic Variation In Maize Adaptation To Temperate Environments, Guangchao Sun, Huihui Yu, Peng Wang, Martha Lopez‑Guerrero, Ravi V. Mural, Olivier N. Mizero, Marcin Grzybowski, Baoxing Song, Karin V. Van Dijk, Daniel P. Schachtman, Chi Zhang, James C. Schnable

Department of Agronomy and Horticulture: Faculty Publications

Background: Transcription bridges genetic information and phenotypes. Here, we evaluated how changes in transcriptional regulation enable maize (Zea mays), a crop originally domesticated in the tropics, to adapt to temperate environments.

Result: We generated 572 unique RNA-seq datasets from the roots of 340 maize genotypes. Genes involved in core processes such as cell division, chromosome organization and cytoskeleton organization showed lower heritability of gene expression, while genes involved in anti-oxidation activity exhibited higher expression heritability. An expression genome-wide association study (eGWAS) identified 19,602 expression quantitative trait loci (eQTLs) associated with the expression of 11,444 genes. A …

Towards A Comparative Map Of White Clover (Trifolium Repens) And Barrel Medic (Medicago Truncatula), M. Febrer, G. Jenkins, M. T. Abberton, D. Milbourne

IGC Proceedings (1977-2023)

Grassland is of pivotal importance to the Irish agricultural industry. This dependence of grass is reflected in the large proportion of land area under grass, approx. 80% of the total land acreage in Ireland. The presence of white clover (Trifolium repens L.) in grassland significantly improves the overall nutritional value of the forage by increasing the relative amounts of nitrogen present. Genetic improvement of white clover through breeding of varieties should increase the productivity of grasslands. Advances in plant biotechnology offer the possibility of developing tools that will radically enhance our ability to breed improved plant varieties. The objective …

Role Of The Banyuls(Ban) Gene From Arabidopsis Thaliana In Transgenic Alfalfa Expression Of Anthocyanins And Proanthocyanidins, S. M. Hesamzadeh Hejazi, Sergio Arcioni, F. Paolocci

IGC Proceedings (1977-2023)

Condensed tannins (CTs) are flavonoid oligomers, many of which have beneficial effects on animal (bloat safe) and human health. The BAN gene encodes anthocyanidin reductase (ANR), an enzyme proposed to convert anthocyanidins to their corresponding 2,3-cis-flavan-3-ols (Xie et al., 2003). Ectopic expression of BAN in Alfalfa transgenic foliage results in accumulation of CTs. Thus, it has been assumed that the BAN gene also acts in starter units for the condensation of tannins in Alfalfa.

Clover Astra: A Web-Based Resource For Trifolium Est Analysis, G. C. Spangenberg, T. Sawbridge, E. K. Ong, C. G. Love, T. A. Erwin, E. G. Logan, D. Edwards

IGC Proceedings (1977-2023)

White clover (Trifolium repens L.) is a major temperate forage legume.

Controlled Flowering Project For Lolium Perenne At Agresearch: An Overview, I. Kardailsky, B. Veit, N. Forester, M. Gagic, K. Richardson, Marty J. Faville, G. Bryan

IGC Proceedings (1977-2023)

Ryegrass (Lolium perenne) is an important forage crop in New Zealand. The work presented here has the goal of developing a system for complete and arbitrary control of the transition from vegetative to floral development. For this, we have pursued an integrated approach utilising genomics with both forward and reverse genetics. Like other model plants, photoperiodic and vernalization pathways are presumed to be operating in ryegrass and control the activity of the meristem identity/floral patterning genes. The candidate gene approach targeting the photoperiodic pathway is described in an accompanying abstract (Gagic et al.). Other candidate genes include …

Monitoring Of Gene Expression Profiles And Identification Of Candidate Genes Involved In Drought Tolerance In Festuca Mairei With Cdna-Aflp, J. P. Wang, S. S. Bughrara

IGC Proceedings (1977-2023)

Drought stress is one of the most complex environmental constraints on plants. Response of plant to drought stress is manifested by various changes in physiological and metabolic processes, which are reflected at the molecular level. cDNA-amplified fragment length polymorphism (cDNA-AFLP) is a high-throughput transcript profiling technique for temporal and spatial gene expression analysis (Bachem et al., 1996). To understand the molecular genetic basis of drought tolerance of grasses, we applied the cDNA-AFLP procedure to identify the genes responding to drought stress of Festuca mairei (Fm), which showed a xeriphytic adaptation (Marlatt et al., 1997).

