Abstract
Selecting crops that express certain reproductive, leaf, and root traits has formed detectable, albeit diverse, crop domestication syndromes. However, scientific and informal on-farm research has primarily focused on understanding and managing linkages between only certain domestication traits and yield. There is strong evidence suggesting that functional traits can be used to hypothesize and detect trade-offs, constraints, and synergies among crop yield and other aspects of crop biology and agroecosystem function. Comparisons in the functional traits of crops vs. wild plants has emerged as a critical avenue that has helped inform a better understanding of how plant domestication has reshaped relationships among yield and traits. For instance, recent research has shown domestication has led important economic crops to express extreme functional trait values among plants globally, with potentially major implications for yield stability, nutrient acquisition strategies, and the success of ecological nutrient management. Here, we present an evidence synthesis of domestication effects on crop root functional traits, and their hypothesized impact on nutrient acquisition strategies in organic and low input agroecosystems. Drawing on global trait databases and published datasets, we show detectable shifts in root trait strategies with domestication. Relationships between domestication syndromes in root traits and nutrient acquisition strategies in low input systems underscores the need for a shift in breeding paradigms for organic agriculture. This is increasingly important given efforts to achieve Sustainable Development Goal (SDG) targets of Zero Hunger via resilient agriculture practices such as ecological nutrient management and maintenance of genetic diversity.
Introduction
Transformations Toward Resilient Agroecosystems
There has been considerable expansion in research focused on better understanding viable pathways toward sustainable agricultural systems, from ecological intensification to diversified farming systems and agroecological practices (DeLonge et al., ). Many scholars and scientists believe we are currently in a watershed moment for transformation in agricultural practices, which are paralleled by efforts to achieve Sustainable Development Goal (SDG) targets of Zero Hunger through resilient agriculture practices, enhanced on-farm diversity, and maintenance of genetic diversity (Blesh et al., ). Within this context, a shift from inorganic inputs to organic amendments has been a central focus for addressing many of our pressing agricultural issues (Chen et al., ; Isaac et al., ). While organic transformations are key for ensuring sustainable food production landscapes into the future, such transitions require (1) well-developed diagnostics of the plant-soil continuum under organic amendments, and (2) a better understanding of the role crop genetic resources play in governing soil nutrient management and crop acquisition strategies.
Soil Amendments, Nutrient Availability, and Crop Performance
Most modern crop species and genotypes are adapted to exploit nutrient-rich habitats through traits that confer fast growth and rapid rates of nutrient uptake (Lambers and Poorter, ). However, as most artificial selection occurs, with some exceptions, under conditions of high resource availability, the transfer of modern crops into low input agricultural systems is often impeded or challenging (Warschefsky et al., 2014). Many growth-supporting soil physical and chemical characteristics can change significantly when shifting from conventional to organic production, where mineral fertilizer and pesticide inputs are minimized (Mäder et al., ; Chen et al., ). As an integrated approach, organic farming seeks to manage soil fertility using ecological approaches by enhancing crop production through a greater reliance on biotic interactions and the mineralization of organic inputs, rather than relying on off-farm chemical inputs (Drinkwater and Snapp, ; Heckman et al., ). In turn, soil environments in organic systems are characterized by slow release of nutrients derived from organic sources which are supported by, or a direct consequence of, (1) longer and more complex crop rotations, (2) coupled carbon and nutrient cycles, (3) holistic farm management, and (4) ecological approaches to pest management.
In organic systems amendments such as composts, manures, and cover crops are a primary source of crop nutrients, with rates of nutrient availability and transfer supported by soil biological mineralization and microbial community interactions. Indeed, in many cases even inorganically fertilized crops obtain 50% of their nitrogen (N) from biologically mineralized organic N pools (Gardner and Drinkwater, ; Yan et al., 2020). But while inorganic fertilizers tend to reduce soil organic carbon (C) and microbial biomass, organic amendments generally enhance soil physiochemical properties including soil organic matter (SOM) and microbial biomass (Drinkwater and Snapp, ). In turn, enhanced SOM from organic amendments contributes to the retention of plant-available nutrients and water, maintenance of soil structure, and sources of soil phosphorus (P) and total N contents, but these contributions tend to be highest in soils with initially low fertility (Chen et al., ). Importantly, the positive effects of organic amendments on microbial biomass -the agent of nutrient mineralization (Cayuela et al., )–do not consistently and predictably increase crop nutrient uptake, in part because of the complex three-way interactions between crops, soil nutrient pools, and soil microbial communities. For example, crops can vary in their ability to compete with soil biota for nutrients, or modify their root environment and associated soil biota to be favorable for organic mineralization.
