Cotton Root Research Articles

Spatial distribution and dynamics of cotton fine root under film-mulched drip irrigation

Fine roots distribution and dynamics (production, mortality, and longevity) significantly impact the crop soil ecosystems. However, the spatial distribution and dynamics of cotton (Gossypium hirsutum L.) fine roots under film-mulched drip irrigation are poorly understood. The present study aims to characterize these distributions and dynamics measured using a minirhizotron technique and the influence of soil conditions. The non-uniform distribution of soil moisture and salinity may lead to the differences of root length density (RLD) distribution. A clear decreased trend for the average RLD was observed in the shallow soil layer due to high localized salinity accumulated after brackish water irrigation. There existed a clear high soil moisture content strip at depth which may lead to a high RLD peak in the 95–100 cm soil layer. Average live root production was characterized by a very high rate during the initial growth stage followed by a decline after budding, which in turn was followed by a slight increase during boll opening. The average number of new roots was highest during the initial growth stages, decreasing after the budding stage. Thinner roots in the deep soil had shorter lifespans than those in shallow soil. Our study indicated that the minirhizotron technique can be used reliably as an in situ, non-destructive method for estimating cotton fine roots distribution and dynamics under film-mulched drip irrigation. To evaluate cotton fine root distribution and dynamics under film-mulched drip irrigation more accurately, a cotton root system architecture model could be parameterized in space and time based on the minirhizotron observations.

Transcriptome-wide N6-methyladenosine profiling of cotton root provides insights for salt stress tolerance

N6-methyladenosine (m6A) is a ubiquitous reversible epigenetic RNA modification which plays a significant role in regulation of gene expression and cell functions. However, m6A abundance, dynamics and topology remain unexplored in cotton. Here, we performed transcriptome-wide m6A profiling and comparative analysis of cotton root tissues under normal and salt stress treatments. Totally, 3360 and 3771 high confidence m6A peaks, involved in 3219 and 3566 expressed genes under normal and salt stress, were identified, respectively. Of them, 1311 mRNA transcripts from salt treatment and 964 in control were specifically detected m6A peaks. Functional analysis indicated that the 1311 methylated genes specifically from salt stress were mainly involved in zeatin biosynthesis, taurine and hypotaurine metabolism, ABC transporters, and anthocyanin biosynthesis, while 964 in control were involved in ribosome and proteasome processes. Furthermore, mRNA m6A sites were enriched around the stop codons and coding regions, and m6A methylation exhibited dynamic changes after salt treatment, with 434 m6A peaks in 430 genes up-regulated and 290 m6A peaks in 287 genes downregulated. Combined with RNA-seq analysis, we found that the m6A deposition specifically in normal or salt treatment is positively correlated with their corresponding gene transcripts abundance. We confirmed that cotton YTH (YT512-B homology) domain gene GhECT6 (evolutionarily conserved C-terminal region 6), a deduced m6A reader, played an important role against salt stress. GhECT6 was significantly induced expression after salt treatment, and silencing GhECT6 caused a decrease in salt tolerance. This first high-throughput epitranscriptomic data provide new insights into understanding the critical mRNA modification in response to salt stress in cotton.

Evaluation of Three Common Root Extraction Methods for Rotylenchulus reniformis Recovery from Cotton Roots

Reniform nematode (Rotylenchulus reniformis) substantially impacts cotton production, reducing yields up to 60%. Evaluating the efficacy of management methods relies on an accurate diagnosis of R. reniformis infection. Therefore, R. reniformis life stages (eggs and vermiform nematodes) were extracted from cotton roots at a long-term research site in Quincy, FL, U.S.A., in June 2017 and June 2018 and the efficiency of three common root extraction methods (blender, modified Baermann funnel, and mist chamber) for R. reniformis recovery from cotton roots was evaluated. Due to its passive extraction nature, the blender method consistently recovered all R. reniformis life stages and also recovered the greatest overall abundances of R. reniformis life stages from cotton roots at midseason. Due to their active extraction natures, modified Baermann funnel and mist chamber methods were only successful at recovering vermiform R. reniformis life stages from cotton roots. This work highlighted the importance of understanding the limitations of commonly used extraction methods to increase the accuracy of reniform nematode recovery from cotton roots and the possible implications for nematode management decisions.

