plsci2110 prelim 2

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188 Terms

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Farming vs cropping system

Farming system: the entire farm or region, multi-year, multi-species

Cropping: Single field over time

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Mono vs polyculture

A single field and year

Differ in # of species grown together

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Continuous cropping vs rotation

Same field over multiple years

Differ in # of species across years

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Strip cropping

Arrangement subtype of polyculture

Single year and field

Distinguished by spatial organization

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Multiple cropping (double and relay)

Single year and field

Distinguished by timing within year

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Farming system

 A complex inter-related unit of soil, plants, animals, implements, power, labor, capital, and other inputs controlled in parts by farming families. It is also influenced by degrees by political, economic, institutional, and social forces that operate at many levels

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Characteristics of farming system

  • Single measures like cover crops & green manure, crop rotation, reduced tillage, intercropping, agroforestry, structural elements

  • Combined practices like conservation ag, mixed crop-livestock, organic agriculture


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Advantages to farming system

  • Advantages to such a farming ecosystem

    • Stable income and better risk management: less risk to uncertain market prices and stressful weather

    • Labour efficiency: spread labor demands to broader time-frames

    • Cost reduction: farm waste replaces expensive inputs (e.g. using animal manure instead of buying chemical fertilizers)

The whole farm is an integrated ecosystem -maximize profit, reduce waste and financial risk

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Cropping (or livestock-pasture) system

 the combination of the type of crop planted, growing and management methods, and the sequence of crops planted on the same land

  • Unlike farming system, cropping system focuses strictly on crops and their management


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Advantages of cropping system

  • specialization

    • More efficient use of specialized equipment and machinery

    • Farmers develop knowledge and deep expertise on narrow set of crops and problems

    • Easier to integrate digital tools like GPS, precision ag, etc

    • Low cost per unit: farmers can buy inputs in massive volumes thus reducing input costs


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Disadvantages of continuous cropping

  1. Reduced fertility 

    1. Same nutrients are removed each year

  2. Increased erosion and runoff 

    1. Poor soil results in wind and water erosion, soil compaction, runoff, etc

  3. Increased pest pressure

    1. Pests (weeds, disease, insects) thrive in same environment year after year

  4. Degradation of soil structure

    1. Same planting, tilling pattern year after year hurts soil structure


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Advantages of crop rotation

  1. Disease prevention

    1. Disturbs root rot complex

  2. Weed control

    1. Most perennial weeds susceptible to late-summer, fall herbicide applications

  3. Insect control

    1. Rotations disturb life cycle of insects and other invertebrate pests

  4. Reduced inputs

    1. Fewer crop inputs when growing crops in rotation (corn after soybean, save on N inputs)

  5. Soil tilth

    1. Forages and pasture crops add OM and remediate soil structure, improving infiltration

  6. Nutrient use efficiency

    1. More efficient use of plant nutrients

  7. Growth and yield

    1. In most cases crop rotations improve yield


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Why do farmers do monoculture

  1. Ease of management

  2. Benefits from specialized production

  3. Highly responsive to technological innovations

  4. Increased amount of agricultural produce


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Disadvantages of monoculture

  1. Deforestation

    1. Most monoculture land comes from deforestation

  2. Loss of biodiversity

  3. Decline of pollinators

  4. Pollution

    1. Reliant on synthetic chemicals

  5. Susceptibility to pest

    1. Acres and acres of pest breeding grounds with plentiful food and no controls

    2. Pesticides sometimes make pests more resistant and aggressive

  6. Degradation of soil quality


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Polyculture (intercrop) definition and advantages

Growing two or more crops together on the same land during the growing season

  1. Advantages

    1. Yield stability (responses to weather, biotic pests)

    2. Better use of resources - complementarity


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Polyculture management challenges

  1. Differing growth optima

  2. Differences in resource requirements

  3. Varying harvesting time and equipment

  4. Differing prices

  5. Herbicide challenges


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Polyculture complementarity examples

  1. N2 fixing legume + non legume

  2. Planting species with differences in rooting depth: so one crop draws water andnutrients from a different soil layer than the other

  3. Light capture: tall with vertical leaves, short with horizontal leaves

  4. Insect and disease pest control by harboring beneficials

  5. Ecosystem services: where the 2nd species provides erosion and weed control, or prevents leaching of NO3 rather than market income