Gene Discovery And Molecular Dissection Of Fructan Metabolism In Perennial Ryegrass (Lolium Perenne), J. Chalmers, A. Lidgett, X. Johnson, K. Terdich, N. Cummings, Y. Y. Cao, K. Fulgueras, M. Emmerling, T. Sawbridge, E. K. Ong, A. Mouradov, G. C. Spangenberg

IGC Proceedings (1977-2023)

Fructans are the main soluble carbohydrate stored in up to a third of the vegetation of the earth, including the economically important temperate grasses. Fructans are polymers of fructose attached to a sucrose precursor. Perennial ryegrass (L. perenne L.) accumulates fructans of the inulin series, inulin neoseries and levan neoseries. Four enzymes are required to produce fructans of this profile: 1-SST (sucrose:sucrose 1- fructosyltransferase), 1-FFT (fructan:fructan 1-fructosyltransferase), 6G-FFT (6-glucose fructosyltransferase) and 6-FFT (fructan:fructan 6-fructosyltransferase) or 6-SFT (sucrose:fructan 6-fructosyltransferase) (Figure 1). Fructan biosynthetic enzymes have evolved from invertases and thus it is argued that fructan metabolism is an extension …

Isolation And Characterization Of A Cbf Gene From Perennial Ryegrass (Lolium Perenne L.), Y. Xiong, S. Fei

IGC Proceedings (1977-2023)

Maximum freezing tolerance of many temperate plant species is achieved after exposure to a period of non-freezing low temperatures, a phenomenon called “cold acclimation”. Multiple mechanisms appear to operate in conferring freezing tolerance in plants. The discovery of a class of transcription factor genes, CBF genes (C-repeat binding factor), in Arabidopsis demonstrated that CBF genes can serve as ‘Master switches’ to activate downstream cold-related (COR) genes during cold-acclimation (Liu et al., 1998). They act by binding to the core sequence (CCGAC) which is present in COR genes and thus activate the expression of COR genes and enhance …

Phenotypic Variation Within Local Populations Of Meadow Fescue Shows Significant Associations With Allele Frequencies At Aflp Loci, S. Fjellheim, Å. B. Blomlie, P. Marum, O. A. Rognli

IGC Proceedings (1977-2023)

To identify markers useful for Marker Assisted Selection (MAS), mapping families are usually constructed and used for Quantitative Trait Loci (QTL) mapping. Association mapping offers an alternative strategy for marker development using already characterized germplasm, preferably from natural populations. Simultaneous phenotypic and molecular screening of gene bank accessions can reveal associations between molecular marker alleles and phenotypic traits, and lead to a more targeted construction of mapping families for fine-mapping. In this investigation, we combine molecular (AFLP) and phenotypic data of 15 Norwegian local populations and 5 Nordic cultivars in order to identify markers associated with phenotypic traits of interest.

Diversity Of Diet Composition Decreases With Conjoint Grazing Of Cattle With Sheep And Goats, A. M. Nicol, M. B. Soper, A. Stewart

IGC Proceedings (1977-2023)

Conjoint or mixed grazing can affect the diet selected by each species (Nicol & Collins, 1990). Diet similarity coefficients are often used to compare pairs of diets (Krebs, 1999). However this approach is awkward when a number of contrasts are required in a multifactorial comparison. Species diversity is a descriptor of a particular environment. Many models provide an estimate of species diversity, the most common of these being a log-normal distribution (Tokeshi, 1996). We tested whether this model could be applied to dietary components selected from a pasture, and thus provide a coefficient of dietary diversity for the individual diets …

A Simple Vegetation Criterion (Ndf Content) May Account For Diet Choices Of Cattle Between Forages Varying In Maturity Stage And Physical Accessibility, Cécile Ginane, R. Baumont

IGC Proceedings (1977-2023)

The management of extensively grazed pastures requires an understanding and prediction of the diet choices of herbivores grazing on vegetation that is qualitatively (maturity stage) and quantitatively (biomass, sward height) heterogeneous. The Optimal Foraging Theory (OFT, Stephens & Krebs, 1986), bases its predictions on the relative energy intake rate (EIR) of forages. However, as EIRs are difficult to assess at pasture and are subject to wide intra- and inter-individual variations, another vegetation criterion was sought (accessibility, quality), by-passing the animal's influence, to predict cattle diet choices quantitatively.

Spatial Scale Of Heterogeneity Affects Diet Choice But Not Intake In Beef Cattle, S. Mark Rutter, J. E. Cook, K. L. Young, R. A. Champion

IGC Proceedings (1977-2023)

Previous research has shown that sheep (Champion et al., 1998) and dairy cattle (Nuthall et al., 2000) have a partial preference for clover of 70%, and achieve higher daily intakes when offered grass and clover as separate but adjacent monocultures compared with animals grazing mixed swards. This intake benefit could be utilised to increase intake and production on farms by grazing from adjacent strips of the two herbages. This study aimed to establish the minimum strip width required to achieve the benefits of monocultures.

Is Biodiversity Declining In The Traditional Haymeadows Of Skye And Lochalsh, Scotland?, G. E. D. Tiley, D. G. L. Jones

IGC Proceedings (1977-2023)

Species-rich haymeadows have developed on crofts in the Isle of Skye and Lochalsh Districts of north-west Scotland as a result of a century or more of traditional land use. This has involved long rotations of late cutting for hay with aftermath grazing by cattle and short breaks for cropping. The traditional haymeadows are increasingly coming under threat from changes taking place in the countryside. A survey of the main haymeadows still remaining in Skye and Lochalsh was carried out during 2003 to assess the current botanical composition, management and conservation value, and to compare with earlier surveys.