Integrating GWAS and Gene Expression Analysis Identifies Candidate Genes for Root Morphology Traits in Maize at the Seedling Stage

Root system plays an essential role in water and nutrient acquisition in plants. Understanding the genetic basis of root development will be beneficial for breeding new cultivars with efficient root system to enhance resource use efficiency in maize. Here, the natural variation of 13 root and 3 shoot traits was evaluated in 297 maize inbred lines and genome-wide association mapping was conducted to identify SNPs associated with target traits. All measured traits exhibited 2.02- to 21.36-fold variations. A total of 34 quantitative trait loci (QTLs) were detected for 13 traits, and each individual QTL explained 5.7% to 15.9% of the phenotypic variance. Three pleiotropic QTLs involving five root traits were identified; SNP_2_104416607 was associated with lateral root length (LRL), root surface area (RA), root length between 0 and 0.5mm in diameter (RL005), and total root length (TRL); SNP_2_184016997 was associated with RV and RA, and SNP_4_168917747 was associated with LRL, RA and TRL. The expression levels of candidate genes in root QTLs were evaluated by RNA-seq among three long-root lines and three short-root lines. A total of five genes that showed differential expression between the long- and short-root lines were identified as promising candidate genes for the target traits. These QTLs and the potential candidate genes are important source data to understand root development and genetic improvement of root traits in maize.

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Phenotypic Diversity for Root Traits and Identification of Superior Germplasm for Root Breeding in Watermelon

HortScience ◽

10.21273/hortsci15093-20 ◽

2020 ◽

Vol 55 (8) ◽

pp. 1272-1279

Author(s):

Dennis N. Katuuramu ◽

W. Patrick Wechter ◽

Marcellus L. Washington ◽

Matthew Horry ◽

Matthew A. Cutulle ◽

...

Keyword(s):

Root System ◽

Surface Area ◽

Root Length ◽

Root Traits ◽

Root Surface ◽

Root Diameter ◽

Root Surface Area ◽

Total Root Length ◽

Root Volume ◽

Diverse Range

Root traits are an important component for productive plant performance. Roots offer immediate absorptive surfaces for water and nutrient acquisition and are thus critical to crop growth and response to biotic and abiotic stresses. In addition, roots can provide the first line of defense against soilborne pathogens. Watermelon crop performance is often challenged by inclement weather and environmental factors. A resilient root system can support the watermelon crop’s performance across a diverse range of production conditions. In this study, 335 four-day-old watermelon (Citrullus spp.) seedlings were evaluated for total root length, average root diameter, total root surface area, and total root volume. Total root length varied from 8.78 to 181 cm (20.6-fold variation), total surface area varied from 2 to 35.5 cm2, and average root diameter and total root volume had an 8- and 29.5-fold variation, respectively. Genotypes PI 195927 (Citrullus colocynthis) and PI 674448 (Citrullus amarus) had the largest total root length values. Accessions PI 674448 and PI 494817 (C. amarus) had the largest total root surface area means. Watermelon cultivars (Citrullus lanatus) had a relatively smaller root system and significantly fewer fibrous roots when compared with the roots of the other Citrullus spp. Positive genetic correlations were identified among total root length, total root surface area, and total root volume. This genetic information will be useful in future breeding efforts to select for multiple root architecture traits in watermelon. Germplasm identified in this study that exhibit superior root traits can be used as parental choices to improve watermelon for root traits.

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Comparison of Root System Morphology of Cucurbit Rootstocks for Use in Watermelon Grafting

HortTechnology ◽

10.21273/horttech04098-18 ◽

2018 ◽

Vol 28 (5) ◽

pp. 629-636 ◽

Cited By ~ 4

Author(s):

Matthew B. Bertucci ◽

David H. Suchoff ◽

Katherine M. Jennings ◽

David W. Monks ◽

Christopher C. Gunter ◽

...

