Agronomy and Crop Sciences Commons^™

Enhancing Selection Intensity With High-Throughput Phenotyping Data In Plant Breeding, Ashmita Upadhyay

Graduate Theses and Dissertations

Genomic prediction (GP) has proven to be an essential tool to accelerate the cultivar development pipeline by predicting the performance of un-phenotyped lines in the field of plant breeding. However, the prediction accuracy is bounded by the heritability of the target trait, limiting the efficiency of the single-trait GP model. To overcome the limitation, a multi-trait genomic prediction model using high-throughput phenotyping (HTP) data can be used to leverage secondary traits to boost the predictive ability of the target trait. This study aimed to assess the efficiency of the multi-trait (MT)- GP model powered by HTP derived secondary traits in …

Diversity Of Gibberellin 2-Oxidase Genes In The Barley Genome Offers Opportunities For Genetic Improvement, Jingye Cheng, Yong Jia, Camilla Hill, Tianhua He, Ke Wang, Ganggang Guo, Sergey Shabala, Meixue Zhou, Yong Han, Chengdao Li

Grain and Other Field Crops Research Articles

Introduction

Gibberellin (GA) is a vital phytohormone in regulating plant growth and development. During the “Green Revolution”, modification of GA-related genes created semi-dwarfing phenotype in cereal crops but adversely affected grain weight. Gibberellin 2-oxidases (GA2oxs) in barley act as key catabolic enzymes in deactivating GA, but their functions are still less known.

Objectives

This study investigates the physiological function of two HvGA2oxgenes in barley and identifies novel semi-dwarf alleles with minimum impacts on other agronomic traits.

Methods

Virus-induced gene silencing and CRISPR/Cas9 technology were used to manipulate gene expression of HvGA2ox9 and HvGA2ox8ain barley and RNA-seq …

Association Mapping For Water Use Efficiency In Soybean Identifies Previously Reported And Novel Loci And Permits Genomic Prediction, Siva K. Chamarthi, Larry C. Purcell, Felix B. Fritschi, Jeffrey D. Ray, James R. Smith, Avjinder S. Kaler, C. Andy King, Jason D. Gillman

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Soybean is a major legume crop cultivated globally due to the high quality and quantity of its seed protein and oil. However, drought stress is the most significant factor that decreases soybean yield, and more than 90% of US soybean acreage is dependent on rainfall. Water use efficiency (WUE) is positively correlated with the carbon isotopic ratio ¹³C/¹²C (C13 ratio) and selecting soybean varieties for high C13 ratio may enhance WUE and help improve tolerance to drought. Our study objective was to identify genetic loci associated with C13 ratio using a diverse set of 205 soybean maturity …

Broad-Spectrum Resistance To Fungal Foliar Diseases In Wheat: Recent Efforts And Achievements, Amira M.I. Mourad, Asmaa A.M. Ahmed, P. Stephen Baenziger, Andreas Börner, Ahmed Sallam

Department of Agronomy and Horticulture: Faculty Publications

Wheat (Triticum spp.) is one of the most important cereal crops in the world. Several diseases affect wheat production and can cause 20-80% yield loss annually. Out of these diseases, stripe rust, also known as yellow rust (Puccinia striiformis f. sp. tritici), stem rust (Puccinia graminis f. sp. tritici), leaf rust (Puccinia recondita), and powdery mildew (Blumeria graminis f. sp. tritici) are the most important fungal diseases that infect the foliar part of the plant. Many efforts were made to improve wheat resistance to these diseases. Due to the continuous advancement in …

Investigating Arbuscular Mycorrhizal Fungi-Cover Crop Interactions To Improve Sustainable Agricultural Practices, Isabel M. Zanartu, Connor Morozumi, Natalie Christian