  6. Three sisters: corn bean squash/pumpkins

  7. Hazel nuts and beans 

  8. Banana and cowpea

  9. Soybean, corn, wheat in adjacent strips

  10. Maize and cowpea

  11. Forage example: alfalfa, orchard grass


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Strip cropping further details (beyond just being spatial complexity)

  1. Growing crops in monocultures in adjacent stirps within a field

  2. Lessens direct competition

  3. Adds complexity to mechanical harvesting, but new equipment is being developed

  4. Types primarily based on the soil topography and the type of erosion to be controlled - wind strip, contour strip cropping, buffer strip and field strip

    1. Corn and soybeans, corn and alfalfa, wheat and cotton

    2. Contour strip cropping


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Double cropping vs and relay cropping - definitions

Double - one in succession after another

Relay - second is sown before first is harvested

  1. Most often practiced in long growing season areas

  2. Utilize both summer and winter annual crops

  3. Pair soybeans with winter wheat

  4. Most prevalent in SE/SW US


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Relay cropping advantages

  1. Potential reduced nitrate leaching

  2. Potential SOC increases

  3. Increase farm income if favorable land equivalent ratio


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Relay cropping disadvantages

  1. Soybean planting process (2nd crop) stresses wheat crop (1st crop), reduces yield 

  2. Wheat harvest stresses soybean growth

  3. Relay cropping requires greater level of management and equipment adjustment

  4. Pest management and control practices must account for more crops being grown in close sequence. System may not have enough time for herbicide carryover to decline and may increase potential for disease or pest infestations if these pests have more than one host in the crop sequence

  5. Time

  6. Crop insurance problems


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How do we know if a cropping system is beneficial?

Land equivalent ratio (LER)

  • With two crops A and B grown together as an intercrop

  • LER = yield of A in intercrop / yield of A as pure stand (monoculture) + yield of B in intercrop / yield of B as pure stand

  • With an LER of 1.43 (correct answer for problem on slides)  - more efficient to crop as an intercrop, need 43% more land for the same yield in a monoculture

Crop equivalent yield (CEY)

  • CEY =  yield (kg) of main crop + (yield of intercrop x price of intercrop / price of main crop)

  • Converting price of intercrop to equivalent in main crop


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Fallow system for drylands

  • Arable land left unseeded and uncultivated for one or more growing seasons

  • Restoring fertility; accumulating soil moisture; starves out pests and break life cycles

  • Great plains: Winter wheat→ grain sorghum → fallow (3 year rotation)


<ul><li><p><span style="background-color: transparent;">Arable land left unseeded and uncultivated for one or more growing seasons</span></p></li><li><p><span style="background-color: transparent;">Restoring fertility; accumulating soil moisture; starves out pests and break life cycles</span></p></li><li><p><span style="background-color: transparent;">Great plains: Winter wheat→ grain sorghum → fallow (3 year rotation)</span></p></li></ul><p></p>
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Soil tillage

a practice of mechanically turning, breaking up, and loosening the top layer of earth to prepare a seed bed

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Soil tillage goals

  1. Incorporate residue (controls diseases and insects)

  2. Incorporation of manures, fertilizers, lime

  3. Alteration of soil physical properties: less compact; more porosity, aeration, drainage channels

  4. Weed control (cut and bury plants)

  5. Preparation of seedbed: uniform, smooth surface so depth of planting is more accurate; achieve a firm soil/seed contact

    1. Seeds safe from birds/rodents


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Evolution of plow

8000 BC → digging tools: hand tools (digging sticks, hoes, thick mollusk shells, sharp edged stones, etc)

6000 BC → draft animals replaced humans in powering the implements for tillage

3500 BC → plowshare, a wedge-shaped implement tipped with iron blade used to loosen top layer of soil

Plows that scratch surface, not inverting soils

1100 AD → horse and oxen drawn wooden moldboard plow with curved blade (moldboard) used to invert soil and bury weeds and residues

Mid 1800s → first smooth steel moldboard plow designed, patented and marketed by multiple people including John Deere; advantage of more easily cutting through the soil and breaking through sod; led to end of walking plows in the US; allowed plowmen to ride on a seat framed onto the plow with adjustable wheels to control a steady plow depth

