Physiological basis of plant productivity

1.1. From Leaf as an Organ to Plant as a System

The leaf is an amazing organ. It concentrates everything necessary for photosynthesis: chloroplasts with pigment systems, stomata for gas exchange, and a developed conducting system for assimilate export. It is no coincidence that the leaf became the main photosynthetic organ of higher plants during evolution (Medvedev, 2012). However, when we speak about yield, we are dealing not with an isolated leaf, but with a whole plant or, even more importantly, with a plant community — a crop stand. And here we encounter the first fundamental limitation: the rules that apply to an isolated leaf do not automatically transfer to the whole plant.

What is the essence of this transition? At any given moment, leaf photosynthesis is its current “labour productivity”. But the plant does not live in an instant; it lives over an extended period during which leaves appear, develop, senesce, and die. For productivity, it is not so much how fast one leaf works, but rather how long and efficiently the entire leaf system works (Tretyakov et al., 2000). Moreover, leaves are not just autonomous sugar factories, but parts of a whole organism, where each organ is in complex relationships with others.

1.2. Leaf Photosynthesis and Plant Growth: A Non‑Obvious Relationship

Researchers have long noticed that the direct correlation between the photosynthetic rate of an isolated leaf and the growth rate of the whole plant is not always observed (Farquhar & Sharkey, 1994). Why is that? Imagine two plants of the same species. The first has leaves with high photosynthetic activity, the second has lower activity. It would seem that the first should grow faster. However, in reality this relationship may break down. First, because leaves with high photosynthetic activity are often thicker and denser, and therefore, all else being equal, consume more carbon per unit area (Farquhar & Sharkey, 1994). Second, under natural conditions, not all leaves work at full capacity: many are shaded by other leaves, and their high potential photosynthesis remains unused.

It is appropriate to recall that growth is an integrative process, depending not only on how much carbon is fixed, but also on how that carbon is distributed among organs. At the whole‑plant level, we must consider not only the “donor” capacity of leaves (source), but also the “acceptor” capacity of consumer organs — roots, stems, fruits, storage tissues. The relationship between donors and acceptors in plant physiology is called source–sink relations, and we will return to them in later lectures when we discuss donor–acceptor relationships.

1.3. Leaf Ontogeny: From Sink to Source

It is important to understand that a leaf passes through several stages during its life. A young, just‑unfolded leaf is a sink; it consumes assimilates coming from other leaves for its own growth. Only after reaching about 30–50% of its final area does it become a source and begin exporting photosynthetic products to other parts of the plant (Morot‑Gaudry et al., 2012; Marschner, 2012). This transition from sink to source is accompanied by profound biochemical changes: the activity of enzymes that hydrolyze sucrose (invertase, sucrose synthase) decreases, while the activity of enzymes that synthesize sucrose for export (sucrose phosphate synthase) increases (Marschner, 2012). Thus, each leaf has its own “working period”, and the productivity of the whole plant is determined by how efficiently the succession of leaf generations is organized and how synchronised their work is with the needs of developing organs.

1.4. Transition to the Plant Community

But even a single plant is not yet a field. In an agroecosystem, plants interact with each other. They compete for light, water, and mineral elements. Competition for light is especially important: leaves in upper layers intercept most of the photosynthetically active radiation (PAR), leaving only a small fraction to the lower layers (Connor et al., 2011).

In an isolated plant, each leaf is more or less uniformly illuminated (unless we are talking about a large tree). In a crop stand, the situation changes dramatically: as leaf area per unit ground area increases, an increasing proportion of leaves find themselves in the shade. This makes the relationship between the productivity of the whole crop and the photosynthesis of an individual leaf even less direct. At the crop‑level, we move from studying a single leaf to studying the photosynthetic apparatus of the crop as a unified system.

1.5. Key Conclusions

So why is one leaf not enough?

1. The leaf is not an autonomous system, but a part of a whole plant with developed source–sink relations.

2. Leaf photosynthesis changes with age, and only during a certain period does it act as a source.

3. A plant in a crop stand is a community where leaves compete for light, and the efficiency of light use is determined not by the activity of a single leaf, but by the work of the entire system.

4. Productivity is determined not so much by the rate of photosynthesis, but by its duration and the efficiency of light and carbon use across the whole crop stand.

That is why, when moving from leaf to plant, we must view productivity not as the sum of photosynthetic activities of individual leaves, but as an integrative result of the work of a complex, dynamic system. The next question we need to answer is how to measure the productivity of this entire system and how it can be improved.

Key terms from the lecture:

• Photosynthetic apparatus of the plant – the totality of all photosynthetic organs that ensure the production process.
• Source–sink relations – the system of connections between assimilate‑source organs (donors) and assimilate‑consuming organs (acceptors), determining the distribution of photoassimilates.
• Leaf transition from sink to source – the ontogenetic stage in leaf development when it ceases to consume assimilates and begins to export them.
• PAR – photosynthetically active radiation (light with wavelengths 400–700 nm) used by plants for photosynthesis.

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2.1. From Illumination of a Single Leaf to the Light Regime of a Crop

Under natural conditions, a single leaf, especially in a well‑lit spot, can receive up to 2000 µmol photons per square metre per second (Taiz et al., 2023). This is a huge value – under direct sunlight at noon. However, the paradox is that the vast majority of agricultural plants never operate in this mode continuously. Why? Because plants form a crop stand – a dense community where upper leaves shade lower ones.

