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Plant breeding and genetics play a major role in the adaptation of plants to meet human needs. The current requirement to make agriculture more sustainable can be partly met by a greater reliance on biological nitrogen fixation by symbiotic diazotrophic microorganisms that provide crop plants with ammonium. Select accessions of the cereal crop sorghum (Sorghum bicolor (L.) Moench) form mucilage-producing aerial roots that harbor nitrogen-fixing bacteria. Breeding programs aimed at developing sorghum varieties that support diazotrophs will benefit from a detailed understanding of the genetic and environmental factors contributing to aerial root formation. A genome-wide association study of the sorghum minicore, a collection of 242 landraces, and 30 accessions from the sorghum association panel was conducted in Florida and Wisconsin and under 2 fertilizer treatments to identify loci associated with the number of nodes with aerial roots and aerial root diameter. Sequence variation in genes encoding transcription factors that control phytohormone signaling and root system architecture showed significant associations with these traits. In addition, the location had a significant effect on the phenotypes. Concurrently, we developed F2 populations from crosses between bioenergy sorghums and a landrace that produced extensive aerial roots to evaluate the mode of inheritance of the loci identified by the genome-wide association study. Furthermore, the mucilage collected from aerial roots contained polysaccharides rich in galactose, arabinose, and fucose, whose composition displayed minimal variation among 10 genotypes and 2 fertilizer treatments. These combined results support the development of sorghums with the ability to acquire nitrogen via biological nitrogen fixation. [ABSTRACT FROM AUTHOR]

Abstract Background Root system architecture (RSA) is an essential characteristic for efficient water and nutrient absorption in terrestrial plants; its plasticity enables plants to respond to different soil environments. Better understanding of root plasticity is important in developing stress-tolerant crops. Non-invasive techniques that can measure roots in soils nondestructively, such as X-ray computed tomography (CT), are useful to evaluate RSA plasticity. However, although RSA plasticity can be measured by tracking individual root growth, only a few methods are available for tracking individual roots from time-series three-dimensional (3D) images. Results We developed a semi-automatic workflow that tracks individual root growth by vectorizing RSA from time-series 3D images via two major steps. The first step involves 3D alignment of the time-series RSA images by iterative closest point registration with point clouds generated by high-intensity particles in potted soils. This alignment ensures that the time-series RSA images overlap. The second step consists of backward prediction of vectorization, which is based on the phenomenon that the root length of the RSA vector at the earlier time point is shorter than that at the last time point. In other words, when CT scanning is performed at time point A and again at time point B for the same pot, the CT data and RSA vectors at time points A and B will almost overlap, but not where the roots have grown. We assumed that given a manually created RSA vector at the last time point of the time series, all RSA vectors except those at the last time point could be automatically predicted by referring to the corresponding RSA images. Using 21 time-series CT volumes of a potted plant of upland rice (Oryza sativa), this workflow revealed that the root elongation speed increased with age. Compared with a workflow that does not use backward prediction, the workflow with backward prediction reduced the manual labor time by 95%. Conclusions We developed a workflow to efficiently generate time-series RSA vectors from time-series X-ray CT volumes. We named this workflow 'RSAtrace4D' and are confident that it can be applied to the time-series analysis of RSA development and plasticity.