Early 1900s → building of implements like tractors with multiple plows that allowed intensive cultivation of vast areas of earth

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Conventional tillage

  1. Type of tillage practiced for 100s of years, intensive form with soil inversion as a key feature

  2. Key stages or steps of conventional tillage

    1. Primary tillage or plowing: invert soil, expose it to surface. Displaces and shatters soil, buries and mixes plant materials, pesticides, fertilizers in tillage layer

    2. Secondary tillage: break up or smooth out mounds created by moldboards and create a fine textured seedbed for planting. Also includes performing shallow post-planting tillage like loosening the soil and/or by mechanical eradication of undesired vegetation

      1. Plowing - primary tillage

      2. Disking with harrow - primary/secondary tillage

      3. Row-crop cultivator - secondary tillage

  3. Equipment used - refer to link on slides for details of diverse equipment used


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Problems with conventional tillage

  1. Soil erosion

  2. Environmental issues caused by soil erosion

    1. Dust bowl 

  3. Soil crusting

    1. Definition: plowing breaks pre-existing soil aggregates and exposes them to rain. Force from raindrops breaks up aggregates, forms a structureless fine soil that forms a crust on the field surface as it dries

  4. Soil compaction

  5. Pollution due to agricultural runoff

  6. Loss of soil organic carbon

    1. Exposes SOM to atmosphere, leading to decomposition and conversion to CO2

  7. Economic losses

    1. Increased need for fertilizers


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No-till

  • Type of conservation tillage method where ½ to 3 inch across grooves are created in planted row and seeds are sown directly in these grooved resulting in minimal soil disturbance

  • Key steps generally include: apply herbicide → plant → apply herbicide → harvest

  • Requirements /facilitators of no tillage:

    • Modern herbicides for weed control

    • Innovations in no-till equipment like seeders


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No till planting requirements to cut and penetrate residue?

Heavy equipment

  1. Requires more pressure

  2. Requires more residue moving and cutting

  • Double disk openers are typically used in no-till or high residue systems

  • They are mounted parallel and equidistant to each other and form a “V” shaped slot in to which the seed is dropped as the planter moves along


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Benefits to no-till

  1. Reduced soil compaction

  2. Reduced soil erosion

  3. Conservation of soil water

  4. Improved soil quality and fertility

  5. Reduced pollution

  6. Increased carbon sequestration

  7. Economic advantages to farmers

  8. Improved yields


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Challenges to no-till adoption

  1. Alternate use of crop residues (Africa + Asia problem) - munch or mulch

  2. Equipment cost

  3. Learning curve

  4. Changes in crop diseases

  5. Problematic in fine-textured and poorly drained soils

  6. Cooler soils

  7. Need for new herbicides

  8. Benefits seen in longer terms


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Strip or zone tilling - implementing no-til

  • Strip (or zone) tilling combines no-till and conventional tillage practices

    • Conservation farming system that tills only narrow bands in the soil where seeds are planted, while leaving the rest of the crop residue and soil between the rows completely undisturbed

    • Width of strips corresponds to type of crop and width of the planter row

    • Seeds, and fertilizers, are usually applied into the strip tilled areas

  • Strip till implement

    • Generally done in the fall but also spring

    • Generally with herbicide weed control

    • GPS/RTK important


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Advantages to strip tillage

  • Many of same benefits to no till:

    • Less soil disturbance

    • Less erosion potential

    • Less SOM breakdown

    • Less tractor energy

  • Better seedbed in tilled strips

  • When used as fall tillage:

    • Deep rip (6-8 inches) drains water from surface during snowmelt and rain in spring, creates microclimate

  • Soil warms faster in spring

    • Dark tilled soil absorbs spring sunshine

  • Earlier planting

    • Drainage

    • Warming


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Importance of N in crop productivity

  1. Constituent of biomass -protein, nucleic acids, chlorophyll, etc

  2. Soils often N-limiting - almost always the case in agricultural systems

    1. Phosphorus in tropical systems

  3. Affects protein productivity of crops, nutritive value, quality

  4. Losses of N from soils and efficiencies of N use by crops pollute ground water, lakes, streams, release NOx to atmosphere

  5. N assimilation represents a high proportion of plant energy expenditure, therefore impacting yield

  6. Provision of N needs for crops, whether by fertilizer or organic residues, represents one of the largest input costs of crop production