Keyword(s):

Root System ◽

Surface Area ◽

Root Length ◽

Dry Weight ◽

Root Systems ◽

Root Surface ◽

Root Diameter ◽

Root Surface Area ◽

Diameter Class ◽

Main Effect

Grafting of watermelon (Citrullus lanatus) is an established production practice that provides resistance to soilborne diseases or tolerance to abiotic stresses. Watermelon may be grafted on several cucurbit species (interspecific grafting); however, little research exists to describe root systems of these diverse rootstocks. A greenhouse study was conducted to compare root system morphology of nine commercially available cucurbit rootstocks, representing four species: pumpkin (Cucurbita maxima), squash (Cucurbita pepo), bottle gourd (Lagenaria siceraria), and an interspecific hybrid squash (C. maxima × C. moschata). Rootstocks were grafted with a triploid watermelon scion (‘Exclamation’), and root systems were compared with nongrafted (NG) and self-grafted (SG) ‘Exclamation’. Plants were harvested destructively at 1, 2, and 3 weeks after transplant (WAT), and data were collected on scion dry weight, total root length (TRL), average root diameter, root surface area, root:shoot dry-weight ratio, root diameter class proportions, and specific root length. For all response variables, the main effect of rootstock and rootstock species was significant (P < 0.05). The main effect of harvest was significant (P < 0.05) for all response variables, with the exception of TRL proportion in diameter class 2. ‘Ferro’ rootstock produced the largest TRL and root surface area, with observed values 122% and 120% greater than the smallest root system (‘Exclamation’ SG), respectively. Among rootstock species, pumpkin produced the largest TRL and root surface area, with observed values 100% and 82% greater than those of watermelon, respectively. These results demonstrate that substantial differences exist during the initial 3 WAT in root system morphology of rootstocks and rootstock species available for watermelon grafting and that morphologic differences of root systems can be characterized using image analysis.

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Study on measurement method for apple root morphological parameters based on Labview

Plant Methods ◽

10.1186/s13007-019-0535-4 ◽

2019 ◽

Vol 15 (1) ◽

Cited By ~ 1

Author(s):

Yu Liu ◽

Ji Qian ◽

Xin Yang ◽

Bao Di ◽

Juan Zhou

Keyword(s):

Root System ◽

Surface Area ◽

Relative Error ◽

Root Length ◽

Average Diameter ◽

Root Surface ◽

Root Diameter ◽

Root Surface Area ◽

Root Volume ◽

Seedling Roots

Abstract Background Traditional measurements of apple seedling roots often rely on manual measurements and existing root scanners on the market. Manual measurement requires a lot of labor and time, and subjective reasons may cause the uncertainty of data; root scanners have limited scanning size and expensive. In case of fruit roots, coverage and occlusion issues will occur, resulting in inaccurate results, but our research solved this problem. Results The background plate was selected according to the color of the seedling roots; the image of the roots of the collected apple seedlings was preprocessed with Vision Development Module by combining image and Labview. The root surface area, average root diameter, root length and root volume of apple seedlings were measured by combining root characteristic parameters algorithm. In order to verify the effectiveness of the proposed method, a set of measurement system for root morphology of apple seedlings was designed, and the measurement result was compared with the Canadian root system WinRHIZO 2016 (Canada). With application of SPSS v22.0 analysis, the significance P > 0.01 indicated that the difference was not significant. The relative error of surface area was less than 0.5%. The relative error of the average diameter and length of the root system was less than 0.1%, and the relative error of the root volume was less than 0.2%. Conclusions It not only proved that the root surface area, average root diameter, root length and root volume of apple seedlings could be accurately measured by the method described herein, which was handy in operation, but also reduced the cost by 80–90% compared with the conventional scanner.

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Complete root specimen of plants grown in soil-filled root box: sampling, measuring, and staining method

Plant Methods ◽

10.1186/s13007-021-00798-3 ◽

2021 ◽

Vol 17 (1) ◽

Author(s):

Takuya Koyama ◽

Shun Murakami ◽

Toshihiko Karasawa ◽

Masato Ejiri ◽

Katsuhiro Shiono

Keyword(s):