In a dense canopy, for example in wheat or maize, only 1–5% of the light falling on the top of the canopy may remain in the lower layers (Connor et al., 2011). The main photosynthetic work under such conditions falls on the upper leaves, while the lower ones are in deep shade. This radically changes our view of productivity: yield is determined not by how a single leaf works in full sun, but by how the whole community intercepts and uses the incident light.

2.2. Leaf Area Index (LAI) as a Key Parameter

To describe the photosynthetic surface of a crop, plant physiologists use the Leaf Area Index (LAI). This is the ratio of the total leaf area (counting only one side of the leaf blade) to the ground area they occupy (Connor et al., 2011). If LAI = 3, it means that for every square metre of ground there are 3 square metres of leaf surface.

LAI is perhaps one of the most important indicators of crop status. At LAI below 3, the soil between plants is still well illuminated, and a significant portion of solar energy is wasted on heating the soil rather than on photosynthesis. At LAI above 5–6, leaves in the lower layers begin to shade each other heavily, and their contribution to photosynthesis becomes minimal. There is a concept of critical LAI – the index value at which the crop intercepts 90–95% of incident photosynthetically active radiation (Tretyakov et al., 2000). For most cereals, this value lies in the range 3–5, and for crops with vertical leaves (e.g., maize or sorghum), the critical LAI can be higher.

Interestingly, during evolution and breeding, the LAI of cultivated plants has increased noticeably. For example, in modern wheat varieties, LAI at flowering can reach 5–8, whereas in wild ancestors this indicator was significantly lower. This came about through two processes: first, breeders selected forms with larger leaves, and second, they developed architecture that allows leaves to be better distributed in space. However, increasing LAI is a double‑edged sword: too high an LAI leads to mutual shading and reduced photosynthetic efficiency, especially in the lower layers (Connor et al., 2011).

2.3. The Law of Light Attenuation in a Crop Canopy

As early as 1953, Japanese scientists Monsi and Saeki showed that light attenuation in a plant canopy obeys a simple law, analogous to the Bouguer–Lambert–Beer law for homogeneous media (Connor et al., 2011):

where:

• I – light intensity at a certain depth within the canopy;
• I₀ – light intensity above the canopy;
• k – extinction coefficient, characterising the ability of leaves to intercept light;
• LAI – leaf area index above that depth.

This equation is a fundamental tool for understanding the light regime of a crop. Imagine: at LAI = 3 and extinction coefficient k = 0.7 (typical for a crop with horizontal leaves, e.g., clover), only about 12% of light remains at soil level: I = I₀ · exp(–0.7×3) = I₀ · exp(–2.1) ≈ 0.12 I₀. That is, 88% of light is intercepted by leaves. At LAI = 5, only about 3% remains (Schopfer & Brennicke, 2016).

The extinction coefficient k is a measure of how effectively each leaf layer shades the layers below. It is determined primarily by canopy architecture – the orientation of leaves in space. In plants with horizontal, plagiotropic leaves (as in many legumes), light is intercepted in the upper layers, and k is high. In plants with vertical, erectoid leaves (as in grasses), light penetrates deeper, and k is lower (Tretyakov et al., 2000).

2.4. Canopy Architecture: How Form Determines Function

In plant physiology, canopy architecture can be compared to an engineering structure that optimises light interception. Take two canopies with the same LAI: one with horizontal leaves, the other with vertical leaves. In the horizontal‑leaf canopy, the upper layers intercept most of the light, leaving the lower leaves in deep shade. In the vertical‑leaf canopy, by contrast, light penetrates deeper, and the distribution of illumination across layers becomes more uniform (Connor et al., 2011).

Which option is more advantageous? It depends on the goal. For plants aiming for maximum biomass under abundant light, horizontal leaves are better – they quickly form a dense canopy and effectively “collect” light. This is the architecture of many plants from open habitats. However, in dense stands where competition for light is especially acute, forms with vertical leaves gain an advantage – they allow the working zone of the canopy to be extended deeper, involving more leaves in photosynthesis (Medvedev, 2012). Therefore, modern high‑yielding cereals, especially rice and maize, have erectoid upper leaves and more horizontal middle and lower leaves (Taiz et al., 2023).

2.5. Sunflecks: Working Under Dynamic Light Conditions

Even in a canopy with high LAI, illumination is not static. Sunflecks – rays of light passing through gaps in the leaf cover – can bring high‑intensity light to the lower layers for short periods (Taiz et al., 2023). These sunflecks can account for up to 50% of the total light energy received by lower leaves during the day. In a forest canopy or dense crop stand, sunflecks are the “windows” of light that allow lower leaves to maintain a positive carbon balance.

Plants adapted to life under a canopy have developed special mechanisms to use these brief flashes of light. For example, they can rapidly activate the photosynthetic apparatus when a sunfleck appears and just as rapidly switch to an “energy‑saving” mode when it disappears. This is one example of fine physiological regulation at the community level (Schopfer & Brennicke, 2016).

2.6. Light Curves at the Canopy Level

If we plot a light‑response curve of photosynthesis for an individual leaf, we see the classic hyperbola with a saturation plateau. However, for a whole canopy, the shape of the curve changes. Because leaves in the canopy are under different light conditions, their individual light curves are superimposed. As a result, the canopy shows light saturation at significantly higher light intensities than a single leaf, and sometimes saturation is not reached at all (Taiz et al., 2023). This means that under real field conditions, light is rarely an absolutely saturating factor for the whole system: there are always leaves working in a limiting regime.