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3 types of nitrogen fixation, N cycle

Inputs: Biological, industrial, atmospheric (lightning) fixation

Biological and atmospheric fixation added to OM

OM mineralized into ammonium

Ammonium nitrifies into nitrate NO3—

Nitrate denitrifies into nitrite, or leaches


<p>Inputs: Biological, industrial, atmospheric (lightning) fixation</p><p>Biological and atmospheric fixation added to OM</p><p>OM mineralized into ammonium</p><p>Ammonium nitrifies into nitrate NO<sub>3</sub><sup>—</sup></p><p>Nitrate denitrifies into nitrite, or leaches </p><p></p>
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Ammonium loss pathways

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Nitrate loss pathways

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Nitrogen fertility, denitrification losses

Low lying areas of fields may flood easily

Denitrification in water-saturated soil a function of temperature

Higher temps and more days saturated = more denitrification losses

<p>Low lying areas of fields may flood easily</p><p>Denitrification in water-saturated soil a function of temperature</p><p>Higher temps and more days saturated = more denitrification losses</p>
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Nitrogen chemical changes in soil and in plant assimilation

  • Green: plants

  • Blue: bacteria in O2

  • Red: bacteria, hypoxic/saturated soil conditions


Higher on this image: reduced substances (GER)

Lower on this image: oxidized substances (LEO)

<ul><li><p><span style="background-color: transparent;">Green: plants</span></p></li><li><p><span style="background-color: transparent;">Blue: bacteria in O<sub>2</sub></span></p></li><li><p><span style="background-color: transparent;">Red: bacteria, hypoxic/saturated soil conditions</span></p></li></ul><p></p><p><span style="background-color: transparent;">Higher on this image: reduced substances (GER)</span></p><p><span style="background-color: transparent;">Lower on this image: oxidized substances (LEO)</span></p>
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How plants convert N to organic forms

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N deficiency symptoms

N deficiency is especially apparent on lower leaves

  • N mobility results in N transport from older to younger leaves

  • Lower leaves display deficiency symptoms

  • Monitoring N status in upper leaves might be less effective monitoring on lower leaves


<p><span style="background-color: transparent;">N deficiency is especially apparent on lower leaves</span></p><ul><li><p><span style="background-color: transparent;">N mobility results in N transport from older to younger leaves</span></p></li><li><p><span style="background-color: transparent;">Lower leaves display deficiency symptoms</span></p></li><li><p><span style="background-color: transparent;">Monitoring N status in upper leaves might be less effective monitoring on lower leaves</span></p></li></ul><p></p>
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Types of N fertilizers

  • 82% N: Anhydrous ammonia - gaseous, everything needs to be handled right

    • Midwest: apply it after harvest, lower temps later in year means lower microbial activity, and nitrogen can be inert over winter

      • Global warming: soils are getting too warm

    • Knifed into soil

    • Inexpensive, but transport and handling is pricey

  • 46% N: Urea

    • Cheapest, more common in developing countries

  • 28-32% UAN (urea ammonium nitrate) - can burn leaves

  • 34% N Ammonium nitrate


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N fixation by rhizobia

Atmosphere N2 converted to ammonium

Plants supply C and host environment

N enters vascular system

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Nodulation of rhizobia

  • Issues

    • cross inoculation groups

    • Inoculation via seed

    • High soil NO3 or NH4 inhibit nodulation and N2 fixation

    • High energy cost

      • Soybean planted in areas where N already exists: plants will not nodulate to save energy


<ul><li><p><span style="background-color: transparent;">Issues</span></p><ul><li><p><span style="background-color: transparent;">cross inoculation groups</span></p></li><li><p><span style="background-color: transparent;">Inoculation via seed</span></p></li><li><p><span style="background-color: transparent;">High soil NO<sub>3</sub> or NH<sub>4</sub> inhibit nodulation and N2 fixation</span></p></li><li><p><span style="background-color: transparent;">High energy cost</span></p><ul><li><p><span style="background-color: transparent;">Soybean planted in areas where N already exists: plants will not nodulate to save energy</span></p></li></ul></li></ul></li></ul><p></p>
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Important sources of N, timed release