Root System ◽

Surface Area ◽

Visual Information ◽

Physiological Function ◽

Physiological Activity ◽

Root Traits ◽

Arbuscular Mycorrhizal ◽

Spatial Arrangement ◽

Root Surface ◽

Root Surface Area

Abstract Background Detailed datasets containing root system and its architecture in soil are required to improve understanding of resource capture by roots. However, most of the root study methods have paid little attention to make and preserve whole root specimens. This study introduces root system sampling equipment that makes the entire root specimen with minimum impairment and without displacement of the spatial arrangement of the root system in root boxes. The objectives are to assess: whether the equipment can rapidly sample the entire root system; whether root surface area is measurable from a scanned digital image of the root specimen; and whether staining of the entire root specimens would provide multidimensional visual information on the interaction between soil and physiological function of root system architecture (RSA). For validation, we examined the root response of two soybean cultivars to arbuscular mycorrhizal (AM) inoculation and the effect of waterlogging stress on the physiological activity of buckwheat RSA. Results The root boxes allowed soybean and buckwheat plants to grow uniformly across the replications. Both species showed significant differences between cultivars and/or among treatments in shoot and root traits. The equipment enabled to sample the whole-root specimens of soybean and buckwheat, where the tips of the fine roots were alive (diameter < 0.2 mm). Also, the whole root specimens of soybean were made in about 7 min. The root surface area calculated from the scanned soybean specimens showed a significant correlation with that calculated from the roots spread out in water (a common method). Staining of the soybean root specimens enabled us to observe the localized root proliferation induced by AM colonization. Moreover, staining of the buckwheat root specimens made it possible to examine the respiratory activity of each root at different depths. Conclusions The present method realized: fast and accurate production of the whole root specimen and precise calculation of the specimens’ root surface area. Moreover, staining of the root specimens enabled analyzing the interaction between soil and physiological function of RSA. The evaluation of root traits, using our methods, will contribute to developing agronomic management and breeding program for sustainable food production.

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Covariation in root traits of Leymus chinensis in response to grazing in steppe rangeland

The Rangeland Journal ◽

10.1071/rj18099 ◽

2019 ◽

Vol 41 (4) ◽

pp. 313

Author(s):

Wei Xiaoting ◽

Zhong Mengying ◽

Liu Yuehua ◽

Wu Ruixin ◽

Shao Xinqing

Keyword(s):

Root Length ◽

Topological Structure ◽

Grazing Intensity ◽

Root Traits ◽

Root Surface ◽

Leymus Chinensis ◽

Root Surface Area ◽

Total Root Length ◽

Grazing Season ◽

Heavy Grazing

Root traits are closely related to nutrient absorption and resource competition and can even influence plant recovery and community succession. Grazing can influence root traits directly through trampling and foraging, or indirectly by changing soil characteristics. In the present study, a grazing experiment that involved combinations of grazing season (from June to September) and intensity (rest, moderate and heavy) was conducted in steppe rangeland, Inner Mongolia, China to investigate how the root traits of Leymus chinensis respond to different grazing regimes in the case of aboveground miniaturisation after long-term overgrazing. Root traits such as root length, root surface area, specific root length, root tissue density, root links (unbranched parts of a root connecting either a tip and a branching point or two branching points) and root topological structure were scanned and analysed using Win-RHIZO image analysis software. The results showed that the size of L. chinensis plants was reduced in response to overgrazing, typically by a smaller plant height, total root length, root surface area, root volume, number of tips and number of links. However, root diameter and link length, branching angle and topological structure (herringbone or dichotomous) were unaffected by grazing. Most root traits showed strong correlations under moderate grazing intensity, but not under heavy grazing, indicating that grazing changed the relationships among root traits. Relationships between plant height and root traits (total root length and number of links) shifted from positive to negative as grazing intensity increased, and the trade-off between aboveground and belowground traits was an important adaptive strategy of L. chinensis under heavy grazing. Decreasing grazing intensity in the late grazing season could benefit plant recovery, and a rest in the early grazing season would mitigate root and shoot damage.

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Identification of Putative Molecular Markers Associated with Root Traits in Coffea canephora Pierre ex Froehner

Molecular Biology International ◽

10.1155/2015/532386 ◽

2015 ◽

Vol 2015 ◽

pp. 1-11 ◽

Cited By ~ 2

Author(s):

Devaraja Achar ◽

Mallikarjuana G. Awati ◽

M. Udayakumar ◽

T. G. Prasad

Keyword(s):