Indigenous arbuscular mycorrhizal fungi play a role in phosphorus depletion in organic manure amended high fertility soil

The species richness and propagule number of arbuscular mycorrhizal fungi (AMF) are high in intensively-managed agricultural soils. Past research has shown that AMF improve crop phosphorus (P) uptake under low soil P conditions, however it is unclear if AMF play a role in high Olsen-P soils. In this study, we investigated whether native fungal benefits exist under high P input field conditions in-situ and contribute to P utilization. We installed in-grow tubes which were sealed with different membrane pore sizes (30 or 0.45 μm) to allow or prevent AMF hyphae access to the hyphal compartment and prevent cotton roots from penetrating the chamber. We used the depletion of soil available P (Olsen-P) in the hyphae accessed compartment to indicate P uptake by the native AMF community. Our results showed that the native AMF mediated P depletion and microbial biomass P (MBP) turnover and caused the largest Olsen-P depletion ratio and MBP turnover ratio in the high P treatments (Olsen-P: 78.29 mg kg−1). The cotton roots in each fertilization regime were colonized by a unique AMF community and Glomus and Paraglomus were the dominant genera, implying the long-term fertilization regimes domesticated the AMF community. We conclude that native AMF caused the P depletion and P turnover even under high soil Olsen-P conditions.

Relationship of Seed Sowing Methods and Feeding Regimen With the Development of Cotton Root

Annotation: According to the obtained 3-year data, changes in planting methods and feeding regime of the "Sultan" variety lead to rapid growth of the root system, early growth of the main root and different levels of (orderly) roots, better absorption activity, 35-38 cm of biomass. Allows to increase by 1.5-1.8 times.

Detailed sphingolipid profile responded to salt stress in cotton root and the GhIPCS1 is involved in the regulation of plant salt tolerance

Sphingolipids are major structural components of membrane and active signaling molecules and play an important role in plant developmental processes and stress responses. As land salinization has increased globally, salinity has compromised the growth and productivity of crops such as cotton. Understanding the mechanisms of plant adaptation to salt stress is essential for breeding salt-tolerant crops. In this study, we explored the comprehensive metabolic profile of sphingolipids in cotton root under salt stress using lipidomics. 118 sphingolipid molecular species were identified, of which PhytoSph, PhytoCer, PhytoCer-OHFA, IPC, and GIPC were relatively high in content, and PhytoSph, PhytoCer, PhytoCer-OHFA, Phyto-GluCer, and IPC showed significant changes after salt stress, especially inositol phosphatidyl ceramide (IPC), which was significantly upregulated after salt treatment. Subsequently, we identified the genes encoding IPC synthase (IPCS), and ectopic expression of GhIPCS1 enhanced salt sensitivity in Arabidopsis, which might result from the disruption on the balance between various sphingolipid classes and/or molecular species. Overall, this study reveals key lipids and genes response to salt stress in cotton and provides a theoretical basis for the use of genetic engineering to improve cotton stress resistance.