Background: Root system architecture (RSA) is an essential characteristic for efficient water and nutrient absorption in terrestrial plants; its plasticity enables plants to respond to different soil environments. Better understanding of root plasticity is important in developing stress-tolerant crops. Non-invasive techniques that can measure roots in soils nondestructively, such as X-ray computed tomography (CT), are useful to evaluate RSA plasticity. However, although RSA plasticity can be measured by tracking individual root growth, only a few methods are available for tracking individual roots from time-series three-dimensional (3D) images. Results: We developed a semi-automatic workflow that tracks individual root growth by vectorizing RSA from time-series 3D images via two major steps. The first step involves 3D alignment of the time-series RSA images by iterative closest point registration with point clouds generated by high-intensity particles in potted soils. This alignment ensures that the time-series RSA images overlap. The second step consists of backward prediction of vectorization, which is based on the phenomenon that the root length of the RSA vector at the earlier time point is shorter than that at the last time point. In other words, when CT scanning is performed at time point A and again at time point B for the same pot, the CT data and RSA vectors at time points A and B will almost overlap, but not where the roots have grown. We assumed that given a manually created RSA vector at the last time point of the time series, all RSA vectors except those at the last time point could be automatically predicted by referring to the corresponding RSA images. Using 21 time-series CT volumes of a potted plant of upland rice (Oryza sativa), this workflow revealed that the root elongation speed increased with age. Compared with a workflow that does not use backward prediction, the workflow with backward prediction reduced the manual labor time by 95%. Conclusions: We developed a workflow to efficiently generate time-series RSA vectors from time-series X-ray CT volumes. We named this workflow 'RSAtrace4D' and are confident that it can be applied to the time-series analysis of RSA development and plasticity. [ABSTRACT FROM AUTHOR]

To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice (Oryza sativa), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 (quantitative trait locus for Number of Crown Root 1). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin (LOC_Os04g55030), a gibberellin 20 oxidase 8 (LOC_Os04g55070), and a cyclic nucleotide-gated ion channel (LOC_Os04g55080). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2. [ABSTRACT FROM AUTHOR]

Changes in root development and growth in upland rice receiving subsurface irrigation were evaluated using root box experiments. Irrigated water was independently applied every day to depths of 0, 5, 10 and 20 cm from the ground surface, and root morphology and aboveground growth were determined after 2 weeks of treatment. Plant length, stem number and leaf age significantly increased along with the irrigation depth, and the aboveground dry weights of rice grown at 5-, 10- and 20-cm depths were significantly greater than those grown at 0 cm. Root surface area significantly increased along with the irrigation depth, which was attributed to the increasing lengths and branch numbers of roots. Subsurface irrigation significantly increased root lengths in deep layers (below 15 cm) and increased the deep layers’ distribution ratios by 1.2 to 5.7 times as the surface layer ratio decreased. This was accompanied with a decrease in the root diameter. This may be associated with the increase in the numbers of branches and the decrease in the numbers of thick nodal roots. These results indicate that subsurface irrigation increases root length and branching in the deep soil layers, inducing deep rooting, even with same amount of irrigation.

Phosphorus (P) acquisition, a key factor in rice productivity, is related to morphological and anatomical root traits. In this study, we examined the root traits of rice that contribute to P acquisition under low P conditions using chromosomal segment substitution lines (CSSLs) grown under nonflooded conditions. Rice plants were grown under low- and high-P conditions in a growth chamber. We tested 39 CSSLs and the parent varieties 'Sasanishiki' and 'Habataki.' Four out of the five selected genotypes from 39 CSSLs had larger root surface areas than that of Sasanishiki due to long fine root and/or coarse roots. The root surface area and shoot P uptake were significantly and positively correlated. Two of the genotypes had higher P use efficiency and shoot dry weight compared to that of Sasanishiki under low P conditions, and nodal root cross-sectional areas were larger in the two genotypes than in Sasanishiki under low P conditions. The root cortical aerenchyma in the nodal roots was well developed in all observed genotypes, which may have reduced the metabolic cost. These results suggest that the thick nodal roots with aerenchyma in contribution to the increase in root surface area are the advantage for growth under low P levels in non-flooded conditions. [ABSTRACT FROM AUTHOR]

Centipedegrass [Eremochloa ophiuroides (Munro) Hack.] is a perennial warm-season grass that originated in China, and its speed of nodal rooting is important for lawn establishment. In our study, centipedegrass nodal rooting ability was limited by node aging. Transcriptome sequencing of nodal roots after 0, 2, 4, and 8 days of water culture was performed to investigate the molecular mechanisms of root development. GO enrichment and KEGG pathway analyses of DEGs indicated that plant hormone signal transduction and transcription factors might play important roles in centipedegrass nodal root growth. Among them, E3 ubiquitin-protein ligases participated in multiple hormone signal transduction pathways and interacted with transcription factors. Furthermore, an E3 ubiquitin protein ligase EoSINAT5 overexpressed in rice resulted in longer roots and more numerous root tips, while knockout of LOC_Os07g46560 (the homologous gene of EoSINAT5 in rice) resulted in shorter roots and fewer root tips. These results indicated that EoSINAT5 and its homologous gene are able to promote nodal root development. This research presents the transcriptomic analyses of centipedegrass nodal roots, and may contribute to elucidating the mechanism governing the development of nodal roots and facilitates the use of molecular breeding in improving rooting ability.