The Cardinal Edge

Arbuscular mycorrhizal fungi (AMF) are fungal species that form beneficial relationships with plants. AMFs are known to help crops acquire important nutrients like nitrogen and phosphorus in the soil, and in return the plants provide carbon to the fungi. At least 80% of all plants partner with AMFs including staple crops such as rice, corn, wheat and soybeans. With so many plants likely relying on AMFs, current farming practices such as planting in monocultures and fallow overwintering may limit these relationships. On top of this, climate change challenges the reliability of these practices in the future. One sustainable agricultural practice …

How Does Herbicide Resistance Change Farmer’S Weed Management Decisions? Evidence From The Roundup Ready Experiment, Huichin Sun, Terrance Hurley, George B. Frisvold, Katherine Dentzman, David Ervin, Wesley J. Everman, Jeffrey Gonsalus, Jason K. Norsworthy, Michae Owen

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Adoption of diverse weed management practices is viewed as essential for slowing the spread of herbicide-resistant (HR) weeds. Yet, adoption of diverse tactics has remained low, while there has been explosive growth of resistant weeds. This study analyzes U.S.-farm-level data to identify factors affecting adoption of diverse weed management practices. This study uses directed acyclic graphs (DAGs) to consider how practice adoption is influenced by different causal pathways between farmer and farm characteristics and farmer awareness of and concern over HR weeds. This study then uses multiple regression analysis to estimate the direct and indirect pathways that influence practice adoption. …

Disentangling Genotype And Environment Specific Latent Features For Improved Trait Prediction Using A Compositional Autoencoder, Anirudha Powadi, Talukder Zaki Jubery, Michael C. Tross, James C. Schnable, Baskar Ganapathysubramanian

Department of Agronomy and Horticulture: Faculty Publications

In plant breeding and genetics, predictive models traditionally rely on compact representations of high-dimensional data, often using methods like Principal Component Analysis (PCA) and, more recently, Autoencoders (AE). However, these methods do not separate genotype-specific and environment-specific features, limiting their ability to accurately predict traits influenced by both genetic and environmental factors. We hypothesize that disentangling these representations into genotype-specific and environment-specific components can enhance predictive models. To test this, we developed a compositional autoencoder (CAE) that decomposes high-dimensional data into distinct genotype-specific and environment-specific latent features. Our CAE framework employed a hierarchical architecture within an autoencoder to effectively separate …

Industrial Hemp Biomass Negatively Affected By Herbicide Drift From Corn And Soybean Herbicides, Milos Zaric, Bruno Canella Vieira, Barbara Houston, Guilherme Sousa Alves, Samuel E. Wortman, Julie A. Peterson, Greg R. Kruger

Department of Agronomy and Horticulture: Faculty Publications

The establishment of industrial hemp (Cannabis sativa L.) fields near row crops has raised concerns about the potential adverse effects of herbicide drift on hemp production. This study examined hemp susceptibility to drift of herbicides registered for use in corn and/or soybeans. Herbicide solutions (2,4-D, dicamba, glufosinate, glyphosate, imazethapyr, lactofen, mesotrione) were applied separately in the wind tunnel (3.6 m s⁻¹ airspeed), simulating drift scenarios, with conventional TP95015EVS (TP) and air inclusion AI95015EVS (AI) flat fan nozzles calibrated to deliver 140 L ha⁻¹ carrier volume at 230 kPa. Mylar cards and hemp plants (20–25 cm tall) were placed …

Effect Of Cereal Rye Cover Crop Termination Timings On Weed Control And Corn Yield Under A Two-Pass Herbicide Program, Amar S. Godar, Jason K. Norsworthy, Tom Barber

Crop, Soil and Environmental Sciences Faculty Publications and Presentations

Cover crops, including cereal rye, are generally known to suppress weeds in various cropping systems; however, research on their effective use is lacking. This study investigated the effects of different cereal rye termination timings on weed control and corn performance in a two-pass herbicide program across 5 site-years (2021–2023) in Arkansas, USA. The herbicide program consisted of one application at cereal rye (Secale cereale) termination (cereal rye environment) or at corn (Zea mays) planting (conventional system) and another at the V4 corn stage. Palmer amaranth (Amaranthus palmeri) at V4 corn was better controlled in …

Towards An Ideal Seed Coating, J M. Scott

IGC Proceedings (1977-2023)

Coated pasture seeds have been formulated in the past based largely on "trial and error" with relatively few objective criteria being employed to define desirable formulations, A description of desirable propelties of various layers of seed coatings and of the seeds themselves is presented.