Crop Trait Variation and Organic Management
Due to relatively limited efforts in breeding crops explicitly for organic systems, most organic farmers in North America currently use modern cultivars that were bred for use in conventional high-input production systems (Murphy et al., 2007). As a result, organic breeding represents an unexplored frontier in crop breeding and ecophysiology. Indeed, understanding and managing the plant-soil-microbial interactions in organic systems with greater precision could contribute to the development of crop cultivars that respond preferentially to organic soil environments. However, due to unique soil systems present in organic vs. conventional systems, plant traits that are of interest to organic crop breeding may differ widely from those favored by conventional crop breeding. Undoubtedly, plant traits selected over the course of long domestication histories can have significant legacies for nutrient acquisition strategies (Figure 1).
Figure 1
Selection for crops that express certain reproductive, leaf, and root traits has formed detectable, albeit diverse, domestication syndromes: suites of plant traits which differ between crops and their wild progenitors. However, scientific and informal on-farm research has primarily focused on understanding and managing linkages between only certain domestication traits and yield, particularly under conventional agricultural management systems (Meyer et al., 2012). There is strong evidence suggesting that functional traits—i.e., the morphological (e.g., leaf area), physiological (e.g., photosynthesis), and chemical (e.g., N concentrations) traits of plants—can be used to hypothesize and detect trade-offs, constraints, and synergies among crop yield, other aspects of crop biology, and agroecosystem function (Martin and Isaac,
Crop Trait Variation and Domestication Syndromes
In agricultural systems, studies have evaluated how interspecific (Buchanan et al.,
In comparison, shifts in root functional traits throughout domestication have largely been overlooked. It appears that relationships between root functional traits, including specific root length (SRL), specific root area (SRA), root N, and root diameter (D), and plant resource acquisition strategies are arguably more complex than leaf trait trade-offs (Isaac and Borden,
Domestication Syndromes, Root Functional Traits, and Organic Agriculture
While literature supports hypotheses surrounding (1) how root traits have changed through the course of crop domestication, and (2) how those root trait syndromes might be expected to influence nutrient acquisition with ecological management, there are few studies that have integrated these two themes. Therefore, here, we seek to chart new territory in the areas of crop breeding and organic management, by synthesizing knowledge on the following questions: (1) has domestication systematically influenced root functional traits in crops vs. wild progenitors?; and if so (2) do root traits have a hypothesized influence on nutrient acquisition in low input systems? Assessing these questions then informs our final question: (3) have transformations toward low input organic systems reframed questions of domestication syndromes in crops?
Methods
To assess our first question, we extracted and analyzed bivariate correlations among three root traits including SRL, root N, and root D, by consolidating data on four crops and their wild progenitors. Data were extracted from the Global root traits (GRooT) database (Guerrero-Ramirez et al.,
We also consolidated data from peer-reviewed papers that quantified root traits in both wild progenitors and domesticated crops. In these papers, plants were grown in the same conditions and traits measured in the same way, thus providing a case by case comparison of effects of domestication on root traits. This systematic review uses a PICO formula: population (crop functional traits), intervention (domestication), comparison (wild plants to artificially selected plants) and outcome (nutrient acquisition). We searched the Web of Science database for terms included in our PICO formula [root trait* AND domestication], which resulted in 200 papers published over the past 20 years. Of these 200 papers, 11 met the following inclusion criteria: papers had to present paired data on wild relatives and domesticated crops grown in similar conditions, and include at least one measure of SLA, root N, root D, or total root length (TRL). We then conducted citation mining on all 11 papers, and with this approach included another three papers. This resulted in a total of 14 papers used in our analysis here (Table 1). Data was compiled from tables and figures in manuscripts and supplementary files, and consolidated and analyzed to depict the percent change (positive or negative) in root trait values (SLA, TRL, root D, root N) between wild relatives and paired domesticated crop. Finally, we used outcomes from our systematic review to inform hypotheses on how domestication syndromes of root traits may impact nutrient acquisition in low input and organic systems, which rely on ecological processes for crop nutrient supply.