MPK homolog GhNTF6 was involved in cotton against Verticillium wilt by interacted with VdEPG1

Mitogen-activated protein kinases (MPKs) are important in regulating plant development and stress response. Rapid activation of MPKs in plants usually depends on its phosphorylated. In view of this situation, a phosphorylated GhNTF6 belonged to MPKs family was screened in cotton roots under Verticillium dahliae challenge by phosphoproteomics analysis. Expression of GhNTF6 in cotton plants was did not induce by V. dahliae infection, while, silencing GhNTF6 results to enhance cotton plants susceptibility to V. dahliae, overexpression – GhNTF6 enhance Arabidopsis plants survivability to V. dahliae. Moreover, the mutation of GhNTF6 at site Thr195 and Thy197 with the phosphorylation decreased the plant resistance to V. dahliae. Therefore, GhNTF6 phosphorylation is important in plants against V. dahliae. Further analysis demonstrated that GhNTF6 interacted with a V. dahliae endopolygalacturonase (VdEPG1) on the cell nucleus. We propose that GhNTF6 is a potential molecular target for improving resistance to Verticillium wilt in cotton.

Differentiation and Variability in the Rhizosphere and Endosphere Microbiomes of Healthy and Diseased Cotton (Gossypium sp.).

The plant microbiome is a key determinant of health and productivity. However, it is still difficult to understand the structural composition of the bacterial and fungal microbiomes of diseased and healthy plants, especially the spatial dynamics and phylogenies of endophytic and rhizosphere microbial communities. We studied the differentiation and variability in the rhizosphere and endosphere microbiomes of healthy and diseased cotton from north and south of the Tianshan Mountains using the methods of PCR-based high-throughput sequencing and real-time quantitative PCR. The endophytic and rhizosphere bacterial abundances in the diseased plants were greater than those of healthy plants. The numbers of endophytic and rhizosphere fungi associated with diseased plants were greater than those associated healthy plants (p < 0.05). Endophytic and rhizosphere bacteria did not share common OTUs. The dominant rhizosphere bacteria were Proteobacteria (29.70%), Acidobacteria (23.14%), Gemmatimonadetes (15.17%), Actinobacteria (8.31%), Chloroflexi (7.99%), and Bacteroidetes (5.15%). The dominant rhizosphere fungi were Ascomycota (83.52%), Mortierellomycota (7.67%), Basidiomycota (2.13%), Chytridiomycota (0.39%), and Olpidiomycota (0.08%). The distribution of dominant bacteria in different cotton rhizosphere soils and roots differed, with the dominant bacteria Pseudomonas (15.54%) and Pantoea (9.19%), and the dominant fungi Alternaria (16.15%) and Cephalotrichum (9.10%) being present in the greatest numbers. At sampling points in different ecological regions, the total numbers of cotton endophytic and rhizosphere microbiome OTUs from southern to northern Xinjiang showed an increasing trend. There were significant differences in the composition and diversity of rhizosphere microbes and endophytes during the entire cotton growth period and in representative ecological regions (p < 0.01), whereas rhizosphere microbes and endophytes showed no significant differences among the four growth periods and in representative ecological regions. RB41, H16, Nitrospira, and Sphingomonas play important roles in the microbial ecology of cotton rhizosphere soil. Pseudomonas accounted for a large proportion of the microbes in the cotton rhizosphere soil. This study provides an in-depth understanding of the complex microbial composition and diversity associated with cotton north and south of the Tianshan Mountains.

Genome Sequence of the Agrobacterium salinitolerans DG3-1 Isolated from Cotton Roots.

Agrobacterium salinitolerans DG3-1 is an endophytic bacterium isolated from cotton root tissue. Our previous work has shown that it can inhibit the growth of Fusarium and Verticillium wilt pathogens as well as increase the chlorophyll content of cotton leaves. Here, we reported the complete genome sequence of strain DG3-1, which was analyzed by sequence reads generated from Nanopore PromethION and Illumina NovaSeq PE150 platforms. This genome sequence could be used to clarify the possible mechanism of DG3-1 at the gene level.[Formula: see text] Copyright © 2021 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Effect of saline land reclamation by constructing the “Raised Field -Shallow Trench” pattern on agroecosystems in Yellow River Delta

