Should Root Plasticity Be a Crop Breeding Target?

Wheat root systems as a breeding target for climate resilience

In the coming decades, larger genetic gains in yield will be necessary to meet projected demand, and this must be achieved despite the destabilizing impacts of climate change on crop production. The root systems of crops capture the water and nutrients needed to support crop growth, and improved root systems tailored to the challenges of specific agricultural environments could improve climate resiliency. Each component of root initiation, growth and development is controlled genetically and responds to the environment, which translates to a complex quantitative system to navigate for the breeder, but also a world of opportunity given the right tools. In this review, we argue that it is important to know more about the 'hidden half' of crop plants and hypothesize that crop improvement could be further enhanced using approaches that directly target selection for root system architecture. To explore these issues, we focus predominantly on bread wheat (Triticum aestivum L.), a staple crop that plays a major role in underpinning global food security. We review the tools available for root phenotyping under controlled and field conditions and the use of these platforms alongside modern genetics and genomics resources to dissect the genetic architecture controlling the wheat root system. To contextualize these advances for applied wheat breeding, we explore questions surrounding which root system architectures should be selected for, which agricultural environments and genetic trait configurations of breeding populations are these best suited to, and how might direct selection for these root ideotypes be implemented in practice.

Can smart nutrient applications optimize the plant's hidden half to improve drought resistance?

Global agriculture is challenged with achieving sustainable food security while the climate changes and the threat of drought increases. Much of the research attention has focused on above-ground plant responses with an aim to improve drought resistance. The hidden half, that is, the root system belowground, is receiving increasing attention as the interface of the plant with the soil. Because roots are a sensing organ for nutrients and moisture, we speculate that crop root system traits can be managed using smart nutrient application in order to increase drought resistance. Roots are known to be influenced both by their underlying genetics and also by responses to the environment, termed root plasticity. Though very little is known about the combined effect of water and nutrients on root plasticity, we explore the possibilities of root system manipulation by nutrient application. We compare the effects of different water or nutrient levels on root plasticity and its genetic regulation, with a focus on how this may affect drought resistance. We propose four primary mechanisms through which smart nutrient management can optimize root traits for drought resistance: (1) overall plant vigor, (2) increased root allocation, (3) influence specific root traits, and (4) use smart placement and timing to encourage deep rooting. In the longer term, we envision that beneficial root traits, including plasticity, could be bred into efficient varieties and combined with advanced precision management of water and nutrients to achieve agricultural sustainability.

Deciphering the genetic basis of wheat seminal root anatomy uncovers ancestral axial conductance alleles

Root axial conductance, which describes the ability of water to move through the xylem, contributes to the rate of water uptake from the soil throughout the whole plant lifecycle. Under the rainfed wheat agro-system, grain-filling is typically occurring during declining water availability (i.e., terminal drought). Therefore, preserving soil water moisture during grain filling could serve as a key adaptive trait. We hypothesized that lower wheat root axial conductance can promote higher yields under terminal drought. A segregating population derived from a cross between durum wheat and its direct progenitor wild emmer wheat was used to underpin the genetic basis of seminal root architectural and functional traits. We detected 75 QTL associated with seminal roots morphological, anatomical and physiological traits, with several hotspots harbouring co-localized QTL. We further validated the axial conductance and central metaxylem QTL using wild introgression lines. Field-based characterization of genotypes with contrasting axial conductance suggested the contribution of low axial conductance as a mechanism for water conservation during grain filling and consequent increase in grain size and yield. Our findings underscore the potential of harnessing wild alleles to reshape the wheat root system architecture and associated hydraulic properties for greater adaptability under changing climate.

Root hairs: the villi of plants

Strikingly, evolution shaped similar tubular structures at the µm to mm scale in roots of sessile plants and in small intestines of mobile mammals to ensure an efficient transfer of essential nutrients from 'dead matter' into biota. These structures, named root hairs (RHs) in plants and villi in mammals, numerously stretch into the environment, and extremely enlarge root and intestine surfaces. They are believed to forage for nutrients, and mediate their uptake. While the conceptional understanding of plant RH function in hydromineral nutrition seems clear, experimental evidence presented in textbooks is restricted to a very limited number of reference-nutrients. Here, we make an element-by-element journey through the periodic table and link individual nutrient availabilities to the development, structure/shape and function of RHs. Based on recent developments in molecular biology and the identification of mutants differing in number, length or other shape-related characteristics of RHs in various plant species, we present comprehensive advances in (i) the physiological role of RHs for the uptake of specific nutrients, (ii) the developmental and morphological responses of RHs to element availability and (iii) RH-localized nutrient transport proteins. Our update identifies crucial roles of RHs for hydromineral nutrition, mostly under nutrient and/or water limiting conditions, and highlights the influence of certain mineral availabilities on early stages of RH development, suggesting that nutritional stimuli, as deficiencies in P, Mn or B, can even dominate over intrinsic developmental programs underlying RH differentiation.