Molecular Markers ◽

Root System ◽

Root Length ◽

Root Traits ◽

Coffea Canephora ◽

Physiological Traits ◽

Phenotypic Variance ◽

Single Marker Analysis ◽

Shoot Ratio ◽

Root To Shoot Ratio

Coffea canephora exhibit poor root system and are very sensitive to drought stress that affects growth and production. Deeper root system has been largely empirical as better avoidance to soil water limitation in drought condition. The present study aimed to identify molecular markers linked to high root types in Coffea canephora using molecular markers. Contrasting parents, L1 valley with low root and S.3334 with high root type, were crossed, and 134 F1 individuals were phenotyped for root and associated physiological traits (29 traits) and genotyped with 41 of the 320 RAPD and 9 of the 55 SSR polymorphic primers. Single marker analysis was deployed for detecting the association of markers linked to root associated traits by SAS software. There were 13 putative RAPD markers associated with root traits such as root length, secondary roots, root dry weight, and root to shoot ratio, in which root length associated marker OPS1850 showed high phenotypic variance of 6.86%. Two microsatellite markers linked to root length (CPCM13400) and root to shoot ratio (CM211300). Besides, 25 markers were associated with more than one trait and few of the markers were associated with positively related physiological traits and can be used in marker assisted trait selection.

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Improvements in the Root Morphology, Physiology, and Anatomy of Platycladus orientalis Seedlings from Air-root Pruning

HortScience ◽

10.21273/hortsci13375-18 ◽

2018 ◽

Vol 53 (12) ◽

pp. 1750-1756

Author(s):

Zhipei Feng ◽

Xitian Yang ◽

Hongyan Liang ◽

Yuhua Kong ◽

Dafeng Hui ◽

...

Keyword(s):

Root System ◽

Surface Area ◽

Root Length ◽

Specific Root Length ◽

Experimental Period ◽

Root Surface ◽

Root Surface Area ◽

Root Pruning ◽

Root Tips ◽

Platycladus Orientalis

Air-root pruning (AP) has been identified as an effective technique for enhancing root growth and development. However, little information is available regarding the temporal changes in the root system of Platycladus orientalis (L.) Franco under AP. We performed integrated morphological, physiological, and anatomical analyses of the roots in P. orientalis seedlings that had been air-root pruned for 120, 150, and 190 days. Our results found that the whole root length, number of root tips, and root surface area of AP seedlings at 120, 150, and 190 days were higher than those of the non–root-pruned (NP) seedlings (P < 0.05), but the average root diameter did not differ significantly between the treatments. Compared with NP treatment, AP increased the root length, surface area, number of tips, and specific root length of the ≤0.5 mm diameter roots in P. orientalis during the experimental periods (P < 0.05), but those of 0.5- to 1-mm-diameter roots were only increased on day 190 (P < 0.05). The AP plants also exhibited higher root vitality and proportion of live fine roots than the NP plants (P < 0.05). Our anatomical evaluation of the ≤0.5 mm roots and taproots revealed features that could account for the morphological differences found between the AP and NP plants. In conclusion, our results indicate that air-root pruning induced changes in the roots that promote the root system development in P. orientalis compared with the NP treatment during the experimental period. These results thus provide experimental evidence to support the use of AP in P. orientalis seedlings.

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The Role of Root Morphology and Pulling Direction in Pullout Resistance of Alfalfa Roots

Frontiers in Plant Science ◽

10.3389/fpls.2021.580825 ◽

2021 ◽

Vol 12 ◽

Author(s):

Qihong Yang ◽

Chaobo Zhang ◽

Pengchong Liu ◽

Jing Jiang

Keyword(s):

Root System ◽

Surface Area ◽

Root Length ◽

Pullout Test ◽

Root Surface ◽

Root Diameter ◽

Root Surface Area ◽

Pullout Resistance ◽

Significant Difference ◽

Morphological Indices

There is a growing consensus on soil conservation by mechanics of plant root system. In order to further study how root system exerts its mechanical properties during soil reinforcing process and which morphological indicator is suitable for reflecting pullout resistance, in-situ vertical pullout test (VPT) and 45° oblique pullout test (OPT) were performed on alfalfa (Medicago sativa L.) roots in the loess area. The results showed that the failure mode of alfalfa roots was pulling out in this study. The peak pullout resistance of the roots increased with root diameter, root length and root surface area, and power law relationships were observed between the pullout resistance and the morphological indices: root diameter, root length and root surface area. The maximum gray relational degree of the morphological indices was 0.841 (VPT) and 0.849 (OPT) for root surface area, suggesting that root surface area was a more significant root morphological index affecting root pullout resistance than root diameter and root length, and was more suitable for characterizing the difference in peak pullout resistance of roots with different size. The index could be used to validate the methods for predicting root pullout capacity. The value of peak pullout resistance was 17.2 ± 2.3 N in VPT test and 28.2 ± 3.8 N (mean ± SE) in OPT test, and a significant difference was observed between the two tests, which showed that the pulling direction significantly affected the peak pullout resistance of alfalfa roots. Vertical pullout test, giving the safety margin, was suggested to determine root pullout resistance for estimate of root reinforcement.