Efficient utilization of the limited water and land resources is critical for global development with a growing population. The widespread saline land remains an important reserved land resource for food security. This study investigated the performance of the raised field-shallow trench pattern on salt removal and water budget in the cotton field by a virtual experiment. The widely-used physically-based HYDRUS (2D/3D) model was used to implement different raise field elevations and slopes. Results showed that the raised land could control the soil salinity in the unsaturated root zone by intensifying the drainage. Compared with the flat land, the desalination effect of the raised land was more effective with the gentler slope and higher raised elevation. Without irrigation, the 30° and 45° slope-raised lands had slight effect on the soil salinity in the unsaturated root zone. Salt removal would be more effective with the addition of irrigation, with the desalination ratio ranging from 10.60% to 41.01% under fresh irrigation, or from 6.76% to 25.92% under saline irrigation, respectively. More importantly, the implementation of irrigation effectively improved the cotton root water uptake, and saline water irrigation for the 15° slope-raised field was proved to nearly meets the cotton water requirement. Therefore, the raised field-shallow trench pattern combined with saline water irrigation may provide local farmers with an alternative solution to saline land reclamation under fresh water scarcity.

Physiological and Comparative Transcriptomic Analysis Provide Insight Into Cotton (Gossypium hirsutum L.) Root Senescence in Response.

Nitrogen (N) deficiency is one of the pivotal environmental factors that induce leaf senescence. However, little is known regarding the impact of low N on root senescence in cotton. Thus, the objective of this study was to investigate the effect of low nitrogen on root senescence. In this study, the molecular mechanism of cotton root senescence in response to nitrogen deficiency was investigated by combing physiological and transcriptomic analysis when no nitrogen and normal nitrogen (138mg N·kg−1 soil). The results showed that: (1) nitrogen starvation induced the premature senescence of leaf, while delaying root senescence. (2) The increase in catalase (CAT) activity at 60, 80, and 100days after emergence (DAE), combined with decrease of malonaldehyde content at 60, 80, and 100 DAE, and the content of abscisic acid (ABA), all of these contributed to the delay of root senescence by low nitrogen treatment. (3) To study the molecular mechanisms underlying root senescence, the gene expression profiling between low nitrogen and normal nitrogen treatments were compared pairwise at 20, 40, 60, 80, and 100 DAE. A total of 14,607 genes were identified to be differentially expressed at these five points. (5) Most genes involved in glutathione (GSH) and ascorbate peroxidase (APX) synthesis were upregulated, while ABA, apoptosis, caspase, and cell cycle-related differentially expressed genes (DEGs) were downregulated. Coupled with the physiology data, these results provide new insights into the effect of nitrogen starvation on root senescence.

A novel raffinose biological pathway is observed by symbionts of cotton≡Verticillium dahliae to improve salt tolerance genetically on cotton

AbstractVerticillium dahliae is a soil‐borne, phytopathogenic fungus that causes Verticillium wilt in cotton. Salt tolerance of cotton plants suffering from Verticillium wilt was significantly improved, but the mechanism is unknown. In this study, we built a symbiont named Cotton≡VD by immersing cotton plant roots into Verticillium dahliae liquid for four days. This resulted in a strong interaction between hyphae and the cotton roots. Under NaCl treatment for 24 h, the Cotton≡VD displayed less leaf wilting and improved root growth compared with the control. Biochemical tests of SOD, POD and CAT showed significant overexpression in Cotton≡VD compared with CK. RNA‐seq data analysis of Cotton≡VD indicated a novel ‘galactose metabolism pathway’ in the KEGG database, in which two key genes, GolS2 and RFS5, were significantly differentially expressed. Symbiotic metabolites inositol galactosyl could be transformed into raffinose to scavenge free radicals and participate in plant osmotic regulation to alleviate salt stress in Cotton≡VD. Functional analysis indicated that silencing of the target gene GhRFS (RFS5) led to a decrease of raffinose content and salt tolerance as compared with CK. Cotton≡VD can significantly improve cotton seedling salt tolerance through improving raffinose content, providing new insights into the salt tolerance mechanism and new salt‐tolerant material in the future.

