How the Root System Affects Yield

Dr. Vijayalaxmi Kinhal

December 12, 2022 at 5:44 pm | Updated December 12, 2022 at 5:44 pm | 9 min read

There is an urgent need to maintain and boost yield, especially as crops face escalating drought and heat stress due to climate change. Therefore, features and functions of the root system that influence the role it plays in providing plants nutrients and water in all kinds of environments are increasingly becoming a focus of crop research. In this venture, the availability of a new generation of tools to scan underground growth is allowing scientists to promote root growth.  

Root System Architecture 

Root system architecture or morphology will differ depending on the species, cultivars, soil conditions, and farm management systems. Over short periods, water availability will also change root distribution.  

It is a fact that any decrease in water can slow down biomass accumulation and, therefore, the yield of crops. Water is a raw material for photosynthesis. Also, roots absorb major and minor nutrients to form the bio compounds that create the plants and biomass. 

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Therefore, the root system architecture is emerging as an important parameter as a selection criterion for crop breeding programs to promote root growth. 

To find out which of the root features can improve plant productivity, Enoch studied how root system architecture affected yield in soybean for his Master’s thesis, submitted in 2021. 

The crop scientist experimented with 11 soybean genotypes for rainfed conditions. The breeding lines used were R01-581F, Boggs, NC-Roy, N06-7023, N09-12854, NC-Raleigh, N09-13890, SC-14-1127, SC07-1518RR, Crockett, and USDA-N8002. The breeding lines were selected as they had different desirable traits like delayed leaf wilting or sustained nitrogen fixation in drought conditions. NC-Raleigh and SC07-1518RR were conventional high-yielding lines.  

He planted them in the compact clayey soils of Pendleton and sandy soils of Florence in South Carolina. The breeding lines were grown as rainfed crops with no irrigation in the summer for two seasons in 2019 and 2020.  

Root system architecture and development were studied, affecting water-use efficiency, leaf area index, biomass production, seed yield, and field yield.

Figure 1: “Process of root imager tube installation and data collection. To install access tubes for the root imager, a hole was made at 45-degree angle using hydraulic probe (A). A hollow acrylic tube was inserted into the hole, and the gap was filled with soil (B). CI-602 root imager was put into the acrylic tube, and the roots were imaged at various depths (C). The collected images were analyzed by RootSnap! Software (D),” Enoch 2021. (Image credits:  

To examine root system architecture non-destructively, a minirhizotron system, the CI-602 Narrow Gauge Root Imager produced by CID-Bioscience, was used. Soil cores were bored, and transparent acrylic root tubes 0.06 m wide and 1.05 m long were installed at an angle of 45 degrees. A cap covered the tube tops to prevent rainwater from entering. These root tubes remained in the soil while the roots grew around them throughout the experiment.  

A cylindrical scanner with a camera head was inserted to scan roots at different soil depths of 0–18, 19–35, 36–52, and 53–70 cm. The camera was rotated, to give a clear 360-degree view of root growth. The images were later analyzed in the laboratory using the associated software RootSnap! 

Root parameters studied were root count and length at the four depths. Each year, scans were made four times in Pendleton and twice at Florence. 

Crop water use was measured by a neutron moisture meter to estimate total stored water at different soil depths and soil water depletion through evapotranspiration.  

The biomass and leaf area index was harvested by hand at intervals from 47 to 146 days after planting. A plant canopy analyzer measured the leaf area index, and biomass was dried to calculate the dry weight. 

At harvest maturity, whole plants were harvested, and seeds were separated and weighed.  

Root growth patterns 

Figure 2: “Changes in total root count and total root length of the soybean genotypes in  

2019 and 2020 at Pendleton and Florence. DAP–days after planting,” Enoch 2021. (Image credits:  

The scientists found root growth was twice as much in sandy soils compared to clay soils. The difference based on genotypes became more apparent later in the crop cycle, 80 days after planting, regardless of soil type. In addition, different genotypes varied in their response to weather in the two years and at different depths of the soils. 

The highest yield or biomass accumulation occurred in three lines- the elite SC07-1518RR, the exotic pedigree line N09-12854, and the slow wilting line N09-13890. These superior results in yields were due to various root responses: 

Parsimonious root phenotype: The exotic N09-12854 had fewer roots and less root length in 2020 with normal rains and the best leaf area index. This genotype prioritized above-ground growth over belowground when resources were abundant. The line improved water use efficiency without increasing water intake with a minor root system. The increased allocation to above-ground parts boosted the yield. This is an example of a parsimonious root phenotype. In 2019, when there was less rainfall, the line increased root production and size to increase access to necessary resources. As a result, good above-ground growth was reflected in the leaf area index, biomass, and seed yield at both locations. 

