Agricultural Science Commons^™

Drought Susceptibility Index; A Preferred Criterion In Screening For Tolerance In Soybean, Muhammad Zeshan Zafer, Muhammad Hammad Nadeem Tahir, Muhammad Amir Bakhtavar, Essam Darwish, Mahmood Alam Khan, Zulqurnain Khan, Chahat Fatima, Ayesha Aftab, Shifa Ur Rahman, Shoaib Ur Rehman

Journal of Bioresource Management

Soybean (Glycine max L.) yield and yield related traits are constrained by drought. Adaptation of soybean to changing environment could be improved by exploitation and introgression of diverse germplasm in breeding program. In present study, the response to drought conditions, especially at flowering stage, was evaluated to determine the potential soybean germplasm for future soybean breeding programs in Pakistan. Field experiment was conducted under two water regimes i.e. well-water and water-limited, to assess the effect of drought in seed yield and yield related traits. Although, drought led to overall reduction of ~15 % in thousand seed weight but still …

Predicting Site‑Specific Economic Optimal Nitrogen Rate Using Machine Learning Methods And On‑Farm Precision Experimentation, Alfonso De Lara, Taro Mieno, Joe D. Luck, Laila A. Puntel

Department of Agronomy and Horticulture: Faculty Publications

Applying at the economic optimal nitrogen rate (EONR) has the potential to increase nitrogen (N) fertilization efficiency and profits while reducing negative environmental impacts. On-farm precision experimentation (OFPE) provides the opportunity to collect large amounts of data to estimate the EONR. Machine learning (ML) methods such as generalized additive models (GAM) and random forest (RF) are promising methods for estimating yields and EONR. Twenty OFPE N trials in wheat and barley were conducted and analyzed with soil, terrain and remote-sensed variables to address the following objectives: (1) to quantify the spatial variability of winter crops yield and the yield response …

A Plea For Scale, And Why It Matters For Invasive Species Management, Biodiversity And Conservation, Nicholas A. Mcmillan, Samuel D. Fuhlendorf, Craig A. Davis, Robert G. Hamilton, Landon. K. Neumann, Samantha M. Cady

Department of Agronomy and Horticulture: Faculty Publications

1. Invasive species are suspected to be major contributors to biodiversity declines worldwide. Counterintuitively, however, invasive species effects are likely scale dependent and are hypothesized to be positively related to biodiversity at large spatial scales. Past studies investigating the effect of invasion on biodiversity have been mostly conducted at small scales (<100 m²) that cannot represent large dynamic landscapes by design. Therefore, replicated experimental evidence supporting a negative effect of invasive plants on biodiversity is lacking across many landscape types, including large grasslands.

2. We collected data across eight large (333–809 ha) grassland landscapes managed with pyric herbivory—that is the recoupling …

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Soil Depth And Geographic Distance Modulate Bacterial Β-Diversity In Deep Soil Profiles Throughout The U.S. Corn Belt, Lucas Dantas Lopes, Stephanie L. Futrell, Emily E. Wright, Gerasimos J. Danalatos, Michael J. Castellano, Tony J. Vyn, Sotirios V. Archontoulis, Daniel P. Schachtman

Department of Agronomy and Horticulture: Faculty Publications

Understanding how microbial communities are shaped across spatial dimensions is of fundamental importance in microbial ecology. However, most studies on soil biogeography have focused on the topsoil microbiome, while the factors driving the subsoil microbiome distribution are largely unknown. Here we used 16S rRNA amplicon sequencing to analyse the factors underlying the bacterial β-diversity along vertical (0–240 cm of soil depth) and horizontal spatial dimensions (~500,000 km²) in the U.S. Corn Belt. With these data we tested whether the horizontal or vertical spatial variation had stronger impacts on the taxonomic (Bray-Curtis) and phylogenetic (weighted Unifrac) β-diversity. Additionally, we …

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 …

Asparagus Breeding: Future Research Needs For Sustainable Production, Daniel Drost

Plants, Soils, and Climate Faculty Publications

Productivity in asparagus (Asparagus officinalis L.) is determined in part by (1) the selection of superior, adaptive genetics, (2) matching the selected genetics to the production environment, and (3) managing the crop production system in ways to maximize harvest potential that are sustainable, profitable, and efficient. Over the last 100 years, a considerable effort by asparagus researchers has gone into breeding superior genetic lines, testing those in numerous locations, and studying how asparagus responds to a multitude of inputs (fertilizers, irrigation, fungicides, herbicides, insecticides). Farmers worldwide have benefited from all of these improvements. However, as we look to the …

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 …

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.