Synergy between a shallow root system with a DRO1 homologue and localized P application improves P uptake of lowland rice

Improved phosphorus (P) use efficiency for crop production is needed, given the depletion of phosphorus ore deposits, and increasing ecological concerns about its excessive use. Root system architecture (RSA) is important in efficiently capturing immobile P in soils, while agronomically, localized P application near the roots is a potential approach to address this issue. However, the interaction between genetic traits of RSA and localized P application has been little understood. Near-isogenic lines (NILs) and their parent of rice (qsor1-NIL, Dro1-NIL, and IR64, with shallow, deep, and intermediate root growth angles (RGA), respectively) were grown in flooded pots after placing P near the roots at transplanting (P-dipping). The experiment identified that the P-dipping created an available P hotspot at the plant base of the soil surface layer where the qsor1-NIL had the greatest root biomass and root surface area despite no genotyipic differences in total values, whereby the qsor1-NIL had significantly greater biomass and P uptake than the other genotypes in the P-dipping. The superior surface root development of qsor1-NIL could have facilitated P uptakes from the P hotspot, implying that P-use efficiency in crop production can be further increased by combining genetic traits of RSA and localized P application.

Soil Water Deficit and Fertilizer Placement Effects on Root Biomass Distribution, Soil Water Extraction, Water Use, Yield, and Yield Components of Soybean [Glycine max (L.) Merr.] Grown in 1-m Rooting Columns

Typical small-pot culture systems are not ideal for controlled environment phenotyping for drought tolerance, especially for root-related traits. We grew soybean plants in a greenhouse in 1-m rooting columns filled with amended field soil to test the effects of drought stress on water use, root growth, shoot growth, and yield components. There were three watering treatments, beginning at first flower: watered daily to 100% of the maximum soil water holding capacity (control), 75% (mild drought stress), or 50% (drought stress). We also tested whether applying fertilizer throughout the 1-m soil depth instead of only in the top 30 cm would modify root distribution by depth in the soil profile and thereby affect responses to drought stress. Distributing the fertilizer over the entire 1-m soil depth altered the root biomass distribution and volumetric soil water content profile at first flower, but these effects did not persist to maturity and thus did not enhance drought tolerance. Compared to the control (100%) watering treatment, the 50% watering treatment significantly reduced seed yield by 40%, pod number by 42%, seeds per pod by 3%, shoot dry matter by 48%, root dry matter by 53%, and water use by 52%. Effects of the 75% watering treatment were intermittent between the 50 and 100%. The 50% treatment significantly increased root-to-shoot dry matter ratio by 23%, harvest index by 17%, and water-use efficiency by 7%. Seed size was not affected by either fertilizer or watering treatments. More than 65% of the total root dry matter was distributed in the upper 20 cm of the profile in all watering treatments. However, the two drought stress treatments, especially the mild drought stress, had a greater proportion of root dry matter located in the deeper soil layers. The overall coefficient of variation for seed yield was low at 5.3%, suggesting good repeatability of the treatments. Drought stress imposed in this culture system affected yield components similarly to what is observed in the field, with pod number being the component most strongly affected. This system should be useful for identifying variation among soybean lines for a wide variety of traits related to drought tolerance.

Linking root and stem hydraulic traits to leaf physiological parameters in Coffea canephora clones with contrasting drought tolerance

Knowing the key hydraulic traits of different genotypes at early seedling stages can potentially provide crucial information and save time for breeding programs. In the current study we investigated: (1) how root, stem and whole plant conductivities are linked to xylem traits, and (2) how the integrated hydraulic system impacts leaf water potential, gas exchange, chlorophyll a fluorescence and the growth of three coffee cultivars (clones of Coffea canephora Pierre ex Froehner cv. Conilon) with known differences in drought tolerance. The Conilon clones CL 14, CL 5 V and CL 109A, classified as tolerant, moderately tolerant, and sensitive to drought respectively, were grown under non-limiting soil-water supply but high atmospheric demand (i.e., high VPD_air). CL 14 and CL 5 V displayed higher root and stem hydraulic conductance and conductivity, and higher whole plant conductivity than CL 109A, and these differences were associated with higher root growth traits. In addition, CL 109A exhibited a non-significant trend towards wider vessels. Collectively, these responses likely contributed to reduce leaf water potential in CL 109A, and in turn, reduced leaf gas exchange, especially during elevated VPD_air. Even when grown under well-watered conditions, the elevated VPD_air observed during this study resulted in key differences in the hydraulic traits between the cultivars corresponding to differences in plant water status, gas exchange, and photochemical activity. Together these results suggest that coffee hydraulic traits, even when grown under non-water stress conditions, can be considered in breeding programs targeting more productive and efficient genotypes under drought and high atmospheric demand.