Genome-Wide Analysis of SRNF Genes in Gossypium hirsutum Reveals the Role of GhSRNF18 in Primary Root Growth.

Root systems are instrumental for water and nutrient uptake and the anchorage of plants in the soil. Root regulating GL2-interacting repressors (GIRs) contain a Short RING-like Zinc-Finger (SRNF) domain, but there has been no comprehensive characterization about this gene family in any plant species. Here, we renamed the GIR-like proteins as SRNF proteins due to their conserved domain and identified 140 SRNF genes from 16 plant species including 24 GhSRNF genes in Gossypium hirsutum. Phylogenetic analysis of the SRNFs revealed both similarities and divergences between five subfamilies. Notably, synteny analysis revealed that polyploidization and whole-genome duplication contribute to the expansion of the GhSRNF gene family. Various cis-acting regulatory elements were shown to be pertinent to light, phytohormone, defense responsive, and meristem regulation. Furthermore, GhSRNF2/15 were predominantly expressed in root, whereas the expression of GhSRNF18 is positively correlated with the primary root (PR) length in G. hirsutum, quantified by quantitative real-time PCR (qRT-PCR). Over-expression of GhSRNF18 in Arabidopsis and virus-induced gene silencing (VIGS) of GhSRNF18 in G. hirsutum has revealed the role of GhSRNF18 in PR growth. The over-expression of GhSRNF18 in Arabidopsis resulted in an increase of meristematic activities and auxin accumulations in PRs, which were consistent with the transcriptomic data. Our results suggested that GhSRNF18 positively regulates PR growth. This study increased our understanding of the SRNF gene family in plants and provided a novel rationale for the further investigation of cotton root morphogenesis regulated by the GhSRNFs.

The Biocontrol and Plant Growth-Promoting Properties of Streptomyces alfalfae XN-04 Revealed by Functional and Genomic Analysis.

Fusarium wilt of cotton, caused by the pathogenic fungal Fusarium oxysporum f. sp. vasinfectum (Fov), is a devastating disease of cotton, dramatically affecting cotton production and quality. With the increase of pathogen resistance, controlling Fusarium wilt disease has become a significant challenge. Biocontrol agents (BCAs) can be used as an additional solution to traditional crop breeding and chemical control. In this study, an actinomycete with high inhibitory activity against Fov was isolated from rhizosphere soil and identified as Streptomyces alfalfae based on phylogenetic analyses. Next, an integrative approach combining genome mining and metabolites detection was applied to decipher the significant biocontrol and plant growth-promoting properties of XN-04. Bioinformatic analysis and bioassays revealed that the antagonistic activity of XN-04 against Fov was associated with the production of various extracellular hydrolytic enzymes and diffusible antifungal metabolites. Genome analysis revealed that XN-04 harbors 34 secondary metabolite biosynthesis gene clusters. The ability of XN-04 to promote plant growth was correlated with an extensive set of genes involved in indoleacetic acid biosynthesis, 1-aminocyclopropane-1-carboxylic acid deaminase activity, phosphate solubilization, and iron metabolism. Colonization experiments indicated that EGFP-labeled XN-04 had accumulated on the maturation zones of cotton roots. These results suggest that S. alfalfae XN-04 could be a multifunctional BCA and biofertilizer used in agriculture.