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Improvement of Root System Architecture in Peach (Prunus persica) Seedlings by Arbuscular Mycorrhizal Fungi, Related to Allocation of Glucose/Sucrose to Root

Notulae Botanicae Horti Agrobotanici Cluj-Napoca ◽

10.15835/nbha3926232 ◽

2011 ◽

Vol 39 (2) ◽

pp. 232 ◽

Cited By ~ 9

Author(s):

Qiang-Sheng WU ◽

Guo-Huai LI ◽

Ying-Ning ZOU

Keyword(s):

Root System ◽

System Architecture ◽

Root Length ◽

Mycorrhizal Fungi ◽

Prunus Persica ◽

Arbuscular Mycorrhizal ◽

Root Surface ◽

Root System Architecture ◽

Root Surface Area ◽

Projected Area

Root system architecture (RSA) is used to describe the spatial configuration of a root system in the soil, which substantially determines the capacity of a plant to take up nutrients and water. The present study was to assess if arbuscular mycorrhizal fungi (AMF), Glomus mosseae, G. versiforme, and Paraglomus occultum would alter RSA of peach (Prunus persica L. Batsch) seedlings, and the alteration due to mycorrhization was related to allocation of glucose/sucrose to root (Aglucose/sucrose). Inoculation with G. mosseae and G. versiforme significantly increased leaf, stem, root and total fresh weights, compared with non-AMF treatment. Mycorrhizal alterations of RSA in peach plants were dependent on AMF species, because only G. mosseae and G. versiforme but not P. occultum markedly increased root length, root projected area, root surface area and root volume. For the distribution of root length classes, AMF mainly increased 0-1 and 3-4 cm root length classes, which is AMF species dependent. Inoculated seedlings with Glomus species recorded significantly higher root sucrose and leaf and root glucose concentrations and lower root sucrose concentrations than un-inoculated control. Compared with the non-AMF treatment, G. mosseae and G. versiforme generally increased the Aglucose and Asucrose, but P. occultum significantly decreased the Aglucose and Asucrose. Asucrose or Aglucose was significantly positive correlated with root length, root projected area and root surface area. The results suggest that AMF modified variables of RSA in peach, which is AMF species dependent and related to Aglucose and Asucrose.

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Shoot and Root Traits Underlying Genotypic Variation in Early Vigor and Nutrient Accumulation in Spring Wheat Grown in High-Latitude Light Conditions

Plants ◽

10.3390/plants10010174 ◽

2021 ◽

Vol 10 (1) ◽

pp. 174

Author(s):

Hui Liu ◽

Fabio Fiorani ◽

Ortrud Jäck ◽

Tino Colombi ◽

Kerstin A. Nagel ◽

...

Keyword(s):

Root System ◽

Leaf Area ◽

Spring Wheat ◽

High Latitude ◽

Root Length ◽

Nutrient Use Efficiency ◽

Root Traits ◽

Plant Production ◽

Nutrient Accumulation ◽

Early Vigor

Plants with improved nutrient use efficiency are needed to maintain and enhance future crop plant production. The aim of this study was to explore candidate traits for pre-breeding to improve nutrient accumulation and early vigor of spring wheat grown at high latitudes. We quantified shoot and root traits together with nutrient accumulation in nine contrasting spring wheat genotypes grown in rhizoboxes for 20 days in a greenhouse. Whole-plant relative growth rate was here correlated with leaf area productivity and plant nitrogen productivity, but not leaf area ratio. Furthermore, the total leaf area was correlated with the accumulation of six macronutrients, and could be suggested as a candidate trait for the pre-breeding towards improved nutrient accumulation and early vigor in wheat to be grown in high-latitude environments. Depending on the nutrient of interest, different root system traits were identified as relevant for their accumulation. Accumulation of nitrogen, potassium, sulfur and calcium was correlated with lateral root length, whilst accumulation of phosphorus and magnesium was correlated with main root length. Therefore, special attention needs to be paid to specific root system traits in the breeding of wheat towards improved nutrient accumulation to counteract the suboptimal uptake of some nutrient elements.

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