Genetics and genomics of root system variation in adaptation to drought stress in cereal crops

Cereals are important crops worldwide that help meet food demands and nutritional needs. In recent years, cereal production has been challenged globally by frequent droughts and hot spells. A plant's root is the most relevant organ for the plant adaptation to stress conditions, playing pivotal roles in anchorage and the acquisition of soil-based resources. Thus, dissecting root system variations and trait selection for enhancing yield and sustainability under drought stress conditions should aid in future global food security. This review highlights the variations in root system attributes and their interplay with shoot architecture features to face water scarcity and maintain thus yield of major cereal crops. Further, we compile the root-related drought responsive quantitative trait loci/genes in cereal crops including their interspecies relationships using microsynteny to facilitate comparative genomic analyses. We then discuss the potential of an integrated strategy combining genomics and phenomics at genetic and epigenetic levels to explore natural genetic diversity as a basis for knowledge-based genome editing. Finally, we present an outline to establish innovative breeding leads for the rapid and optimized selection of root traits necessary to develop resilient crop varieties.

Challenges to design-oriented breeding of root system architecture adapted to climate change

Roots are essential organs for capturing water and nutrients from the soil. In particular, root system architecture (RSA) determines the extent of the region of the soil where water and nutrients can be gathered. As global climate change accelerates, it will be important to improve belowground plant parts, as well as aboveground ones, because roots are front-line organs in the response to abiotic stresses such as drought, flooding, and salinity stress. However, using conventional breeding based on phenotypic selection, it is difficult to select breeding lines possessing promising RSAs to adapted to abiotic stress because roots remain hidden underground. Therefore, new breeding strategies that do not require phenotypic selection are necessary. Recent advances in molecular biology and biotechnology can be applied to the design-oriented breeding of RSA without phenotypic selection. Here I summarize recent progress in RSA ideotypes as "design" and RSA-related gene resources as "materials" that will be needed in leveraging these technologies for the RSA breeding. I also highlight the future challenges to design-oriented breeding of RSA and explore solutions to these challenges.

An Analysis of Soil Coring Strategies to Estimate Root Depth in Maize (Zea mays) and Common Bean (Phaseolus vulgaris)

A soil coring protocol was developed to cooptimize the estimation of root length distribution (RLD) by depth and detection of functionally important variation in root system architecture (RSA) of maize and bean. The functional-structural model OpenSimRoot was used to perform in silico soil coring at six locations on three different maize and bean RSA phenotypes. Results were compared to two seasons of field soil coring and one trench. Two one-sided T-test (TOST) analysis of in silico data suggests a between-row location 5 cm from plant base (location 3), best estimates whole-plot RLD/D of deep, intermediate, and shallow RSA phenotypes, for both maize and bean. Quadratic discriminant analysis indicates location 3 has ~70% categorization accuracy for bean, while an in-row location next to the plant base (location 6) has ~85% categorization accuracy in maize. Analysis of field data suggests the more representative sampling locations vary by year and species. In silico and field studies suggest location 3 is most robust, although variation is significant among seasons, among replications within a field season, and among field soil coring, trench, and simulations. We propose that the characterization of the RLD profile as a dynamic rhizo canopy effectively describes how the RLD profile arises from interactions among an individual plant, its neighbors, and the pedosphere.

Maize lateral root developmental plasticity induced by mild water stress. II: Genotype-specific spatio-temporal effects on determinate development

Maize lateral roots exhibit determinate growth, whereby the meristem is genetically programmed to stop producing new cells. To explore whether lateral root determinacy is modified under water deficits, we studied two maize genotypes (B73 and FR697) with divergent responses of lateral root growth to mild water stress using an experimental system that provided near-stable water potential environments throughout lateral root development. First-order laterals of the primary root system of FR697 exhibited delayed determinacy when grown at a water potential of -0.28 MPa, resulting in longer and wider roots than in well-watered (WW) controls. In B73, in contrast, neither the length nor width of lateral roots was affected by water deficit. In water-stressed FR697, root elongation continued at or above the maximum rate in WW roots for 3 days longer, and was still 45% of maximum when WW roots approached their determinate length. Maintenance of root elongation was associated with sustained rates of cell production. In addition, kinematic analyses showed that reductions in tissue expansion rates with aging were delayed in the longitudinal, radial and tangential planes throughout the root growth zone. Thus, this study reveals large genotypic differences in the interaction of water stress with developmental determinacy of maize lateral roots.