This effect has practical significance. That is why crop productivity often correlates with the total amount of intercepted PAR, rather than with the photosynthetic rate of an individual leaf. Each additional leaf increases total light interception, but with diminishing returns (Connor et al., 2011).

2.7. Optimal LAI: Finding the Balance

Thus, the agronomist’s task is to find the optimal balance between LAI and canopy architecture. At low LAI, light is lost to the soil; at high LAI, it is lost in the shaded lower layers where leaves do not justify their maintenance costs. This balance depends on many factors: crop, variety, region, and moisture conditions.

It is important to remember that LAI can be regulated:

• by breeding – creating varieties with a specific architecture and leaf area formation dynamics;
• by agronomic practices – changing planting density, sowing dates, and plant arrangement.

In modern crop production, we strive for the crop to reach the optimal LAI as quickly as possible and maintain it for as long as possible. This is one of the tasks that breeders address when creating high‑yielding varieties.

Key terms of this section:

• Leaf Area Index (LAI) – the ratio of leaf area to the ground area they occupy.
• Extinction coefficient (k) – a measure of light attenuation when passing through the leaf canopy (reflects light‑interception efficiency).
• Canopy architecture – the spatial structure of the crop, determined by the orientation and arrangement of leaves in space.
• Erectoid leaves – leaves with a vertical orientation, allowing light penetration deep into the canopy.
• Plagiotropic leaves – leaves with a horizontal orientation, efficiently intercepting light in the upper layers.
• Critical LAI – the leaf area index value at which the canopy intercepts 90–95% of incident PAR.
• Sunflecks – brief flashes of light that reach the lower canopy layers through gaps in the leaf cover.

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3.1. The Big Picture: Energy Balance of a Crop

On a clear summer day, about 30–50 MJ of solar energy falls on the crop surface per square metre per day (Connor et al., 2011). Of this energy, only a strictly defined part falls within wavelengths that can be used by plants. And even from that fraction of photosynthetically active radiation (PAR), ultimately only about 3–5% (in the best cases) is converted into biomass. How does this happen?

Let us trace the path of a sunbeam from the moment it hits a leaf until it is converted into dry matter gain, step by step, noting all the losses.

3.2. First Loss: Spectral Composition of Light

The solar spectrum covers the entire range of wavelengths – from ultraviolet to infrared. But only a limited region – from 400 to 700 nanometres – is suitable for photosynthesis; this is called photosynthetically active radiation (PAR) (Taiz et al., 2023). PAR accounts for only about 45% of the total solar energy reaching the Earth’s surface. The remaining 55% is infrared radiation (heat) and ultraviolet, which plants hardly use for photosynthesis. Infrared rays are vital for thermal balance, but not for chemical transformations.

Thus, even before meeting the leaf, the first major “cut‑off” occurs: more than half of the solar energy cannot be used in principle. And this is just the beginning.

3.3. Losses at the Leaf Level: Reflection, Transmission, Thermal Dissipation

When light reaches the leaf surface, it is divided into three streams:

• part is reflected (5–10% of PAR in many crops, and up to 30–50% in plants with waxy coatings or pubescence);
• part passes through the leaf (transmitted);
• and only the remainder is absorbed by pigments (Kuznetsov & Dmitrieva, 2006; Medvedev, 2012).

The fraction of absorbed PAR depends on leaf type, age, and illumination. In general, a mature green leaf absorbs 80–90% of the PAR falling on it. But even from the absorbed energy, not all goes into photochemistry. A significant portion is converted to heat – this is a protective mechanism, especially important on bright sunny days when light absorption exceeds the capacity of the photosynthetic apparatus. This process, called non‑photochemical quenching, allows excess energy to be dissipated as heat via the xanthophyll cycle, preventing damage to reaction centres (Taiz et al., 2023).

Thus, even after absorption by the leaf, we lose energy to heat. But the main losses await us further – at the stage of photochemical and biochemical transformations.

3.4. Photochemical Limit: Quantum Yield

Let us move to the molecular level. The primary photochemical reaction is the excitation of electrons in the reaction centres of photosystems. This requires the energy of a light quantum. The theoretical quantum yield of photosynthesis is the maximum number of CO₂ molecules that can be fixed per absorbed light quantum. Based on the stoichiometry of light reactions and the Calvin cycle, at least 8 quanta of light are required to fix one CO₂ molecule in C₃ plants (4 quanta per photosystem) (Morot‑Gaudry et al., 2012; Schopfer & Brennicke, 2016). This means that the quantum yield ideally cannot exceed 0.125 mol CO₂ per mol of quanta.

Under real conditions, especially in the presence of photorespiration, the quantum yield for C₃ plants is about 0.05–0.07 mol CO₂ per mol of quanta. For C₄ plants, in which photorespiration is suppressed, this value remains at 0.06–0.07, but it is not higher because of the additional energy costs of the C₄ concentrating mechanism (Taiz et al., 2023). Why do we not reach the theoretical maximum? The main reason is photorespiration, which we will discuss separately. In addition, part of the energy of excited electrons is inevitably lost as fluorescence and heat.