Lolium Endophyte Viability: Effect Of Seed Storage, M P. Rolston, J R. Crush, M D. Hare, K K. Moore

IGC Proceedings (1977-2023)

The effects of seed storage on the endophyte Acremonium lolii in ryegrass (Lolium perenne L.) were evaluated over 7 years. The long• term effects of 4 seed moisture contents (SMC) 8.6-13.1 %: tempemture (ambient, 5, O, -15°C) 'aitd packaging types: calico, polyethylene fi,Jm. 9-140 µm, and aluminium-polyethylene (AIP) on endophyte viability were assess·ed. • Endophyte viability was maintained by lower seed moisture content and low temperatures. In ambient warehouse conditions endophyte viability declined to zero in 12 months in calico bags,' but was maintained for 3 years at 8.6% SMC in AIP: • Endophyte viability was maintained for …

Effect Of Dormancy-Releasing Treatments On Germination Of Bahiagrass Seed, J. Jeffrey Mullahey, D S. Fisher

IGC Proceedings (1977-2023)

Low seed germination and dormant seed in bahiagrass (Paspalum nonatutum Flugge.) necessitate high seeding rates for successful pasture establishment. A study of dormancy-releasing treatments and age of seed on germination of bahiagrass was conducted in an incubator at the Southwest Florida Research and Education Center near Immokalee, Florida. Five seed treatments (Crop-Start (Solid Matrix Seed Priming, Kamterter Products Inc., Lincoln, NB), potassium nitrate (KNO3), heat/humidity, palea removed, and a check), 2 cullivars (Pensacola, Tifton 9) of bahiagrass and 2 ages (10 and 16 months) of seed were used. A significant (P<0.05) age ·x treatment interaction occurred for all response variables. Based on total germination at 28 days, % dormant seed and rate of germination, Crop-Start and heat/humidity were consistently the best treatments. Additional research on germination with dormancy-releasing treatments is needed to study the Interaction of seed age and bahiagrass cultivar.

Weed Seed Contamination: Use Of A Seed Testing Database To Identify Processing Limitations, J S. Rowarth, M P. Rolston, A A. Johnson

IGC Proceedings (1977-2023)

A computerised database maintained by the Official Seed Testing Station of New Zealand provided the opporlunity to survey weed seed contamination in clover and grass seed-lots. Broad-leaf weeds such as Slierardia arvensis, Stellaria ,nedia and Chenopodium album were the major contaminants in Trifolium repens seed-lots. In grass seed-lots the main contaminants were seeds of other grasses such as Bromus hordaeceus, Vulpia spp. and Holcus lanatus. Weed seeds were found to be a major reason for downgrading or rejection from certification of clover and grass seed-lots in New Zealand; this reflects strict quality control measures.

An Investigation In To The Effect Of Some Factors On The Germination Of Erodium Seeds, Myrna Johnston, Alfredo Olivares, Gladys Fernandez

IGC Proceedings (1977-2023)

Erodiurn seeds present variable dormancy in and even within each species. Thus, it is important to know the factors that determine this variation as related to the persistence of its species. E. rnoschatmn and E. rnalacoides seeds were collected at the end of the annual cycle at La Rinconada de Maipli (33°28'S and 7S050'W). Effects of seed sour.ce (collecting in 1986, 1988 and 1990), age (keeping seeds under laboratory conditions) and maternal factors (cutting plants at early flowering) were analysed. Seeds were tested for germination capacity and germination rate at a constant temperature of 15°C on Petri dishes provided with …

