Cotton Root Research Articles

Dual Transcriptome Analysis Reveals the Changes in Gene Expression in Both Cotton and Verticillium dahliae During the Infection Process

Cotton is often threatened by Verticillium wilt caused by V. dahliae. Understanding the molecular mechanism of V. dahlia–cotton interaction is important for the prevention of this disease. To analyze the transcriptome profiles in V. dahliae and cotton simultaneously, the strongly pathogenic strain Vd592 was inoculated into cotton, and the infected cotton roots at 36 h and 3 d post infection were subjected to dual RNA-seq analysis. For the V. dahliae, transcriptomic analysis identified 317 differentially expressed genes (DEGs) encoding classical secreted proteins, which were up-regulated at least at one time point during infection. The 317 DEGs included 126 carbohydrate-active enzyme (CAZyme) and 108 small cysteine-rich protein genes. A pectinesterase gene (VDAG_01782) belonging to CAZyme, designated as VdPE1, was selected for functional validation. VdPE1 silencing by HIGS (host-induced gene silencing) resulted in reduced disease symptoms and the increased resistance of cotton to V. dahliae. For the cotton, transcriptomic analysis found that many DEGs involved in well-known disease resistance pathways (flavonoid biosynthesis, plant hormone signaling, and plant–pathogen interaction) as well as PTI (pattern-triggered immunity) and ETI (effector-triggered immunity) processes were significantly down-regulated in infected cotton roots. The dual RNA-seq data thus potentially connected the genes encoding secreted proteins to the pathogenicity of V. dahliae, and the genes were involved in some disease resistance pathways and PTI and ETI processes for the susceptibility of cotton to V. dahliae. These findings are helpful in the further characterization of candidate genes and breeding resistant cotton varieties via genetic engineering.

Diversity of Oomycetes From Alabama Cotton Soils Using Culture-Independent Methods.

Seedling disease management recommendations rely on comprehensive identification of the pathogens. A recent manuscript isolated oomycetes from diseased cotton (Gossypium hirsutum L.) roots to identify the species associated. However, culture-dependent surveys may miss species because of the microbiological medium and work required to isolate and maintain all cultured organisms. Alternatively, culture-independent methods using PCR amplification and high-throughput sequencing can identify species' presence and relative abundance, including obligate pathogens and rare members of communities. We used culture-independent sequencing from the same cotton soils in the culture-based survey to determine the oomycete species in oomycete-containing soils. The results of the two methods were generally similar regarding the species identified. Similarly to the culture-based method, Globisporangium irregular accounted for 24% of the relative abundance and was encountered in all fields sequenced. In contrast, we identified three operational taxonomic units matching Globisporangium ultimum, but accounted for less than 0.06% of total relative abundance, potentially explaining why it was not isolated from cotton roots in the original survey. Phytophthora nicotianae was identified in soils but not at the concentrations recorded in the culture-based study. The results of this study, combined with the results of the culture-based survey, demonstrate the most comprehensive identification of oomycetes associated with cotton in the cotton belt and the oomycetes related to seedling disease. The combined results will be essential for future research into the specific pathogen species mentioned and stimulate similar research in other states.

Molecular characterization of Fusarium isolates from Upland cotton roots in Uzbekistan and whole-genome comparison with isolates from the USA.