Livestock and green manures

  • Mineralization - “timed release” 50% in year 1 (10 tons of manure applied, only 5 tons would be available the year it is applied)

    • Lignin, phenol

  • Manure - N and P imbalances, to get enough N you end up with too much P

    • Overapply manure for N since it is timed release, then P is in excess - NYS soils


<p>Livestock and green manures</p><ul><li><p><span style="background-color: transparent;">Mineralization - “timed release” 50% in year 1 (10 tons of manure applied, only 5 tons would be available the year it is applied)</span></p><ul><li><p><span style="background-color: transparent;">Lignin, phenol</span></p></li></ul></li><li><p><span style="background-color: transparent;">Manure - N and P imbalances, to get enough N you end up with too much P</span></p><ul><li><p><span style="background-color: transparent;">Overapply manure for N since it is timed release, then P is in excess - NYS soils</span></p></li></ul></li></ul><p></p>
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Yield based N recommendations

Left graph: 1970s, 1980s

Right graph - shows yield vs N rate was actually not very effective for recommending N rates

<p><span style="background-color: transparent;">Left graph: 1970s, 1980s</span></p><p><span style="background-color: transparent;">Right graph - shows yield vs N rate was actually not very effective for recommending N rates</span></p>
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N fertilization rate and economic response

  • New approach called MRTN in midwest - maximum return to N

  • Data-driven recommendations sensitive to measured N response and grain responses


<ul><li><p>New approach called MRTN in midwest - maximum return to N</p></li><li><p>Data-driven recommendations sensitive to measured N response and grain responses</p></li></ul><p></p>
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“Black box” of N cycle

Black box - many factors affecting nitrogen efficiency

  • Very hard to attach firm numbers to, varies across landscape

  • Unavoidable losses of N when harvest is moved off the farm, and other losses: never get 100% efficiency


<p><span style="background-color: transparent;">Black box - many factors affecting nitrogen efficiency</span></p><ul><li><p><span style="background-color: transparent;">Very hard to attach firm numbers to, varies across landscape</span></p></li><li><p><span style="background-color: transparent;">Unavoidable losses of N when harvest is moved off the farm, and other losses: never get 100% efficiency</span></p></li></ul><p></p>
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What makes estimating available soil N diffciult?

  • Dynamic cycling

    • Mineralization timed releases

    • Denitrification losses

  • Weather

    • Rainfall

    • Temp

  • Soil characteristics

    • Drainage

    • Percolation

    • OM content and quality

  • Plant needs for N vary over the season

    • Highest during stem elongation


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Methods for estimating nitrogen

  • Soil testing inadequate

    • Cycling dyanmic

  • Plant tissue testing

    • Stem NO3 test

    • Leaf color

  • Calculate N supply with model of dynamic cycling (AdaptN)

    • Simulation with weather, soil, history, crop needs accounted for


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Obstacles to better N management

  • Recommendations state based, sometimes outdated and fertilizer focused

  • Unease and unresolved issues between public and private sectors and regulations

    • Cannot assess how much N being lost off individual farms, violates privacy laws

  • skepticism about technologies


<ul><li><p>Recommendations state based, sometimes outdated and fertilizer focused</p></li><li><p><span style="background-color: transparent;">Unease and unresolved issues between public and private sectors and regulations</span></p><ul><li><p><span style="background-color: transparent;">Cannot assess how much N being lost off individual farms, violates privacy laws</span></p></li></ul></li><li><p>skepticism about technologies</p></li></ul><p></p>
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Adapt-N

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Grey, green, blue nitrogen

Grey ammonia - produced as is

Blue ammonia - given carbon capture storage, practicality dubious (some call it a “fantasy” and impractical at scale)

Green ammonia - renewable electricity, electrolysis for hydrogen, thus green ammonia has significantly less emissions 

  • Higher cost at present


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Crop yield and economic development progression over time graph

(NUE, N surplus vs practical limit to NUE)

SSA - NUE over 1, N outputs > inputs, more nitrogen in grain than nitrogen applied, mining soil for nitrogen

<p><span style="background-color: transparent;">SSA - NUE over 1, N outputs &gt; inputs, more nitrogen in grain than nitrogen applied, mining soil for nitrogen</span></p>
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Global NUE graph

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Nitrogen functions

Component of amino acids, nucleic acids, protein and chlorophyll; promotes vegetative growth