Alternative Land Use Options For Philippine Grasslands: A Bioeconomic Modeling Approach Using The Wanulcas Model, D. B. Magcale-Macandog, E. Abucay, P. A. B. Ani

IGC Proceedings (1977-2023)

In the Philippines, pure grasslands occupy 1.8 million ha and another 10.8 million ha (33% of the country’s total land area) is under extensive cultivation mixed with grasslands and scrub. Most of these grasslands are under-utilised and dominated by Imperata cylindrica. Imperata grasslands generally represent areas of degraded soils that are acidic, low in organic matter and susceptible to erosion. However, conversion of these grassland areas into upland farms planted to annual crops and perennial trees is proliferating at a fast rate. This is triggered by the interacting factors of rapidly increasing population, the system of landholding, scarcity of …

Forage Development In The Nepal Mid-Hills: New Perspectives, A. D. Robertson

IGC Proceedings (1977-2023)

Nepali hill farming communities are typically poor and remote, and are currently severely affected by conflict. The challenge is to define simple approaches which can generate results within this context. Livestock are central to livelihoods and to the sustainability of farming, with rain-fed agriculture dependent on inputs of manure-based compost. Stall feeding has increased dramatically with the adoption of community forestry and general preclusion of grazing. A broad landscape approach to forage development is increasingly being adopted, with concurrent on-farm interventions, such as intercropping and back-yard forage, and off-farm interventions, such as landslide stabilisation with forages, development of forest understory, …

How To Simplify Tools For Natural Grassland Characterisation Based On Biological Measures Without Losing Too Much Information?, P. Ansquer, P. Cruz, J. P. Theau, E. Lecloux, M. Duru

IGC Proceedings (1977-2023)

In marginal areas, such as the Pyrenees, natural grasslands are the only available resource for livestock feeding. Despite this, there is a lack of simple and efficient tools for advisers to aid the management of the complex vegetation of these grasslands. Therefore, we tested an approach derived from functional ecology, to construct such tools: using biological traits to inform on the agronomic characteristics and the way farmers’ practices act on them (Ansquer et al., 2004). Nevertheless, the required protocol of measurement is still time-consuming and difficult. In this paper, we test different ways of simplifying this protocol by reducing …

Herders And Wetland Degradation In Northern Cameroon, E. Tedonkeng Pamo, F. Tendonkeng, J. R. Kana

IGC Proceedings (1977-2023)

Livestock rearing in Northern Cameroon is carried out under two majors systems: the nomadic and the transhumance production systems (Pamo & Pamo, 1991). Nomadism is the practice of wandering from place to place, while transhumance involves seasonal displacement of flocks from one area to another by herders. These production systems involved large grazing areas, which may encompass different ecosystems. The Yaére, the only wetland of the northern Cameroon, is the major dry season grazing lands for livestock and wildlife. The main characteristic of this wetland is that the whole area is excluded from grazing during the growing season as a …

Recombination Hotspots In Soybean [Glycine Max (L.) Merr.], Samantha Mcconaughy, Keenan L. Amundsen, Qijian Song, Vince Pantalone, D. Hyten

Department of Agronomy and Horticulture: Faculty Publications

Recombination allows for the exchange of genetic material between two parents, which plant breeders exploit to make improved cultivars. This recombination is not distributed evenly across the chromosome. Recombination mostly occurs in euchromatic regions of the genome and even then, recombination is focused into clusters of crossovers termed recombination hotspots. Understanding the distribution of these hotspots along with the sequence motifs associated with them may lead to methods that enable breeders to better exploit recombination in breeding. To map recombination hotspots and identify sequence motifs associated with hotspots in soybean [Glycine max (L.) Merr.], two biparental recombinant inbred lines …

The Investigation Of Flowering Control In Late/Rare Flowering Lolium Perenne, S. Byrne, I. S. Donnison, L. J. Mur, E. Guiney

IGC Proceedings (1977-2023)

Flowering in Lolium perenne (perennial ryegrass) results in reduced digestibility and its inhibition would enhance forage quality. Flowering regulation has been well studied in Arabidopsis thaliana (Simpson and Dean, 2002) and orthologs of Arabidopsis flowering genes underlying heading date Quantitative Trait Loci (QTL) have been identified in rice (Yano, M et al., 2000). However it is not clear yet how universally applicable such studies are to Lolium. The project goals are to characterise the gene expression profiles of late/rare flowering L. perenne plants to determine factors affecting flowering and to map the genes involved in the flowering process. Initial …