Centipedegrass [ Eremochloa ophiuroides (Munro) Hack.] is a perennial warm-season grass that originated in China, and its speed of nodal rooting is important for lawn establishment. In our study, centipedegrass nodal rooting ability was limited by node aging. Transcriptome sequencing of nodal roots after 0, 2, 4, and 8 days of water culture was performed to investigate the molecular mechanisms of root development. GO enrichment and KEGG pathway analyses of DEGs indicated that plant hormone signal transduction and transcription factors might play important roles in centipedegrass nodal root growth. Among them, E3 ubiquitin-protein ligases participated in multiple hormone signal transduction pathways and interacted with transcription factors. Furthermore, an E3 ubiquitin protein ligase EoSINAT5 overexpressed in rice resulted in longer roots and more numerous root tips, while knockout of LOC_Os07g46560 (the homologous gene of EoSINAT5 in rice) resulted in shorter roots and fewer root tips. These results indicated that EoSINAT5 and its homologous gene are able to promote nodal root development. This research presents the transcriptomic analyses of centipedegrass nodal roots, and may contribute to elucidating the mechanism governing the development of nodal roots and facilitates the use of molecular breeding in improving rooting ability. [ABSTRACT FROM AUTHOR]

The root of wheat consists of seminal and nodal roots. Comparatively speaking, fewer studies have been carried out on the nodal root system because of its disappearance at the early seedling stage under indoor environments. In this study, 196 accessions from the Huanghuai Wheat Region (HWR) were used to identify the characteristics of seminal and nodal root traits under different growth environments, including indoor hydroponic culture (IHC), outdoor hydroponic culture (OHC), and outdoor pot culture (OPC), for three growing seasons. The results indicated that the variation range of root traits in pot environment was larger than that in hydroponic environment, and canonical coefficients were the greatest between OHC and OPC (0.86) than those in other two groups, namely, IHC vs. OPC (0.48) and IHC vs. OHC (0.46). Most root traits were negatively correlated with spikes per area (SPA), grains per spike (GPS), and grain yield (GY), while all the seminal root traits were positively correlated with thousand-kernel weight (TKW). Genome-wide association study (GWAS) was carried out on root traits by using a wheat 660K SNP array. A total of 35 quantitative trait loci (QTLs)/chromosomal segments associated with root traits were identified under OPC and OHC. In detail, 11 and 24 QTLs were significantly associated with seminal root and nodal root traits, respectively. Moreover, 13 QTLs for number of nodal roots per plant (NRP) containing 14 stable SNPs, were distributed on chromosomes 1B, 2B, 3A, 4B, 5D, 6D, 7A, 7B, and Un. Based on LD and bioinformatics analysis, these QTLs may contain 17 genes closely related to NRP. Among them, TraesCS2B02G552500 and TraesCS7A02G428300 were highly expressed in root tissues. Moreover, the frequencies of favorable alleles of these 14 SNPs were confirmed to be less than 70% in the natural population, suggesting that the utilization of these superior genes in wheat root is still improving.