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Phosphorus

Energy transfer (ATP) and protein metabolism; seed germination, root growth, essential for N fixation in legumes

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Potassium

Regulates stomata, enzyme activation for starch and protein metabolism; water balance, drought tolerance, disease resistance

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Calcium

Cell wall constituent, cell division, regulates nutrient transport, increases fruit set

  • Cornell media mix deficient in it


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Mg

Major constituent of chlorophyll and ribosomes, enzyme activation for carbohydrate metabolism

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Sulfur

Synthesis of amino acids, chlorophyll formation, promotes nitrogen fixation in legumes

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Micronutrients

Essential constituents of numerous enzymes or key in activating enzymes

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Nutrient acquisition

  • very little gaseous form may enter through stomata

    • Mostly through mass flow or diffusion

  • Mass flow (NO3, SO4,Ca, Mg, K, micros) - order of centimeters

  • Diffusion (P, K, S, Fe, Zn) - order of millimeters

    • Must be near site of uptake (i.e the root)


<ul><li><p>very little gaseous form may enter through stomata</p><ul><li><p>Mostly through mass flow or diffusion</p></li></ul></li><li><p><span style="background-color: transparent;">Mass flow (NO<sub>3</sub>, SO<sub>4</sub>,Ca, Mg, K, micros) - order of centimeters</span></p></li><li><p><span style="background-color: transparent;">Diffusion (P, K, S, Fe, Zn) - order of millimeters</span></p><ul><li><p><span style="background-color: transparent;">Must be near site of uptake (i.e the root)</span></p></li></ul></li></ul><p></p>
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Plants assimilate mineral nutrients as ions

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Factors affecting nutrient availability to plants

  • Parent material

  • Soil pH

    • On acid soils, H+ overwhelms exchange sites, leading to issues with Mg, Ca

  • Moisture content

  • Temperature

  • Redox conditions



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How plant respiration impacts soil pH

CO2 released from respiration by plants, and H+ pumped into the soil by roots, acidify the soil solution and trigger cation exchange

Consider for fertility

  • What is the pH

  • Can you modify it?

  • Where are the charges coming from: OM, clay?


<p><span style="background-color: transparent;">CO<sub>2</sub> released from respiration by plants, and H<sup>+</sup> pumped into the soil by roots, acidify the soil solution and trigger cation exchange</span></p><p><span style="background-color: transparent;">Consider for fertility</span></p><ul><li><p><span style="background-color: transparent;">What is the pH</span></p></li><li><p><span style="background-color: transparent;">Can you modify it?</span></p></li><li><p><span style="background-color: transparent;">Where are the charges coming from: OM, clay?</span></p></li></ul><p></p>
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Impacts of pH on nutrient availability

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Global soil pH

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Nutrient constraints to crop productivity

  • N - most limiting worldwide

  • P - highly weathered soils, esp. In tropical areas

  • K - intensive cropping systems with high residue removal

  • S - particularly in reduced, paddy rice agroecosystems

  • Ca, Mg - highly weathered and acidic soils

  • Zn - micronutrient deficiency especially in paddy rice

  • B - problem for grain legumes, wheat and vegetables (high pH)


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Temporal patterns and remobilization

  • Most uptake during vegetative period: N, K and Mg

  • Season-long uptake: P, S and Zn

  • Remobilization from leaves, stalks: N, P

    • Less remobilization: K, Mg, S


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Determining crop nutrient status

Hard to apply so many macronutrients to reach toxicity, but micronutrients have a more narrow optimal concentration range

<p><span style="background-color: transparent;">Hard to apply so many macronutrients to reach toxicity, but micronutrients have a more narrow optimal concentration range</span></p>
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Approaches toward identifying deficiencies



  1. Deficiency Symptoms - simple, no cost diagnostic based on characteristic visual symptoms and novel approaches such as remote sensing

    1. Symptoms can be confused with non-nutrient stresses (diseases, drought, flood)

  2. Plant Analysis - nutrient analysis of specific plant parts at specified growth stages

    1. Nutrient concentrations compared to known sufficiency ranges

    2. Good for monitoring crop nutrition status; effectiveness of fertilizer applications

    3. May come too late in the plant life cycle

  3. Soil Testing - measurement of soil nutrient/pH status to use as basis for fertilizer/lime recommendations

    1. Nutrient status before planting; supplement level

    2. Functional relationship between soil nutrient extracted & crop yield

    3. Must be used before deficiencies occur


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Symptoms of major nutrient deficiencies

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Mobile vs immobile nutrient deficiency symptoms - mobile nutrient deficiency symptoms appear in old plants

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Physiological functions of beneficial mineral elements


<p></p>
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Plant breeding definition

  • Plant breeding is the genetic improvement of plants for human benefit

  • Plant breeding is the art and science of the genetic improvement of plants


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Why breed plants?