The slow wilting line also has a parsimonious root system. The N09-13890 had less root count and length regardless of water availability. Yet this line showed the best water use efficiency and biomass accumulation.   

Deep rooting type: The SC07-1518RR had one of the best biomass accumulation, seed yield, and leaf area indexes in both years. Its root count and length were intermediary, but it had most roots in deep soils at 53-70 cm. This occurred even in compacted clay-type soils, showing good root penetrability. Roots were deeper in the drier season than in the wetter 2020. This line promotes root growth and distribution during drier seasons without sacrificing above-ground growth.  

Based on the results, Enoch recommended the three high yielders for growing soybeans where conditions are optimal and also in drought. In addition, the SC07-1518RR is useful for developing varieties for compacted and clayey soils. 

Root Anatomy 

Scientists are investigating if root anatomy can explain the observed yield gap in soybean between potential and actual yield in drought conditions but not in well-watered soils.  

Xylem, the tissue that conducts water from roots into the above-ground parts to the leaves, is another root phene or trait that influences water uptake and use. Plant scientists from the University of Missouri reasoned that improving water uptake and use in soybean could solve the problem and wanted to test if xylem could provide a solution in these cases.  

Plastic genotypes that can change in morphological and anatomical response to environmental conditions have been reported in many pulses.   

Thus, the plant scientists Prince, Murphy, Mutava, Durnell, Valliyodan, Shannon, and Nguyen tested if increasing the number of metaxylem increased yield in drought and well-watered conditions, in 41 accessions, in addition to root system architecture. Furthermore, these genotypes were grown in varying environmental conditions like greenhouses and fields. 

Metaxylem are formed after protoxylems in the vascular bundles in the interior and are not affected by stress. 


Figure 3: “Root anatomical analysis of soybean LG05-4317 using Rootscan software with various root anatomical features shown. A: aerenchyma; CCFN: cortical cell file number; P: phloem; MX: metaxylem,” Prince et al. 2017. (Image credits:  

The plant scientist conducted four experiments, two in greenhouses and two in open fields. 

Greenhouse trials – Soyabean seeds were germinated and removed at the first leaf stage. The Soybean roots were scanned to study seedling architecture using a destructive method. Cross-sections were also taken from other seedlings to show metaxylem, see Figure 3. 

A greenhouse trial also grew all the accessions with irrigated and drought treatments without water for 28 days. Then leaf area, gas exchange, and leaf wilting symptoms were recorded. Roots were also harvested, and cross-sections were made at the root-shoot junction to count xylem vessels and measure their size.  

Field trails– The 41 accessions were grown in irrigated and drought conditions (under rain shelter). Water available to plants and gas exchanges were recorded at three stages- early vegetative, early productive, and mid-seed filling stages. The Handheld Laser Leaf Area Meter CI-203 from CID Bio-Science Inc. was used for leaf area measurements at the last stage.  

Two other field trials at locations with different climates and soils (sandy and clayey) and watering conditions were conducted to evaluate biomass partitioning and allocation and water use efficiency. Shoot biomass was measured at pod filling and full maturity, as was field yield after harvest. Carbon and nitrogen isotopic analyses were also carried out for seeds.  

The plant scientist found variations in root length and metaxylem traits during drought.  

High-yielding varieties had total root length at the seedling stage and were crucial for determining yield also.  

In general, leaf area was less in drought conditions, except in three cases LG04-4717, LD02-4485, and Maverick. In these three genotypes, photosynthesis increased during the drought, accompanied by less stomatal conductance. In addition, one high-yielding variety PI 427136 has less leaf area, which helps to reduce water use and improve yield during drought.  

There were also a lot of variations in photosynthesis and stomatal conductance between genotypes and watering levels. High-yielding varieties had lower stomatal conductance and more photosynthesis, while lower yielders showed the reverse trend. 

Metaxylem positively influenced stomatal conductance and internal carbon dioxide levels, which improved photosynthesis and yield, as seen in high-yielding varieties. Metaxylem increased in numbers when canopy temperatures fell and enabled better water uptake. While xylem diameter increased water uptake hydraulic conductivity, the plant could reduce biomass allocation to root growth into deeper soils to access water. This biomass was allocated to produce flowers and late reproductive stages, even during a drought. This is the first study to show how metaxylem plasticity can help drought-stressed plants. It can be used as a selection criterion to identify enhanced water and nutrient uptake and used to improve yield. 