Screening of Bacillus for the development of bioprotectants for the control of Fusarium oxysporum f. sp. vasinfectum and meloidogye incognita

Fusarium oxysporum f. sp. vasinfectum and Meloidogyne incognita cause large losses in cotton productivity. These pathogens can occur simultaneously, resulting in a Fusarium-nematode complex, which strengthens the destructive power when compared to the pathogens alone. Due to the ineffectiveness of chemicals, and to the fact that chemicals pesticides are responsible for releasing residues into the environment, more attention has been given to biocontrol. Bacillus are recognized by their ability to control plant-parasitic pathogens. However, since Fusarium and Meloidogyne often occur simultaneously, and the resulting complex causes more losses than each pathogen alone, selecting bioagents that act against both pathogens simultaneously is important, and this is the objective of this study. Among 40 Bacillus strains obtained from cotton rhizosphere and other sites, the most efficient ones were selected to inhibit mycelial growth and spore germination of Fusarium, cause J2 mortality and inhibit hatching of M. incognita. Forty Bacillus strains were evaluated both through biochemical tests related to plant growth promotion (indoleacetic acid, siderophores, and cyanhydric acid production; catalase activities; nitrogen fixation and phosphate solubilization) and root colonization. Strains S2531, S2535, S2545, S2548, S2552, S2554, S2555, and S2557 showed >4 positive responses for biochemical tests. Strains S2527, S2535, S2538, S2545, S2573, AP03, AP115, AP117, AP210, QST713 colonized cotton roots. Strains S2535, S2543, S2545, S2557, S2560, S2564, AP03, AP10, AP115, and AP117 inhibited mycelial growth of Fusarium. The most efficient strains for the inhibition of microconidia germination were S2545, S2548, AP115, AP03, and S2543. Strains AP117, S2527, S2530, S2538, S2560, and S2569 showed the highest mortality of J2. Strains S2527, S2557, S2569 and AP03 were the ones with the lowest area under hatching progress curve. Overall, strains AP03, S2527 and S2545 were selected to evaluate the control of the complex Fusarium-nematodes in cotton plants. These three strains were identified as Bacillus velezensis.

GhADF6-mediated actin reorganization is associated with defence against Verticillium dahliae infection in cotton.

Several studies have revealed that actin depolymerizing factors (ADFs) participate in plant defence responses; however, the functional mechanisms appear intricate and need further exploration. In this study, we identified an ADF6 gene in upland cotton (designated as GhADF6) that is evidently involved in cotton's response to the fungal pathogen Verticillium dahliae. GhADF6 binds to actin filaments and possesses actin severing and depolymerizing activities in vitro and in vivo. When cotton root (the site of the fungus invasion) was inoculated with the pathogen, the expression of GhADF6 was markedly down‐regulated in the epidermal cells. By virus‐induced gene silencing analysis, the down‐regulation of GhADF6 expression rendered the cotton plants tolerant to V. dahliae infection. Accordingly, the abundance of actin filaments and bundles in the root cells was significantly higher than that in the control plant, which phenocopied that of the V. dahliae‐challenged wild‐type cotton plant. Altogether, our results provide evidence that an increase in filament actin (F‐actin) abundance as well as dynamic actin remodelling are required for plant defence against the invading pathogen, which are likely to be fulfilled by the coordinated expressional regulation of the actin‐binding proteins, including ADF.

In situ Root Phenotypes of Cotton Seedlings Under Phosphorus Stress Revealed Through RhizoPot.

Phosphorus (P) deficiency is a common challenge in crop production because of its poor mobility through the soil. The root system plays a significant role in P absorption from the soil and is the initial indicator of low P levels. However, the phenotypic dynamics and longevity of cotton roots under P stress remain unknown. In this study, RhizoPot, an improvised in situ root observation device, was used to monitor the dynamics of root phenotypes of cotton seedlings under P-deficient (PD) and P-replete (PR) conditions. Low P stress reduced P absorption and accumulation in the roots, leading to low dry weight accumulation. Cotton seedlings responded to low P stress by increasing the number of lateral roots, specific root length, branch density, root length density, and length of root hairs. Additionally, the life span of root hairs was prolonged. Low P stress also reduced the average diameter of roots, promoted root extension, expanded the root coverage area, and increased the range of P acquisition. Principal component analysis revealed that the net root growth rate, root length density, root dry weight, P absorption efficiency, average root hair length, and taproot daily growth significantly influenced the cotton root architecture. Collectively, these results show that low P stress reduces the net growth rate of cotton seedling roots and restricts plant growth. Plants respond to P deficiency by extending the life span of root hairs and increasing specific root length and lateral root branch density. This change in root system architecture improves the adaptability of plants to low P conditions. The findings of this study may guide the selection of cotton varieties with efficient P utilization.