Long-Term Seed Dormancy In Poa Pratensis L. Northern Norway, Trygve S. Aamlid, Dagfinn Arntzen

IGC Proceedings (1977-2023)

Inadequate gennination has often been obseived when planting Poa pratensis L. cv. Lavang (69°N) in northern Norwegian grasslands. This investigation was intended to elucidate whether this was due lo long­term seed dormancy, Seed-lots grown in different years in northern and southern Norway and stored at O-to•c, were germinated in Jakobsen­type germinators al various combinations of temperature and light. Significant dormancy was expressed at 21 °C even after 10 years of storage. Al this constant temperature, germination was promoted by 8 h fluorescent light compared with darkness and continuous light. Al 21/ I 2°C alternating temperature, seed genninated well irrespective of …

Seed Vigour In Lucerne And White Clover, Y R. Wang, J G. Hampton

IGC Proceedings (1977-2023)

Accelerated ageing (AA) was used to assess the seed vigour of 5 lucerne (Medicago sativa L, cv. Wairau) and 8 white clover (Trifolium repens L. cv. Grasslands Huia) seed-lots. Germination prior to AA ranged from 86-94% and 87-94% for the lucerne and white clover seed-lots respectively. All seed-lots hl\d been harvested in 1988 and were certified either as basic or first generation. Germination after 72 h at 40:t0.5°C (AA test) ranged frcim 31-76% for the lucerne seed­lots and 15-56% for che white clover seed-lots, indicating significant differences in seed.vigour among lots of both species. Time of ageing influenced …

Growing Methods For The Morphological Assessment Of White Clover Cultivars Purity, J G. Hampton, E J. Musukwa

IGC Proceedings (1977-2023)

Three growing methods (field sward, field spaced plants, glasshouse plants) were compared for the morphological assessment of white clover (Trifolium repens L.) cultivar purity. Three cerlified (breeders, basic and first generation) seed-lots of cv. Grasslands Kopu and one first generation Kopu seed lot which had been mixed with seed of another cultivnr (10:1) were used to generate data. After analysis of variance (ANOVA), significant (P<0.05) reductions from the breeders seed lot siandnrd for leaf size, stolon number and leaf length/width ratio were recorded for the mixed seed· 101 in nil three growing methods, and for petiole length with the sward method only. With the glasshouse and spaced-plant melhods, slolon numbers of the basic and first generation seed-lots were reduced (P<0.05), while leaf size was lower (P<0.05) for the first generation seed-lot in lhe glasshouse. However, under OECD certification requirements, leaf size of the mixed seed lot was the only characler for which "off types" were detecled. Data coefficients of variation were no greater for the glasshouse method than the required OECD plot-test method.

Importance Of Tropical Pasture Seed Quality And Factors Affecting It In Smallholder Farming System, H F. Chin, C C. Wong

IGC Proceedings (1977-2023)

Most tropical pastures are associated with and confined to smaJlholder animal production in developing countries of the tropics, with the exception of Australia. At present, tropical pasture seeds are very variable and poor in quality, as tropical herbage seed production is relatively new compared with that for temperate systems. Many tropical species are relatively wild and have yet to be domesticated and selected for pasture use, let alone for seed production characteristics. The unfavourable production and storage environment of the wet tropics, coupled with a lack of appropriate technology, also contributes towards poor quality in tropical pasture seeds. In this …

The Benefits Of Seed Quality In Intensive Temperate Forage Systems, Jeffrey J. Steiner

IGC Proceedings (1977-2023)

Seed quality has traditionally been considered to consist of two components: physiologic and genetic quality. The benefits of using high quality seeds have been widely documented and are generally not questioned. These henefits came about as a result of a first­generation of seed quality aware11ess which began more than a century ago. In intensive temperate forage production systems, the producer usually has a ready supply of high-quality seeds available for purchase. For the consumer, seed quality is not a major constraint to system productivity, However, many forage producers are not realising all of the potential benefits from using high quality …