Table 1
| Source | Wild relative | Crop | Root traits |
|---|---|---|---|
| Nakhforoosh et al., 2021 | Triticum dicoccoides | Triticum durum (durum wheat) | SRL; TRL |
| Marques et al., | Cicer reticumlatum | Cicer arietinum (chickpea) | SRL |
| Schmidt et al., 2020 | Pre1942 Zea mays mays hybrids | Post 1942 Zea mays mays hybrids (maize) | TRL; root N |
| Barel et al., | Arrhenatherum elatius Festuca rubra Trifolium pratense Vicia cracca Raphanus raphanistrum Cichorium intybus | Avena sativa (oat) Lolium perenne (ryegrass) Trifolium repens (clover) Vicia sativa (vetch) Raphanus sativus (fodder raddish) Cichorium endive (endive) | Root N |
| Berny Mier y Teran et al., | Wild Phaseolus vulgaris | Phaseolus vulgaris | SRL |
| Martín-Robles et al., 2019 | Cicer reticulatum Zea mexicana Triticum dicoccoides | Cicer arietinum (chickpea) Zea mays mays (maize) Triticum durum (durum wheat) | SRL, root D |
| Pastor-Pastor et al., 2019 | Physaria pinetorum Physaria mendocina | Physaria (high seed-yield accession) | SRL; root N |
| Junaidi et al., | Aegilops tauschii | Triticum aestivum (wheat) | SRL, root D, TRL |
| Roucou et al., 2018 | Triticum dicoccoides | Triticum durum (durum wheat) | SRL, root D |
| Pérez-Jaramillo et al., 2017 | Wild Phaseolus vulgaris | Phaseolus vulgaris (bean) | SRL |
| Chinchilla-Ramírez et al., | Zea mays parviglumis | Zea mays mays (maize) | TRL |
| Gioia et al., | Triticum dicoccoides | Triticum durum (durum wheat) | TRL |
| Szoboszlay et al., 2015 | Zea mays parviglumis | Zea mays subsp. mays (maize) | TRL, root D |
| Gaudin et al., | Zea mays parviglumis | Zea mays mays (maize) | SRL, TRL |
Sources identified through a systematic literature review, with associated wild relative, crop and suite of root traits in each source.
TRL, Total Root Length; SRL, Specific Root Length; root N (nitrogen); root D (diameter).
Results and Discussion
Root Trait Patterns Globally
Crop root traits co-vary in patterns consistent with established trait trade-offs in wild plants globally (Figure 2). In bivariate space, root D and SRL are negatively correlated, such that species expressing large root D and low SRL fall on the resource conservative end of the relationship, and species expressing high SRL and constrained root D fall on the resource acquisitive end of the relationship. Broadly, wild relatives express more resource acquisitive root traits compared to their domesticated counterparts, with systematic shifts toward resource conservation in crops, especially for rice and maize.
Figure 2

Bivariate relationships among root traits [root diameter and specific root length (A) and root N and specific root length (B)] of crops. In order to visualize the extent of root trait trade-offs, crops and their wild relatives are included, as well as trait relationships observed across the whole GRooT dataset (Guerrero-Ramirez et al.,
Root trait variation between wild relatives and domesticated crops is a function of conscious and unconscious artificial selection and in response to soil environments (Zohary, 2004). The wild progenitors of many crops already existed in the acquisitive end of the root economic spectrum (Milla et al., 2015), but here we show a shift toward resource conservation in root trait expression with domestication. This finding is (1) counter to evidence from studies on leaf traits, which are shown to express leaf-level trait values that reflect highly resource acquisitive strategies with domestication (Cunniff et al.,
Changes in Crop Root Functional Traits With Domestication–Data Comparison
We compared trait values of domesticated crops and their wild relatives, covering a range of crop-wild relative complexes including wheat (Aegilops tauschii), durum wheat (Triticum durum ssp. dicoccoides), maize (Z. mays mexicana), Chickpea (Cicer reticulatum). Figure 3 illustrates the percent change in root trait values through domestication, ordered by phylogenetic relatedness. Results from published literature are mixed. In some instances, SRL, TRL, root D, and root N values are higher in wild relatives vs. crops, while the opposite pattern is true for other crop-wild relative combinations. However, root D is generally larger in wild relatives vs. crops, expressing a negative percent change in trait values with domestication. Interestingly, SRL tends to have positive percent change in trait values with domestication, indicating a shift toward higher SRL in domesticated crops as compared to wild relatives (Figure 3). However, this trend is opposite for leguminous species Phaseolus: the percent change in trait values through domestication for beans is consistently negative.
Figure 3

Percent change in trait values for 12 crops, organized according to their phylogenic relationships, and their paired wild relatives. Specific root length (SRL), total root length (TRL), root diameter (root D), and root nitrogen (root N) are depicted.