3.5. Energy Balance of the Calvin Cycle and Respiration

Even if quanta have successfully launched electron transport and produced ATP and NADPH, that is not yet biomass. Next comes the Calvin cycle – and here we face energy costs. To synthesise one molecule of glucose (C₆H₁₂O₆), 18 molecules of ATP and 12 molecules of NADPH are required (Farquhar & Sharkey, 1994; Schopfer & Brennicke, 2016). This is a large “payment” for carbon reduction. But even this is not all the losses – part of the synthesised organic matter is immediately consumed by respiration.

Respiration (mitochondrial) proceeds in all living cells, both in the light and in the dark. It oxidises part of the photoassimilates, providing cells with energy for all life processes. Over a day, respiration can consume from 25 to 50% or even more of the carbohydrates synthesised during the day (Connor et al., 2011; Lambers & Oliveira, 2019). The proportion of respiratory losses is especially high in slow‑growing species and under stress conditions.

In addition, in C₃ plants, photorespiration plays a significant role – a process in which oxygen competes with carbon dioxide for the active site of the enzyme Rubisco, leading to the formation of glycolate and the loss of some previously fixed carbon as CO₂. Under conditions of high temperature and low CO₂ concentration, photorespiration can “eat up” up to 30–40% of the carbon assimilated during the light phase (Medvedev, 2012; Tretyakov et al., 2000). This is one of the main reasons why C₃ plants are less efficient in hot climates than C₄.

3.6. What Is RUE and Why Is It So Low?

All these losses can be combined into one integral indicator – Radiation Use Efficiency (RUE). RUE is the ratio of accumulated biomass (dry matter) to the amount of intercepted PAR. Units: grams of dry matter per megajoule of intercepted PAR (g/MJ) (Connor et al., 2011).

The theoretical maximum of RUE can be estimated as follows (Connor et al., 2011; Farquhar & Sharkey, 1994). Assume that 1 MJ of solar energy contains about 2.06 mol of PAR quanta. Of these, about 8% is reflected, 10% is absorbed inefficiently (heat), leaving 1.69 mol of quanta for photosynthesis. With a quantum yield of 0.10 mol CO₂ per mol of quanta (an optimistic estimate), 0.169 mol of CH₂O is formed, which corresponds to 5.07 g of glucose per 1 MJ. But respiration consumes about one third, leaving a net production of about 3.4 g dry matter per MJ. This is the theoretical maximum of RUE (Connor et al., 2011).

However, in a real crop, actual RUE is much lower. Even in the best C₄ crops (maize, sorghum, sugarcane) during short periods of maximum productivity, RUE can reach 2.5–3.5 g/MJ, while in C₃ crops it is 1.5–2.5 g/MJ (Connor et al., 2011). Average values over the entire growing season are even lower. Why is even the theoretical maximum not reached? Because we have not considered many factors:

• Non‑ideal canopy architecture: some light falls on the soil or on non‑functioning organs.
• Leaf senescence: with age, the photosynthetic apparatus degrades, and RUE drops.
• Stress: drought, salinity, nutrient deficiency, diseases – all reduce photosynthetic efficiency and increase respiratory losses.
• Sink limitation: if the plant does not have sufficient demand for assimilates (e.g., because of a small number of flowers or fruits), photosynthesis is inhibited by negative feedback – accumulation of carbohydrates suppresses the expression of photosynthetic genes.

3.7. Comparison of RUE in C₃ and C₄ Plants

The differences in RUE between C₃ and C₄ plants are a classic example of physiological adaptation. C₄ plants have almost no photorespiration, so under high temperatures and bright light they have an advantage: their RUE is 30–50% higher (Connor et al., 2011; Taiz et al., 2023). However, C₃ plants have their own “niches”: at low temperatures and under low light (e.g., at the beginning and end of the growing season, or under diffuse light), their efficiency can be higher because the C₄ mechanism requires additional energy for the CO₂ pump, and under cold conditions this mechanism works inefficiently.

That is why in temperate latitudes we grow wheat, barley, oats, potatoes – C₃ crops – while in the tropics and subtropics we grow maize, sorghum, sugarcane – C₄ crops. Global warming may shift the balance in favour of C₄ species in some regions.

3.8. Why Is Canopy RUE Lower Than That of an Individual Leaf?

Interestingly, the RUE of an individual leaf, measured under ideal conditions, is often higher than the RUE of the whole canopy. This is because in the canopy, leaves do not all operate at full capacity simultaneously. Upper leaves may be light‑saturated and work inefficiently (excess light, part goes to heat), while lower leaves are light‑limited. In addition, the spectral composition of light changes within the canopy: the proportion of far‑red light increases, which is absorbed less strongly, also reducing quantum efficiency. Finally, respiration of the entire biomass (including stems, roots, senescing organs) reduces net gain. Therefore, when calculating yield, we always deal with an averaged RUE, which determines how much dry matter accumulates by the end of the season (Connor et al., 2011; Schopfer & Brennicke, 2016).

3.9. Summary of the Section: Why Most Energy Is Lost

Let us briefly summarise the losses:

1. Spectral losses (~55%): only PAR (400–700 nm) can be used.

2. Reflection and transmission (~10–20% of PAR): part of the light is not absorbed by leaves.

3. Thermal dissipation and fluorescence (~10–15% of absorbed): part of the excitation energy does not reach photochemistry.

4. Photorespiration (in C₃) and respiration (all plants): up to 30–50% of fixed carbon is consumed for maintenance.

5. Non‑ideal canopy performance: light is distributed unevenly, some falls on the soil.

As a result, even in the most productive crops, the efficiency of conversion of solar energy into chemical energy of biomass is no more than 3–5%, and most often 0.5–2%. This may seem negligible, but it is this small efficiency that feeds all of humanity. That is why any way to increase RUE – whether through breeding more efficient varieties, improving canopy architecture, or combating stress – has a huge agronomic impact.