New Realities For The Management Of Tussock Grasslands In New Zealand, I.G C. Kerr

IGC Proceedings (1977-2023)

Concerns about the potential demise of the tussock grasslands of the Soulh Island of New Zealand have been well recorded in the scientific and official literature. Little effective action has been taken to arrest the process of land degradation that has occurred during the 125 years of utilisation of !he tussock grasslands for pastoralism. A substantial decline in the pastoral productivity and conservation value of the "unimproved" tussock grasslands has been the result, Much of the cause has been the failure of the administrators and the occupiers of the high country to understand, and act on, the evidence. Occupiers and …

Integration Of Recreation With Pastoral Use And Conservation In The High Country Of South Island, New Zealand, P H. Murray, D M. Robertson, C R. Mason

IGC Proceedings (1977-2023)

Over 3 000 000 ha of the South Island high country is Crown (i.e. Govemmcnt)-owned land, held under pastoral lease or conservation estate. There is increasing pressure from recreationists for access to land under both tenures. Permits from Crown agents, with agreement from land occupiers, are required for commercial recreation. Access for non-commercial recreation on pastoral lease land is generally through direct negotiation with the lessee. Conflicts between high country users are occurring where recreation pressure is greatest. A case study in the Remarkables Range near the mountain resort of Queenstown, shows domination by the primary users (pastoral lessees and …

Tradition And Pastoral Sustainability- An Exercise In The Applied Human Ecology Of Mountain Rangelands, David Pitt

IGC Proceedings (1977-2023)

The paper presents the case for regarding some traditional practices and customs as a ba��e for sustainable development in winter cold temperate rangeland pastoralism, The emphasis is on the social forms which maintain a system in which low intensity production, usufruct, kinship dynamics, co-operation, environmentally friendly practices and nomadism are maintained in the face of extreme outside pressures, A typology is elaborated including five situations: independence, coexistence, fluctuation, absorption and interaction. Case studies _are presented from the Middle East, Andes, North Africa, the Alps, the Himalaya and the former Soviet Union. Although these situations are basically historical, or at best …

Integration Of Pastoral And Non-Pastoral Uses On Temperate Rangelands With Cold Winters In Developed Countries, T J. Maxwell, W A. Laycock

IGC Proceedings (1977-2023)

The demands of the relatively wealthy and sophisticated societies of developed countries, with their substantial amounts of leisure time and discretionary income, are having an increasing impact on temperate rangelands in a variety of ways. Some parts of these societies are concerned to protect the landscapes, habitats, wildlife and solitude that can be found there, and wish to constrain any further development within these ecosystems; others also wish .to gain ready access to these resources for hunting, recreation and sport and believe that this requires the exclusion of domesticated livestock. Temperate rangelands are frequently used as water catchments and some …

Effects Of Date Of Harvest On Yield And Quality Of Meadow Fescue Seed, Uwe Simon

IGC Proceedings (1977-2023)

A seed-shattering-resistant cultivar and a normal cultivar of meadow rescue (Festuca pratensis Huds.) were harvested for seed 10 times in regular intervals during a period of 30 days, The effects of harvesting time on yield, water content, germination and weight of seeds, and on costs of seed processing were studied in the 2 types of cultivar. Yield losses due to premature harvest were greater than losses due to delayed harvest. Seed losses due to shattering were smaller in the shattering-resistant cultivar compared with the normal cultivar. The water content of the seeds decreased with advancing maturity, from =50% to .. …

After-Effects Of Grass Seed Production On Subsequent Field Crops, Uwe Simon

IGC Proceedings (1977-2023)

Forage grasses grown for the production of seed are usually components of a crop rotation. The after-effects of 3 grass species compared with 4 crop species on the yields of 5 field crops in the first and second year after grass seed harvest were investigated. Significant differences between the grass species, and between grasses and other field crops on subsequent crops, and between the subsequent crops in their reactions to the preceding crops were obvious in both years after grass seed harvest, Annual and perennial ryegrass excited the most positive effects on subsequent crop yields. Corn and sugarbeets responded particularly …