The root of wheat consists of seminal and nodal roots. Comparatively speaking, fewer studies have been carried out on the nodal root system because of its disappearance at the early seedling stage under indoor environments. In this study, 196 accessions from the Huanghuai Wheat Region (HWR) were used to identify the characteristics of seminal and nodal root traits under different growth environments, including indoor hydroponic culture (IHC), outdoor hydroponic culture (OHC), and outdoor pot culture (OPC), for three growing seasons. The results indicated that the variation range of root traits in pot environment was larger than that in hydroponic environment, and canonical coefficients were the greatest between OHC and OPC (0.86) than those in other two groups, namely, IHC vs. OPC (0.48) and IHC vs. OHC (0.46). Most root traits were negatively correlated with spikes per area (SPA), grains per spike (GPS), and grain yield (GY), while all the seminal root traits were positively correlated with thousand-kernel weight (TKW). Genome-wide association study (GWAS) was carried out on root traits by using a wheat 660K SNP array. A total of 35 quantitative trait loci (QTLs)/chromosomal segments associated with root traits were identified under OPC and OHC. In detail, 11 and 24 QTLs were significantly associated with seminal root and nodal root traits, respectively. Moreover, 13 QTLs for number of nodal roots per plant (NRP) containing 14 stable SNPs, were distributed on chromosomes 1B, 2B, 3A, 4B, 5D, 6D, 7A, 7B, and Un. Based on LD and bioinformatics analysis, these QTLs may contain 17 genes closely related to NRP. Among them, TraesCS2B02G552500 and TraesCS7A02G428300 were highly expressed in root tissues. Moreover, the frequencies of favorable alleles of these 14 SNPs were confirmed to be less than 70% in the natural population, suggesting that the utilization of these superior genes in wheat root is still improving. [ABSTRACT FROM AUTHOR]

Changes in root development and growth in upland rice receiving subsurface irrigation were evaluated using root box experiments. Irrigated water was independently applied every day to depths of 0, 5, 10 and 20 cm from the ground surface, and root morphology and aboveground growth were determined after 2 weeks of treatment. Plant length, stem number and leaf age significantly increased along with the irrigation depth, and the aboveground dry weights of rice grown at 5-, 10- and 20-cm depths were significantly greater than those grown at 0 cm. Root surface area significantly increased along with the irrigation depth, which was attributed to the increasing lengths and branch numbers of roots. Subsurface irrigation significantly increased root lengths in deep layers (below 15 cm) and increased the deep layers' distribution ratios by 1.2 to 5.7 times as the surface layer ratio decreased. This was accompanied with a decrease in the root diameter. This may be associated with the increase in the numbers of branches and the decrease in the numbers of thick nodal roots. These results indicate that subsurface irrigation increases root length and branching in the deep soil layers, inducing deep rooting, even with same amount of irrigation. [ABSTRACT FROM AUTHOR]

Summary: Ethylene plays a critical role in many diverse processes in plant development. Recent studies have demonstrated that overexpression of the maize ARGOS8 gene reduces the plant's response to ethylene by decreasing ethylene signaling and enhances grain yield in transgenic maize plants. The objective of this study was to determine the effects of ethylene on the development of nodal roots, which are primarily responsible for root‐lodging resistance in maize. Exogenous application of the ethylene precursor 1‐aminocyclopropane‐1‐carboxylic acid (ACC) was found to promote the emergence of nodal roots. Transcriptome analysis of nodal tissues revealed that the expression of genes involved in metabolic processes and cell wall biogenesis was upregulated in response to ACC treatment, supporting the notion that ethylene is a positive regulator for the outgrowth of young root primordia. In BSV::ARGOS8 transgenic plants with reduced ethylene sensitivity due to constitutive overexpression of ARGOS8, nodal root emergence was delayed and the promotional effect of ACC on nodal root emergence decreased. Field tests showed that the BSV::ARGOS8 plants had higher root lodging relative to non‐transgenic controls. When ARGOS8 expression was controlled by the developmentally regulated promoter FTM1, which conferred ARGOS8 overexpression in adult plants but not in the nodal roots and nodes in juvenile plants, the FTM1::ARGOS8 plants had no significant difference in root lodging compared with the wild type but produced a higher grain yield. These results suggest that ethylene has a role in promoting nodal root emergence and that a delay in nodal root development has a negative effect on root‐lodging resistance in maize. Significance Statement: Root‐lodging resistance is a critically important trait for high‐yield maize hybrids and has been selected in maize breeding programs over the past 100 years. In maize, the stem‐borne nodal roots are formed in the normal developmental process and play a major role in root‐lodging resistance. Using the ethylene precursor 1‐aminocyclopropane‐1‐carboxylic acid (ACC) and ARGOS8 transgenic plants which have reduced ethylene sensitivity, we found that ACC promotes nodal root emergence and that ARGOS8 transgenic plants have delayed nodal root development and increased root lodging. These results suggest a positive role for ethylene in root‐lodging resistance. These findings have applications in maize breeding for improved agronomic traits. [ABSTRACT FROM AUTHOR]