Key terms of this section:

• PAR (photosynthetically active radiation) – the part of the solar spectrum (400–700 nm) used for photosynthesis.
• Quantum yield – the number of CO₂ molecules fixed per absorbed quantum of light; theoretical maximum 0.125, actual 0.04–0.07.
• RUE (Radiation Use Efficiency) – efficiency of radiation use (g dry matter per MJ of intercepted PAR).
• Non‑photochemical quenching – a mechanism for dissipating excess light energy as heat via the xanthophyll cycle.
• Photorespiration – a process in which Rubisco fixes O₂ instead of CO₂, leading to carbon loss and reduced quantum yield.
• Theoretical maximum of RUE – about 3.4 g/MJ; actual in C₄ crops up to 3.5 g/MJ, in C₃ up to 2.5 g/MJ.

In the next section, we will look at how gross photosynthesis and respiration combine to form the net carbon balance of the crop, and how this determines the final yield.

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4.1. Gross and Net Photosynthesis: A First Approximation

Let us start with formal definitions. Gross photosynthesis is the total amount of CO₂ fixed by photosynthetic organs per unit time. Net photosynthesis (or apparent photosynthesis) is the difference between the amount of CO₂ fixed and the amount of CO₂ released by respiration (Farquhar & Sharkey, 1994; Schopfer & Brennicke, 2016).

In classic experiments, this is measured as leaf gas exchange. If you place a leaf in a closed chamber in the dark, it will release CO₂ (respiration). In the light, it will begin to absorb CO₂ (photosynthesis), but complete absorption will not occur until light intensity exceeds the light compensation point – the moment when photosynthesis and respiration are balanced (Schopfer & Brennicke, 2016). Above this point, net carbon accumulation (net photosynthesis) begins.

However, at the whole‑crop level the situation is more complex because:

• the crop contains not only leaves, but also stems, roots, flowers, fruits – all of which respire, but not all photosynthesise;
• respiration does not stop even in the light (although part of it is suppressed by the Kok effect);
• in addition, C₃ plants have photorespiration, which also releases CO₂, and it is difficult to separate from mitochondrial respiration in gas‑exchange measurements (Farquhar & Sharkey, 1994).

Therefore, the full carbon balance of a crop is described by an equation similar to that of Ivanov (Tretyakov et al., 2000):

where “losses” may include root exudates, volatile organic compounds, and “litter” – dead parts (leaves, roots).

4.2. Respiration: Not Just Loss, but a Necessity

Respiration is often perceived only as an unavoidable cost. In fact, respiration is a fundamental process that supports all life functions of the plant. It supplies energy (ATP) and carbon skeletons for the synthesis of new cells, active ion transport, maintenance of membrane potentials, and protein turnover. The carbon “lost” through respiration is the price paid for life and growth.

In plant physiology, respiration is usually divided into three functional components (Lambers & Oliveira, 2019; Marschner, 2012):

1. Growth respiration – energy and substrates spent on synthesising new biomass. This is an obligatory cost for creating every new cell. It accounts for approximately 20–30% of total respiration in fast‑growing plants and depends on the chemical composition of the tissue being synthesised (proteins, lipids, cellulose require different costs).

2. Maintenance respiration – costs for protein turnover, maintenance of ion gradients, membrane repair, and other processes necessary to preserve existing biomass. In old or slow‑growing plants, the maintenance fraction increases to 50–80%.

3. Ion transport respiration – costs for ion uptake from the soil and their transport in xylem and phloem. In roots, this fraction is especially large and can account for up to 30–50% of total root respiration, especially under low nutrient availability (Lambers & Oliveira, 2019).

Thus, total plant respiration can be written as:

And each of these components depends strongly on environmental conditions and the state of the plant.

4.3. How Much Carbon Does Respiration “Consume”?

To estimate the scale of losses, we can give the following data (Lambers & Oliveira, 2019; Connor et al., 2011):

• On average, plants spend 25 to 50% (and sometimes up to 70%) of the carbon fixed in photosynthesis on respiration per day.
• In young, actively growing plants, the proportion of growth respiration is high, but it “pays off” quickly: new photosynthetic surface is created.
• In senescing or stress‑exposed plants (drought, salinity, nitrogen deficiency), the proportion of maintenance respiration increases because costs for repair and osmotic regulation rise.

Interestingly, in slow‑growing species (e.g., perennial grasses or trees), the share of respiration in the balance is often higher than in fast‑growing cultivars (Lambers & Oliveira, 2019). This is one reason why breeders aim for fast‑growing varieties with a high proportion of growth respiration (compensated by rapid yield formation) and minimal maintenance costs.

At the canopy level, total respiration is the sum of:

• respiration of all above‑ground green parts (leaves, stems, ears);
• root respiration, which is especially high in cereals and legumes with developed root systems;
• respiration of soil microflora, which oxidises root exudates and litter (so‑called heterotrophic soil respiration).

In the field, soil respiration can account for 30–60% of the total agroecosystem respiration, making assessment of the crop carbon balance a complex task that requires accounting for soil processes.