A New Power Airflow Harvester Improves Grass Seed Yield And Quality In Central Queensland, Australia, J H. Wildin, Dingfa Zhou, A Dobson

IGC Proceedings (1977-2023)

Most perennial tropical grasses produce new seedheads over a period extending up to 4 weeks, Seeds mature and ripen up to 4 weeks after inflorescence emergence. The dilemma for seed producers using one­pass harvesting has been to time the harvesting operation to maxmise. recovery of mature seed, Harvested immature seeds and inert material adversely affect seed purity and germination tests. Light fluffy seeds such as buffel and bluegrasses are generally difficult to harvest with grain crop harvesters, and paddle beater harvesters have been used for simplicity and economy. Over the last 3 years, tractor-mounted brush harvesters using 4 rows of …

Evaluation And Development Of Brush Harvesting For Chaffy-Seed Grasses In Queensland, Australia, T A. Jensen, D S. Loch, B G. Robotham

IGC Proceedings (1977-2023)

Lack of an effective seed harvester has limited the commercial availability of many chaffy-seeded grasses in Australia. A brush harvester similar to the Woodward Plail-Vac. Seed Stripper was evaluated successfully across a range of chaffy-seeded grasses in southern Queensland. A second machine with increased harvesting and storage capacity plus a facility for primary cleaning of seed was designed and built for large-scale commercial use. A third harvester is currently being developed for opportunist harvesting of small discontinuous seed areas, particularly of chaffy-seeded native grasses in the, semi-arid mulga lands in south-western Queensland; it is designed for low-cost construction and maintenance …

The Woodward Flail-Vac Seed Stripper: Recent Progress In Harvesting Chaffy Seed, C L. Dewald, P L. Sims, L M. White

IGC Proceedings (1977-2023)

The Woodward Flail-Vac Seed Stripper was developed and tested in Woodward County, Oklahoma during 1980-82. Since its introduction we estimate that more than 500 strippers are now used to harvest the majority of seed used to establish over one million ha of Old World bluestem (OWB) grasses. Recent progress includes manufacture of units from aluminum with 40% less weight, and modifications to allow for multiple harvests. Lower brush rotation speeds resulted in a higher quality product and were less destructive lo immature seed heads, A 25 mm increase in brush diameter and· a redesigned shroud increased the air flow and …

Mechanical Harvesting And Processing Of Temperate Zone And Tropical Pasture Seed, J M. Hopkinson, P.T P. Clifford

IGC Proceedings (1977-2023)

Temperate zone herbage seed harvesting continues to evolve round combine•harvesters designed principally for large-seeded grain and pulse crops. Most research emphasis has been placed on increasing efficiency of systems for presenting the crop to the auger platform. Timing of harvest, precutting treatment, cutting and pickup alternatives including airblast assistance vary in relation to species and environmental conditions. With the development of drying-cooling systems considerable advantages in the harvesting and processing of grass seed have occurred. An understanding of the range and use of seed cleaning equipment available to meet purity standards is given, along with additional options to meet end.user …

Harvesting And Processing Techniques Of Tropical Grass And Legume Seeds For Smallfarmers, Lumyai Kowithayakorn, Chaisang Phaikaew

IGC Proceedings (1977-2023)

For smallfarmers of forage legumes and grasses in Thailand, manual harvesting and cleaning of leguminous seeds have been widely practised because of cheap and available labour. Tropical grasses produce more seeds than can be harvested; hence it is necessary to find means to improve harvesting and processing techniques in order to obtain high standards of both quality and quantity of seed. The main obstacles could be due to prolonged flowering nnd grain filling periods of individual seedheads resulting in the uneven ripening of seeds at harvest. Premature seeds cause low yields and low quality nt harvests in many species. Flowering …