Deep rooting of wheat has been suggested that it influences the tolerance to various environmental stresses. In this study, the nodes from which the deepest penetrated roots had emerged were examined in winter wheat. The wheat was grown in long tubes with or without mechanical stress and in large root boxes. The length and growth angle of each axile root were examined to analyze the difference in the vertical distribution of the roots between the two wheat cultivars, one with a deep and one with a shallow root system. In Shiroganekomugi, a Japanese winter wheat cultivar with a shallow root system, the rooting depths of the seminal and nodal roots decreased as the rooting nodes advanced acropetally. Six out of nine deepest roots were seminal root in the non-mechanical stress conditions. In Mutsubenkei, a Japanese winter wheat cultivar with a deep root system, grown in root boxes, not only the seminal roots but also the coleoptilar and the first nodal roots penetrated to a depth of more than 1.3 m in the root box, and became the deepest roots. In both cultivars, the seminal roots became the deepest roots under the mechanical stress conditions. There were no clear tendencies in the root growth angles among the rooting nodes in the wheat root system. This indicates that the length of the axile roots can explain the differences in the rooting depths among axile roots in a wheat root system. On the other hand, the axile roots of Mutsubenkei elongated significantly more vertically than those of Shiroganekomugi. This suggests that not only seminal but also nodal roots exhibit strong positive gravitropism and penetrate deeply in a cultivar with a deep root system. In wheat cultivars, it is likely that the extent of its Root Depth Index results partly from the gravitropic responses of both seminal and nodal roots.

Nodal root anatomy was compared among twelve upland and lowland rice (Oryza sative L.) varieties with tropical origin which were grown in hydroponic culture and under field conditions. The traditional upland japonica varieties showed the largest diameter of root, stele, and xylem vessel followed by modern upland varieties. There was a clear varietal difference in the ratio of stele to root diameter, which was associated with the genetic group rather than with the ecosystems. The japonica varieties had a significantly larger stele diameter relative to the root diameter than indica and aus varieties. The indica and aus varieties displayed more xylem vessels per unit area of stele than the japonica varieties, but the diameter of xylem vessel was smaller. Equivalent xylem vessel diameter (De) was more dependent on the number of xylem in the indica varieties than in the japonica varieties. Distinctly different types of sclerenchyma anatomy were identified among the varieties. The development of sclerenchyma was classified into four different types based on thickening of cell wall in the outer cortical parenchyma and the number of sclerenchymatous cell layers. Like the xylem anatomy, the varietal differences in sclerenchyma development were more associated with genetic group rather than the ecotype. The japonica varieties had higher frequency of the types which have a doubled cell layer in sclerenchyma with thick cell wall than indica and aus. The difference among the genetic groups was nearly consistent across growing conditions, aerobic and submerged soils. These results indicated that sclerenchyma development is controlled by a genetic factor.

Rice plants in the rainfed areas are mostly grown under fluctuating soil moisture. We examined responses in dry matter production, root development and water use to changing soil moisture in diverse rice cultivars. Rice plants were grown in polyvinyl chloride tubes under glasshouse conditions. Progressive drought right after planting greatly inhibited the shoot dry matter production, tiller development, nodal root development and water uptake in all cultivars tested. When the plants experienced soil submergence before being exposed to drought, all the cultivars exhibited higher dry matter production than their well-watered counterparts. Cultivar differences were clearly noted in the growth responses to rewatering after these plants were droughted. With well–watered control as basis, IRAT 109 and KDML 105 plants increased efficiency in converting available dry matter to increase their total root length by means of enhanced lateral root development. In the latter, however, the dry weight of roots also increased and so did root water uptake. In Dular, droughted plants did not show a clear response in terms of root development and water uptake to rewatering while its shoot growth was much more severely inhibited than the other cultivars. These findings suggest that phenotypic plasticity in the root system structure exhibited by promoted lateral root development and new nodal root production play a key role in the growth of rice under changing moisture level in the soil.