The responses of lateral roots and root hairs to nitrogen stress in cotton based on daily root measurements

AbstractLateral roots and root hairs are essential portions of cotton roots. However, the morphology and lifespan of cotton (Gossypium hirsutum L.) lateral roots and root hairs in response to nitrogen stress have remained unknown. Two cotton cultivars were assessed when no nitrogen and normal nitrogen (138 mg N·kg−1 soil) were added. The daily acquisitions of root phenotype information including the lateral root angle, lateral root density, lateral root diameter, lateral root lifespan, root hair length, root hair density, and root hair lifespan, were obtained in situ by a self‐designed platform of RhizoPots equipped with high‐resolution scanners. Nitrogen starvation significantly reduced the growth of shoots and roots, although there was less reduction of roots than shoots. Root hairs were the first organ to respond to nitrogen deficiency through morphological changes. The lateral root diameter and angle as well as the root hair lifespan decreased significantly under nitrogen stress. However, nitrogen deficiency dramatically increased the lateral root lifespan, root hair density and length. Our results demonstrate that low nitrogen can induce notable changes in lateral roots and root hairs, which may play a crucial role in the adjustment to nitrogen uptake, particularly in species that can adapt to low nitrogen availability.

Intercropping of Maize (Zea mays) and Cotton (Gossypium hirsutum L.) vs. Monoculture: Plant Growth, Root Development, and Yield

In Xinjiang Uygur Autonomous Region of China, we conducted an experimental study to evaluate the root morphology and crop yield for the intercropping of maize and cotton. Due to the shading effect of maize and the reduced root surface area of cotton root system, intercropped cotton yield was smaller (14.7%) than monoculture cotton yield. By contrast, intercropped maize with cotton yield was higher than monoculture maize yield. Compared with typical production of each crop separately, intercropping of maize and cotton showed several benefits: increased the land utilization rate, with a land equivalent ratio (LER) greater than 1; and increased the root length, root surface area, and light interception in maize, which contributed to an increase in maize yield.

Semantic segmentation model of cotton roots in-situ image based on attention mechanism

The growth and distribution of root system in the soil has an important influence on the growth of plants and is one of the important factors affecting crop production. However, the root system of plants is located in the dark and closed soil. Even if we can obtain high-definition root image from the complex soils, the interference of the soil particles on root system and the small difference of color between them will pose challenges for further root segmentation. In this experiment, the cotton mature root system is used as the research object. Based on the introduction of sub-pixel convolution DeepLabv3+ semantic segmentation model, we further added the attention mechanism to the model, assigning more weight to the pixel points of fine roots and their root hairs, and designed a semantic segmentation model of cotton roots in-situ image based on the attention mechanism. The experimental results show that the model has higher segmentation accuracy and operational efficiency than only introduces sub-pixel convolution DeepLabv3+ model, U-Net model and SegNet model. The precision value, recall value and F1-score are 0.9971, 0.9984 and 0.9937 respectively, and the IoU value of 161 untrained root image segmentation tasks was 0.9875. At the same time, we also performed segmentation experiments on the early cotton root images. The results show that the DeepLabv3+ model which only introduces sub-pixel convolution, U-Net model and SegNet model have poor segmentation effects. The semantic segmentation model based on attention mechanism proposed in this paper can be segmented accurately. The above results show that the proposed model can distinguish the cotton root system from the complex soil background accurately and has good segmentation effect. It can realize the accurate segmentation of root image in early and mature period in the process of cotton root growth, and provide important theoretical value and practical application reference for deep learning in plant root segmentation.