  • Yield - food for rising population

    • Evaluate performance of diverse varieties in diff places

    • G x E x M

      • Genotype x env x management

  • Increase disease and insect resistance

  • Enhance abiotic stress resistance

  • Quality – taste, nutritional value

  • Harvestability

    • Lodging resistance, uniform maturity, shatter resistance, dry down rate; adaptable to mechanical harvest

  • Persistence

    • Esp for perennials that winterkill e.g alfalfa


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How do we know how much of yield increase is from breeding?

Era study

More than half of yield gains in major cereal crops are a result of genetic improvement

Genetic yield gain / total yield gain = % genetic gain

<p>Era study</p><p><span style="background-color: transparent;">More than half of yield gains in major cereal crops are a result of genetic improvement</span></p><p><span style="background-color: transparent;">Genetic yield gain / total yield gain =  % genetic gain</span></p>
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How diverse are crop species

  • Based on DNA sequence we now know that, on average, two maize lines are as genetically different as humans are from chimpanzees

  • Toolbox of genes to utilize


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Driver of new genetic combinations?

Meiosis

Regular plant cell is diploid - 2 copies of each chromosome, one from each parent

  • Recombination leads to genetic diversity

    • Plant breeders make use of this process of recombination


<p>Meiosis</p><p><span style="background-color: transparent;">Regular plant cell is diploid - 2 copies of each chromosome, one from each parent</span></p><ul><li><p><span style="background-color: transparent;">Recombination leads to genetic diversity</span></p><ul><li><p><span style="background-color: transparent;">Plant breeders make use of this process of recombination</span></p></li></ul></li></ul><p></p>
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Mendelian genetics 3 principles

  1. Paired factors

    1. Every gene has variant forms i.e alleles

    2. Individual inherits a pair of alleles for each gene, one from egg and one from pollen parent

  2. Law of segregation

    1. Offspring receive one copy of each gene from each parent via egg or sperm gametes (haploid)

  3. Law of Independent assortment

    1. Genes inherited from each parent are passed independently to offspring, conferring separate traits

  • Used mathematical ratios rather than microscope to develop these 3 principles

    • Think of punnett squares


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What shapes breeding strategy?

Reproductive strategy

  1. Self pollinating plants

    1. Naturally homozygous

    2. Selfed inbreds reveal their true character – more predictable, easier to study

  2. Open pollinating plats

    1. Floral structure facilitates outcrossing

    2. Self-incompatibility genes in some species

  3. Hybrids are crosses of two inbred lies

    1. Inbreds made in self-pollinating or open-pollinating crops

    2. Inbreeding depression

  4. Many crops vegetatively propagated as clones

    1. Sweet potato, sugarcane, cassava, potato


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Plant breeding steps

  1. Identify breeding goals

  2. Identify parent germplasm

  3. Create variable population

  4. Select from variable population

    1. If selections are unfavorable, back to step 2

  5. Test progeny

    1. If progeny is unfavorable, back to step 2

  6. Release new cultivar

  7. Distribute seed to growers


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  1. Identify breeding goals expanded


  1. Shape, flavor, color, storage capacity, disease/pest resistance


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  1. Identify germplasm


Seed sources, genetic resources from other programs, varieties, seed banks, wild relatives (e.g queen anne’s lace), potential parent lines provided by collaborators

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  1. Variable population


Control pollen movement, so that only desired parents contribute genes

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  1. Select from population


  1. Select a group of desirable plants from population

  2. Bulk seed and intimate in next generation

  3. Repeat for several generations

  4. Family selections - rather than individual plants, breeders keep track from a family of plants, assess sibling performance 