Root systems determine the capacity of a plant to access soil water and their architecture can influence adaptation to water-limited conditions. It may be possible to associate that architecture with root attributes of young plants as a basis for rapid phenotypic screening. This requires improved understanding of root system development. This study aimed to characterise the morphological and architectural development of sorghum and maize root systems by (i) clarifying the initiation and origin of roots at germination, and (ii) monitoring and quantifying the development of root systems in young plants. Three experiments were conducted with two maize and four sorghum hybrids. Sorghum produced a sole seminal (primary) root and coleoptile nodal roots emerged at the 4th–5th leaf stage, whereas maize produced 3–7 seminal (primary and scutellum) roots and coleoptile nodal roots emerged at the 2nd leaf stage. Genotypic variation in the flush angle and mean diameter of nodal roots was observed and could be considered a suitable target for large scale screening for root architecture in breeding populations. Because of the relatively late appearance of nodal roots in sorghum, such screening would require a small chamber system to grow plants until at least 6 leaves had fully expanded. [ABSTRACT FROM AUTHOR]

To explore the genetic resources that could be utilized to help improve root system architecture phenotypes in rice ( Oryza sativa ), we have conducted genome-wide association studies to investigate maximum root length and crown root number in 135 10-day-old Japanese rice accessions grown hydroponically. We identified a quantitative trait locus for crown root number at approximately 32.7 Mbp on chromosome 4 and designated it qNCR1 ( quantitative trait locus for Number of Crown Root 1 ). A linkage disequilibrium map around qNCR1 suggested that three candidate genes are involved in crown root number: a cullin ( LOC_Os04g55030 ), a gibberellin 20 oxidase 8 ( LOC_Os04g55070 ), and a cyclic nucleotide-gated ion channel ( LOC_Os04g55080 ). The combination of haplotypes for each gene was designated as a haploblock, and haploblocks 1, 2, and 3 were defined. Compared to haploblock 1, the accessions with haploblocks 2 and 3 had fewer crown roots; approximately 5% and 10% reductions in 10-day-old plants and 15% and 25% reductions in 42-day-old plants, respectively. A Japanese leading variety Koshihikari and its progenies harbored haploblock 3. Their crown root number could potentially be improved using haploblocks 1 and 2., (Copyright © 2022 by JAPANESE SOCIETY OF BREEDING.)

In plagiotropic plants, axillary buds on the stolon can be exposed to low red:far-red (R:FR) ratios, while the leaves may be positioned in the uppermost layer of the sward where they are exposed to a high R:FR ratio. We tested whether the light environment of unfolded leaves influences outgrowth of the axillary buds and the formation of nodal roots of Trifolium repens. Single plants were grown in a growth cabinet with high photosynthetic photon flux rate (PPFR) and a high R:FR ratio (FHRH, control), low PPFR and high R:FR (FLRH) or low PPFR and low R:FR (FLRL). In an additional treatment (SS), only stolons were shaded so that developing leaves grew into light conditions similar to the control treatment. Neutral shading (FLRH) had a minor effect on branching and did not influence root formation. A reduction in the R:FR ratio (FLRL) significantly delayed the outgrowth of axillary buds so that, compared to the control plants, the percentage of branched phytomers was reduced by 43% on the parent axis and by 75% on primary branches. Furthermore, the number of nodal roots per plant was reduced by about 30%. When only the stolons were shaded (SS), the percentage of branched and rooted phytomers was similar to that of the control plants. Extension of petioles and leaves was very variable, increasing the values in the FLRL treatment at least 2.5-fold compared with the control plants. It was concluded that the light environment of the unfolded leaves had a significant influence on the regulation of the outgrowth of axillary buds and that the high plasticity in petiole growth allows the positioning of the leaves in a light environment conducive to the stimulation of branch outgrowth. [ABSTRACT FROM AUTHOR]