4.4. Photorespiration as an Additional Loss in C₃ Plants

A special case is photorespiration, which we have already briefly mentioned. In C₃ plants, which include most temperate crops (wheat, barley, rice, potato, soybean, sunflower), about 25–30% of fixed carbon may be lost as CO₂ through photorespiration, and at high temperatures and low CO₂ concentration (e.g., when stomata are closed at midday), losses can reach 40–50% (Medvedev, 2012; Tretyakov et al., 2000). In C₄ plants, photorespiration is virtually absent (less than 5–6%) because CO₂ is concentrated in bundle‑sheath cells, suppressing the oxygenase activity of Rubisco (Medvedev, 2012; Kuznetsov & Dmitrieva, 2006).

Thus, in C₃ plants gross photosynthesis may be high, but net gain is significantly lower because of photorespiration. This explains why in hot regions C₄ crops (maize, sorghum) are often more productive.

4.5. Carbon Balance and Growth: Dependence on Developmental Stage

The carbon balance of a crop is not static – it changes during the growing season. At early development, when the leaf apparatus is just forming, growth respiration may exceed or be comparable to photosynthesis, so net gain is small. Then, when the critical LAI is reached, net photosynthesis is maximal, and the crop rapidly accumulates biomass. At flowering and grain filling, respiration of the whole plant (especially respiration of stems, roots, and developing fruits) may increase again, and net biomass gain slows down or even becomes negative (if respiration of old leaves and roots exceeds photosynthesis of the remaining green parts) (Connor et al., 2011; Tretyakov et al., 2000).

This is well illustrated in annual crops: first exponential growth of leaf mass, then linear growth of total biomass, and finally carbon accumulation in reproductive organs through remobilisation of assimilates from vegetative parts (Farquhar & Sharkey, 1994). At this stage, the carbon balance of the whole crop may become negative if respiration of old leaves and roots is not compensated by photosynthesis of the ear or fruits.

4.6. Measuring Carbon Balance at the Canopy Level

For practical assessment of crop carbon balance, several approaches are used:

1. Gas‑exchange methods (infrared gas analysers) – measurement of CO₂ and H₂O above the crop (micrometeorological methods) or in chambers (Tretyakov et al., 2000). They allow calculation of net ecosystem exchange (NEE).

2. Harvest (biomass) method – periodic sampling and determination of dry mass (direct method).

3. Photosynthetic potential method – integral of leaf area index over time. This indicator correlates with yield (Connor et al., 2011; Tretyakov et al., 2000).

However, all these methods give only an approximate picture. A true carbon balance is only possible with simultaneous accounting of photosynthesis, respiration of all organs (including roots and soil microflora), and carbon fluxes into the soil.

4.7. Practical Significance: How Carbon Balance Drives Yield

Understanding the carbon balance is important for practice. If we know that yield is determined by the difference between photosynthesis and respiration, then yield can be managed in two ways:

• Increase gross photosynthesis (through improved light interception, elevated CO₂, breeding for more efficient photosynthesis).
• Reduce respiratory losses (by breeding for lower maintenance respiration, optimising water supply, combating diseases that increase respiration in affected tissues).

However, breeding for lower respiration is not always beneficial, because respiration supports growth. The goal is not simply to reduce respiration, but to change its structure: increase the proportion of growth respiration and reduce maintenance. This is achieved through accelerated development, early yield formation, and shortening of the growing period.

Another important point: under stress conditions (drought, salinity, high temperatures), the proportion of maintenance respiration increases sharply due to the need for osmoprotectant synthesis, membrane repair, and activation of defence systems (Lambers & Oliveira, 2019). Therefore, drought‑tolerant varieties are not only those that transpire less, but also those in which respiratory losses under stress are minimal.

4.8. Summary of the Section: Net Productivity and Its Components

Thus, the carbon balance of a crop is an integral result of:

• Gross photosynthesis – determined by light interception, Rubisco activity, and CO₂ availability.
• Respiration – composed of three components (growth, maintenance, transport), each depending on developmental stage, environment, and genotype.
• Photorespiration – an additional loss in C₃ plants, which can be reduced by CO₂ enrichment or breeding.

Ultimately, net crop productivity (net biomass increment) is what remains for yield formation. Agricultural practice aims to maximise this: through management of plant density, sowing dates, nitrogen fertilisation, and irrigation. Understanding all components of the carbon balance is the key to sound crop management.

Key terms of this section:

• Gross photosynthesis – total amount of CO₂ fixed without considering respiration.
• Net photosynthesis (apparent photosynthesis) – the difference between gross photosynthesis and respiration (including photorespiration).
• Growth respiration – energy and substrates spent on synthesising new biomass.
• Maintenance respiration – costs for protein turnover, gradient maintenance, repair.
• Ion transport respiration – costs for ion uptake and transport from the soil.
• Photorespiration – a carbon‑loss process in C₃ plants due to the oxygenase activity of Rubisco.
• Net primary productivity – gross photosynthesis minus all respiratory losses (mitochondrial + photorespiration).

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5.1. Breeding for Improved Light Interception and Canopy Architecture

As we have discussed, light interception is determined by two key parameters: leaf area index (LAI) and canopy architecture (extinction coefficient k). Both are heritable traits that can be improved by breeding.

Optimising LAI. In modern high‑yielding cereal varieties, LAI at flowering reaches 5–8, whereas in older varieties and wild forms it was much lower (Connor et al., 2011). Breeders have deliberately selected forms with larger leaves and more leaves per stem to reach critical LAI faster and maintain it longer. However, there is a limit: too high an LAI leads to excessive shading of the lower layers and, consequently, to increased respiration of old leaves without additional photosynthesis. Therefore, modern breeding aims not simply for maximum LAI, but for the optimal LAI for specific conditions (light availability, growing season length, water supply).