These shifts in root trait values reported between paired domesticated crop traits with wild relatives, are not consistent with trends reported from global datasets as shown in Figure 2. While these trends of crops and wild relatives fall into established trait trade-off patterns, they do not reflect the nuances of pairing crops and wild relatives in the same growing conditions with the same measurements. In doing so here, we show a clearer trend of domesticated crops expressing acquisitive traits (higher SRL and lower root D) than those compiled from unpaired global datasets; a finding that is more consistent with leaf trait changes that occur through domestication. Our paired data highlights another critical area of root trait shifts as a result of domestication: the strength of relationships between root traits and arbuscular mycorrhiza. Older crop varietals may be more able to form these symbiotic relationships regardless of nutrient availability, while modern varietals only benefit from the symbiosis when under nutrient stress (Martín-Robles et al., 2018). Plant-microbial symbiosis that destabilize systematic trait trades-offs (Bergmann et al.,
Hypothesized Outcomes for Nutrient Acquisition
Variation in root traits may either facilitate or inhibit organic nutrient mineralization and nutrient acquisition. Plants exhibit diverse root acquisition strategies to enable nutrient uptake, including mechanisms that regulate nutrient bioavailability (Hinsinger,
Specifically, higher SRL and TRL are linked with foraging and higher resource uptake zones (Cahill et al.,
Systematic shifts in crop root traits can also indirectly affect nutrient availability and acquisition by altering soil microbial community composition (Cantarel et al.,
Acquisition strategies emerging through domestication may be confounded by nutrient allocation patterns within crops (Løes et al.,
Implications of Root Trait Variation for Breeding Programs for Ecological and Organic Nutrient Management
Due to the inherent and multi-faceted differences in growing environment between organic and conventional production systems (see Box 1 for a long-term research case study on soil biochemistry in organic vs. conventional systems), increased efforts in organic breeding have the potential to reduce the yield gap by developing crop cultivars that respond well to organic environments. For instance, the spatial and temporal heterogeneity in organic agricultural soils requires crops with high root plasticity, which in turn confers an advantage for successful nutrient acquisition in low-input systems. Conventional seeds often perform poorly in organic agricultural systems (Boyle,
Box 1 Three decades of organic agriculture research at Glenlea, Manitoba, Canada.
Factors affecting plant nutrient acquisition in organic production have been studied in the Canadian context at the Glenlea study for three decades. Within the first 15 years of organic production, researchers observed a shift in the soil P pools, with less plant available P (Welsh et al., 2009) and more organic P (Braman et al.,
Cultivar selection is a critical aspect for organic farmers to consider in relation to soil fertility, as well as pest and weed management (Bond and Grundy,
Drawing on global datasets and published data, we show detectable shifts in root trait strategies with domestication. Relationships between domestication syndromes in root traits, and the subsequent impact on acquisition strategies in low input systems, underscores the need for a shift in breeding paradigms for organic agriculture. Such efforts are under way in many different field and horticultural crops, for instance in Canada for wheat (Wiebe et al., 2016; Entz et al.,
Funding
This research was partially funded by the Canada Research Chairs program to MI.
Publisher's Note
All claims expressed in this article are solely those of the authors and do not necessarily represent those of their affiliated organizations, or those of the publisher, the editors and the reviewers. Any product that may be evaluated in this article, or claim that may be made by its manufacturer, is not guaranteed or endorsed by the publisher.
Statements
Data availability statement
The original contributions presented in the study are included in the article/supplementary material, further inquiries can be directed to the corresponding author.
Author contributions
MI conceived and coordinated the study. JS generated the illustration. AM generated the figures. All authors contributed to the formulation of ideas, manuscript writing, and final approval for publication.
Acknowledgments
We thank two reviewers for insightful comments. We thank Thanuka Sivanathan and Rachel Mariani for assistance with literature review and data compilation.
Conflict of interest
The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.
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Summary
Keywords
agroecology, breeding, ecological nutrient management, food security, functional traits, wild relatives, sustainable development goals
Citation
Isaac ME, Nimmo V, Gaudin ACM, Leptin A, Schmidt JE, Kallenbach CM, Martin A, Entz M, Carkner M, Rajcan I, Boyle TD and Lu X (2021) Crop Domestication, Root Trait Syndromes, and Soil Nutrient Acquisition in Organic Agroecosystems: A Systematic Review. Front. Sustain. Food Syst. 5:716480. doi: 10.3389/fsufs.2021.716480
Received
28 May 2021
Accepted
11 August 2021
Published
14 September 2021
Volume
5 - 2021
Edited by
Sudhakar Srivastava, Banaras Hindu University, India
Reviewed by
Ana Aurora Fontes-Puebla, Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP), Mexico; Johnattan Hernández Cumplido, National Autonomous University of Mexico, Mexico
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© 2021 Isaac, Nimmo, Gaudin, Leptin, Schmidt, Kallenbach, Martin, Entz, Carkner, Rajcan, Boyle and Lu.
This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner(s) are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.
*Correspondence: Marney E. Isaac marney.isaac@utoronto.ca
This article was submitted to Agroecology and Ecosystem Services, a section of the journal Frontiers in Sustainable Food Systems
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