In addition, the study showed that other anatomical features, like the percentage of stele (the central tube in roots containing the xylem) and the surrounding cortex cells area, correlate with seed yield.  

Genotypes that could assimilate carbon and nitrogen at the leaf level increased seed yield in drought conditions. So, the concentrations of two elements can also be used as selection criteria to identify crop performance in drought. 

Root Physiology 

Physiology and biochemical reactions that promote root growth need to be well documented.  

Wu, S. Gu, H. Gu, Cheng, Li, Guo, Wang, He, Li, and Chen, horticulturists at the Zhengzhou Fruit Research Institute, Chinese Academy of Agricultural Sciences, checked the roles that root hormones in kiwifruit could play in promoting growth in response to the environment.  

Hormones provide regulatory signals and are involved in root structure, elongation, and lateral root formation. Brassinosteroids (BR) are one such group of endogenous hormones. However, its role in kiwifruits was unknown.  

They grew young seedlings of the variety Hongyang. The horticulturists treated kiwifruit roots with the BR hormone in four concentrations (0. 0.1, 1, 10, and 100 nM BR) and with 2 μM brassinazole (BRZ) that inhibits BR production for five weeks, once a week. Then they tested root length, surface area, and volume. Root hair growth was checked with the help of a microscope. Above-ground traits like stem diameter and plant height were recorded. Leaf area was measured non-destructively by the CI-203 Handheld Laser Leaf Area Meter, from CID Bioscience Inc.  

The best-growing plants from the BR, BRZ, and control were sent for transcriptome sequencing. Later gene expression, functional annotation, and enrichment analyses were carried out, besides polymerase chain reaction tests.  


Figure 4: “The phenotype of kiwifruit seedlings in response to brassinosteroid (BR) and brassinazole (BRZ) treatment. (A) Macromorphology of ‘Hongyang’ seedlings before and after treatment (scale bar = 1 cm). (B–G) Quantitation of the root and aerial part (root length, root surface area, root volume, stem diameter, plant height, leaf area),” Wu et al. 2022. (Image credits: 

The horticulturists found the roots of kiwifruits are fleshy and, therefore, easily affected by the environment. They often can’t absorb enough water and nutrients, weakening the kiwifruit tree and lowering productivity. External applications of BR do help but are dependent on doses in enhancing root length, volume, and lateral growth. The most effective dose was 1nM BR in promoting all three root traits. This also was the best treatment to increase leaf area, stem diameter, and plant height, see Figure 4.  

As expected BRZ inhibited root and shoot growth, see Figure 4.  

 BR improves lateral root growth, vital for the root structure, by controlling auxin distribution by upregulating the genes for its production and the auxin transporters. However, the transcription studies showed that the BRZ had the opposite effect. Also, the gene AcLBD16/18, which promotes lateral roots, was upregulated by BR and down-regulated by BRZ.  

Moreover, BR resulted in auxin accumulation by promoting the expression of the gene AcSAUR, which inhibits AcPP2C-D, further helping lateral root growth. This chain of events also enables the proton pump causing the cell wall to relax and absorb water.  

Morphology, Anatomy, and Physiology Promote Root Growth 

Scientists think root architecture, anatomy, and physiological traits or phenes can be used as selection criteria in crop breeding, as they all promote root growth and influence yield. In addition, using these phenes and modifying them should help develop cultivars with the plasticity to adapt to acute changes in water availability and other environmental cues to grow and produce in drought conditions.  


Alexopoulos, C., Moore, David J., and Vernon, A. (2020, February 27). Fungus. Encyclopedia Britannica. 


Noh, E. (2021). Root System Architecture that Improves Biomass Production and Yield of Soybean. [Master’s thesis, Graduate School of Clemson University]. All Theses. 3596. 


Prince, S. J., Murphy, M., Mutava, R. N., Durnell, L. A., Valliyodan, B., Grover Shannon, J., & Nguyen, H. T. (2017). Root xylem plasticity to improve water use and yield in water-stressed soybean. Journal of Experimental Botany. 


Wu, Z., Gu, S., Gu, H., Cheng, D., Li, L., Guo, X., Wang, M., He, S., Li, M., & Chen, J. (2022). Physiological and transcriptomic analyses of brassinosteroid function in Kiwifruit Root. Environmental and Experimental Botany, 194, 104685. 

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