Canopy architecture. Leaf angle is another important breeding trait (Taiz et al., 2023; Connor et al., 2011). In most modern rice, wheat, and maize varieties, the upper leaves have an erectoid (vertical) orientation, which improves light penetration into the canopy and increases photosynthesis in the lower layers. Middle leaves are often at intermediate angles, while lower leaves are more horizontal to capture diffuse light. This is achieved by selecting forms with specific internode lengths, leaf sheath stiffness, and photoperiod sensitivity.

Breeding for canopy architecture is a classic example of a physiological approach: we do not just increase leaf area, but create a spatial arrangement that maximises total light interception and ensures uniform illumination across layers. Such varieties allow denser planting without the risk of reduced productivity in lower leaves.

5.2. Increasing RUE: From Photosynthesis to Yield

Improving light interception is only half the battle. The second half is increasing the efficiency of using the intercepted light – that is, RUE (Farquhar & Sharkey, 1994; Connor et al., 2011). Here physiology opens several avenues.

Increasing quantum yield. The theoretical maximum for C₃ plants is 0.125 mol CO₂ per mol of quanta, but actual values are 0.05–0.07 because of photorespiration and other losses. Reducing photorespiration is one goal. This can be done by:

• breeding for higher Rubisco specificity for CO₂ over O₂ (however, in most species this specificity is already close to the evolutionary optimum);
• creating varieties with more efficient glycolate metabolism (e.g., enhanced carbon re‑utilisation from the glycolate cycle);
• genetic engineering aimed at introducing elements of the C₄ CO₂‑concentrating mechanism into C₃ plants (this is one of the most ambitious tasks in modern physiology).

For C₄ plants, the task is different: their photosynthesis is already close to the quantum limit at high temperatures, but at low temperatures their RUE drops because of the extra energy cost of the C₄ pump. Therefore, breeding C₄ crops for cold tolerance is also a physiological challenge.

Improving Rubisco performance. Rubisco is a slow enzyme; its catalytic turnover number (molecules of substrate converted per unit time) is only 3–5 s⁻¹, whereas most enzymes have orders of magnitude higher rates. Therefore, increasing the amount or activity of Rubisco is a direct route to higher photosynthesis (Farquhar & Sharkey, 1994). However, there is a nuance: Rubisco contains a lot of nitrogen (up to 25% of total leaf nitrogen in C₃ plants). Thus, increasing Rubisco requires additional nitrogen nutrition, and under nitrogen deficiency this becomes limiting. Breeders seek forms with more efficient Rubisco (high ratio of maximum velocity to nitrogen content) or with optimised nitrogen distribution among leaves of different ages (Taiz et al., 2023).

Improving RuBP regeneration. The rate of photosynthesis is often limited not by carboxylation, but by the regeneration of ribulose‑1,5‑bisphosphate (RuBP) – a process dependent on electron transport and ATP production. Increasing the efficiency of electron transport, raising the content of cytochromes and plastoquinones, and improving coupling with phosphorylation are all potential targets for breeding and biotechnology (Farquhar & Sharkey, 1994).

5.3. Managing Source–Sink Relations: The Role of the Sink

We have already mentioned that photosynthesis is not always limited by light or CO₂. Often it is limited by the plant’s ability to use assimilates – so‑called sink limitation (Marschner, 2012; Farquhar & Sharkey, 1994). If the plant has few fruits, tubers, or other storage organs, excess carbohydrates in leaves suppress photosynthesis through feedback – accumulation of sugars represses genes encoding photosynthetic enzymes, and also causes starch accumulation in chloroplasts, which mechanically disrupts their structure.

The physiological approach to solving this problem is to create a balanced source–sink system. This is achieved in two ways:

• breeding to increase the number and capacity of acceptor organs (e.g., number of grains per ear, tuber size, fruit mass);
• agronomic practices that stimulate acceptor growth (e.g., fertilisation at critical stages, regulation of plant density).

Interestingly, in many crops, breeding has effectively proceeded along the path of increasing sink strength: selection for large ears, high grain number, and high harvest index (the proportion of economically valuable part in total biomass) (Connor et al., 2011). This has led to modern varieties where sink is often no longer limiting, and efforts are now directed at increasing photosynthesis – to supply this enhanced sink with assimilates. Thus, we return to the task of increasing RUE and gross photosynthesis, but now in combination with a strengthened sink.

5.4. Reducing Respiratory Losses: How Not to Lose Yield

Respiration, as we have seen, can consume up to half or more of fixed carbon. Breeding to reduce respiratory losses is a major task of physiology (Lambers & Oliveira, 2019). But care must be taken: we cannot simply reduce respiration without disrupting growth. Therefore, the strategy is:

• Reducing maintenance respiration. This is achieved by selecting forms with more stable membranes, lower protein turnover rates (while maintaining functionality), and more efficient ion pumps. Resistance to stress is also important – under drought or salinity, maintenance respiration increases sharply, so drought‑tolerant varieties often also have lower maintenance respiration under water deficit.
• Optimising growth respiration. In fast‑growing varieties, growth respiration accounts for a larger share than maintenance respiration, and this is beneficial because it is compensated by rapid biomass production. Breeding for accelerated development and early yield formation is essentially breeding to shift the balance towards growth respiration.
• Reducing photorespiration (for C₃ plants) – one of the most effective ways to cut losses, but so far real success in breeding for reduced photorespiration without yield loss has not been achieved (Farquhar & Sharkey, 1994). However, genetic approaches (e.g., introducing bacterial glycolate utilisation pathways that do not release CO₂) promise a breakthrough in the future.