    1. Among and within families


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  1. Evaluate progeny


  1. After several generations of selections, how do breeders know if they are making progress?

  2. 5% selection intensity from parent (highlighted yellow) used for the progeny population

  3. Entire progeny population has shifted to the right, indicating improvement


<ol><li><p><span style="background-color: transparent;">After several generations of selections, how do breeders know if they are making progress?</span></p></li><li><p><span style="background-color: transparent;">5% selection intensity from parent (highlighted yellow) used for the progeny population</span></p></li><li><p><span style="background-color: transparent;">Entire progeny population has shifted to the right, indicating improvement</span></p></li></ol><p></p>
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6 and 7: release cultivar, distribute seed

  1. Seed production

  2. Marketing

  3. Intellectual property


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Genetic modification - engineering/transformation vs editing

  • Key breeding steps of step 3 - create variable population

  • Gene modification to change genes of interest

    • Genetic Engineering / Transformation: moving a gene from one species to another

    • Gene Editing: deleting or changing particular nucleotide(s) within a species’ DNA

  • Small number of genes at a time

    • For traits determined by one or a few genes, like herbicide and insect resistance

  • Differences in the level of regulatory approval

    • Significant approval process required to release a "genetically engineered" variety (e.g., RoundUp Ready soybean or Bt cotton)

    • Gene edited varieties require minimal regulatory oversight (e.g. non-browning mushroom, Arctic apple (non-browning), seedless blackberry, pitless cherry).


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Genetic engineering/transformation

knowt flashcard image
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Gene editing

knowt flashcard image
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Marker assisted selection

  • Accelerates step 4. Selection from variable population

  • DNA marker is a landmark - a sequence close to gene of interest, often inherited together with gene of interest


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Genomic selection

  • Effective for complex traits controlled by many genes

  • Uses genome-wide markers

  • Trains genomic prediction model on a population that associates genotype with phenotype

  • Predicts genomic estimated breeding values for individuals without needing to wait for phenotypes to be exhibited

    • Predict variety performance without field trial


<ul><li><p><span style="background-color: transparent;">Effective for complex traits controlled by many genes</span></p></li><li><p><span style="background-color: transparent;">Uses genome-wide markers</span></p></li><li><p><span style="background-color: transparent;">Trains genomic prediction model on a population that associates genotype with phenotype</span></p></li><li><p><span style="background-color: transparent;">Predicts genomic estimated breeding values for individuals without needing to wait for phenotypes to be exhibited</span></p><ul><li><p><span style="background-color: transparent;">Predict variety performance without field trial</span></p></li></ul></li></ul><p></p>
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Ecological vs weed science vs agronomical definition of a weed

Ecology def of weed - a plant thriving on human disturbance of growing unchecked

Weed science: a plant interfering with any human objective

Agronomy: a plant interfering with crop productivity or harvest

Essentially: a plant at the wrong place at the wrong time

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Common characteristics of weeds

Rapid growth rate

  • Abundant reproduction

  • Effective dispersal

  • Persistent propagules (ability to emerge over time)

    • Weed seedbank

    • Vegetative growth (tuber, tiller)

  • Phenotypic plasticity

    • Can change physiology/morphology in response to environmental changes


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“ideal” (biggest pain) weed



  • Flexible in

    • Germination (seed dormancy e.g in Chenopodium album)

    • Pollination (generalists or some self-compatibility) (e.g Thlaspi arvense)

    • Seed production (high when favorable, limited when unfavorable) (e.g Amaranthus sp.)

    • Dispersal (seeds + rhizomes) (e.g Cirsium arvense)


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Losses from weeds

  • Production

    • Constraints on limited resources (light, nutrients, water)

  • Increased cost

    • Control (herbicides, fuel)

    • Crop reseeding

  • Product quality or spoilage

    • Dockage e.g weed seeds in wheat harvest

    • Forage contamination

  • Disease or insect hosts

    • Powdery mildew from wild oats


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Physical weed control

  • Uproot, severing, burying

    • TIllage (5-10” deep)

      • Primary: uproot established weeds and stubble

        • Moldboard

      • Secondary: for soil tilth and seedbed prep or incorporating herbicides or fertilizer

        • Tine weeding

        • Flicking weeds between crop rows

  • Mowing

  • Heat

    • Flame weeding

    • Steam

  • Mulching

  • Flooding