It is also important to consider that root respiration depends strongly on nutrient availability. Under nitrogen or phosphorus deficiency, roots must spend more energy on ion uptake, increasing the transport respiration fraction (Lambers & Oliveira, 2019). Therefore, optimising mineral nutrition is also a physiological way to reduce respiratory losses and increase the share of carbon going to yield.

5.5. Using Physiological Markers in Breeding

Breeding for yield is a long and labour‑intensive process, especially when the trait is polygenic. Physiology offers rapid and informative markers that allow assessment of potential productivity even before harvest. Among them:

• Stable carbon isotopes (¹³C). As we discussed, the Δ¹³C/¹²C ratio in plant tissues reflects the ratio of internal to atmospheric CO₂ concentration (c_i/c_a), which in turn relates to water status and photosynthesis (Farquhar & Sharkey, 1994; Taiz et al., 2023). In C₃ plants, more negative Δ¹³C values correspond to more open stomata and, consequently, higher photosynthetic activity, but also higher transpiration losses. This marker is widely used for selecting drought‑tolerant forms.
• Chlorophyll fluorescence. A rapid and non‑destructive method for assessing photosystem II efficiency. Parameters F_v/F_m (maximum quantum yield) and Ψ_PSII (actual quantum yield) allow evaluation of the state of the photosynthetic apparatus, degree of photodamage, and overall plant health (Taiz et al., 2023). This enables selection of forms resistant to stress (drought, high temperature, salinity) or having high photosynthetic potential.
• Gas‑exchange measurements. Direct measurement of CO₂ gas exchange in the field (using portable infrared gas analysers) allows assessment not only of current photosynthesis, but also of stomatal conductance and intercellular CO₂ concentration, providing information on limiting factors (Tretyakov et al., 2000).
• Leaf chlorophyll and nitrogen content. Although, as we mentioned, the direct relationship between chlorophyll content and photosynthesis is not always clear, this indicator is often used as an integral indicator of nitrogen status and potential photosynthetic activity (Marschner, 2012).

These methods allow breeders to perform early selection of promising genotypes without waiting for the end of the growing season, and to evaluate the physiological status of plants over time.

5.6. Physiological Crop Management: From Theory to Practice

Besides breeding, physiological knowledge is applied directly in crop management:

• Optimising plant density – to reach critical LAI at the right time, but not exceed it. This is a calculation based on knowledge of variety architecture and regional radiation regime (Connor et al., 2011).
• Regulating nitrogen nutrition – nitrogen affects not only growth, but also photosynthesis (Rubisco synthesis) and respiration. The timing and rates of nitrogen application are chosen to prolong the active work of the photosynthetic apparatus and avoid excessive vegetative growth at the expense of yield (Marschner, 2012; Tretyakov et al., 2000).
• Irrigation and drought management – knowledge of how water deficit affects stomatal conductance and photosynthesis allows the choice of irrigation strategies (e.g., drip irrigation to maintain optimal moisture, or hardening droughts to induce adaptation).
• Use of growth regulators – some phytohormones (e.g., cytokinins) can stimulate assimilate export from leaves and delay senescence, thereby increasing photosynthetic potential (Marschner, 2012). Others (e.g., retardants) reduce vegetative growth, redirecting assimilates to fruits.

It is important to understand that physiological approaches do not replace agronomic practices – they justify and refine them. Knowing how the photosynthetic apparatus and respiration actually work, the agronomist can make informed decisions rather than follow templates.

5.7. The Main Conclusion: Physiology as the Foundation of Intelligent Crop Production

Thus, we have completed our journey from leaf to yield. What have we learned?

1. High photosynthesis of an individual leaf is a necessary but not sufficient condition for high yield. Yield is determined by light interception, RUE, carbon balance, and source–sink relations at the whole‑crop level.

2. Physiology provides keys to improving each of these parameters: canopy architecture, photosynthetic efficiency, reduction of respiratory losses, source–sink balance – all are manageable physiological traits.

3. Breeding armed with physiological markers allows targeted development of varieties with desired properties, accelerating progress.

4. Agronomic practices based on physiological principles allow the genetic potential of a variety to be realised, adapting it to specific conditions of the year and region.

Ultimately, plant physiology is the science of how to obtain a crop from a sunbeam, water, and CO₂. And every percentage increase in the efficiency of this process means additional tonnes of grain, root crops, or other products so essential to humanity.

Key terms of this section:

• Source–sink relations – the system of connections between source organs (donors) and consumer organs (acceptors) of assimilates, determining carbon distribution.
• Physiological markers – measurable indicators (isotopic composition, fluorescence, gas exchange) that allow assessment of potential productivity and stress tolerance of genotypes.
• Harvest index – the proportion of the economically valuable part of the plant in total biomass; a breeding trait closely related to source–sink relations.
• Sink limitation – a situation where photosynthesis is limited not by light or CO₂, but by the plant’s ability to use assimilates for growth and storage.
• Retardants – growth regulators that reduce vegetative growth and redirect assimilates to reproductive organs.