Fusarium oxysporum f. sp. vasinfectum (FOV) is a significant cotton (Gossypium spp.) pathogen causing vascular wilt, browning of the vascular tissues, and plant death in the most severe cases. This global disease is responsible for sizeable crop losses annually and is found in many cotton producing regions, including the Republic of Uzbekistan and the USA. Specifically, FOV race 4 (FOV4) has been disrupting production for years. This study aimed to genetically characterize FOV4 isolates causing disease in the main cotton producing region of Uzbekistan and compare with FOV4 isolates from the USA. A field study conducted in the Bukhara region of the Republic of Uzbekistan in the spring of 2022 identified both FOV4 and new Fusarium isolates from Upland cotton exhibiting typical Fusarium wilt symptoms. Molecular markers were initially used to identify isolates of interest, and a phylogenetic analysis was performed using partial EF1-α sequences, followed by a comparative genomic analysis. We also report for the first time the isolation of F. solani and F. commune causing Fusarium wilt in Uzbekistan. Furthermore, we show that the FOV4 population within our sampling region of Uzbekistan may be dominated by a single biotype with an effector profile similar to that of FOV race 7 (FOV7). One of these effector proteins is also present in the F. commune isolate showing virulence to cotton. Whole genome comparisons between FOV races can identify unique genetic markers for FOV4 and aid in the development of tools for breeding FOV resistant cotton varieties.

Optimizing nitrogen fertilizer for improved root growth, nitrogen utilization, and yield of cotton under mulched drip irrigation in southern Xinjiang, China

The root system plays a crucial role in water and nutrient absorption, making it a significant factor affected by nitrogen (N) availability in the soil. However, the intricate dynamics and distribution patterns of cotton (Gossypium hirsutum L.) root density and N nutrient under varying N supplies in Southern Xinjiang, China, have not been thoroughly understood. A two-year experiment (2021 and 2022) was conducted to determine the effects of five N rates (0, 150, 225, 300, and 450 kg N ha−1) on the root system, shoot growth, N uptake and distribution, and cotton yield. Compared to the N0 treatment (0 kg N ha−1), the application of N fertilizer at a rate of 300 kg N ha−1 resulted in consistent and higher seed cotton yields of 5875 kg ha−1 and 6815 kg ha−1 in 2021 and 2022, respectively. This N fertilization also led to a significant improvement in dry matter weight and N uptake by 32.4% and 53.7%, respectively. Furthermore, applying N fertilizer at a rate of 225 kg N ha−1 significantly increased root length density (RLD), root surface density (RSD), and root volume density (RVD) by 49.6–113.3%, 29.1–95.1%, and 42.2–64.4%, respectively, compared to the treatment without N fertilization (0 kg N ha−1). Notably, the roots in the 0–20 cm soil layers exhibited a stronger response to N fertilization compared to the roots distributed in the 20–40 cm soil layers. The root morphology parameters (RLD, RSD, and RVD) at specific soil depths (0–10 cm in the seedling stage, 10–25 cm in the bud stage, and 20–40 cm in the peak boll stage) were significantly associated with N uptake and seed cotton yield. Optimizing nitrogen fertilizer supply within the range of 225–300 kg N ha−1 can enhance root foraging, thereby promoting the interaction between roots and shoots and ultimately improving cotton production in arid areas.

Negatively Charged Carbon Dots Employed Symplastic and Apoplastic Pathways to Enable Better Plant Delivery than Positively Charged Carbon Dots.

Efficient delivery of nanoparticles (NPs) to plants is important for agricultural application. However, to date, we still lack knowledge about how NPs' charge matters for its translocation pathway, i.e., symplastic and apoplastic pathways, in plants. In this study, we synthesized and used negatively charged citrate sourced carbon dots (C-CDs, -37.97 ± 1.89 mV), Cy5 coated C-CDs (Cy5-C-CDs, -41.90 ± 2.55 mV), positively charged PEI coated carbon dots (P-CDs, +43.03 ± 1.71 mV), and Cy5 coated P-CDs (Cy5-P-CDs, +48.80 ± 1.21 mV) to investigate the role of surface charges and coatings on the employed translocation pathways (symplastic and apoplastic pathways) of charged NPs in plants. Our results showed that, different from the higher fluorescence intensity of P-CDs and Cy5-P-CDs in extracellular than intracellular space, the fluorescence intensity of C-CDs and Cy5-C-CDs was similar between intracellular and extracellular space in cucumber and cotton roots. It suggests that the negatively charged CDs were translocated via both symplastic and apoplastic pathways, but the positively charged CDs were mainly translocated via the apoplastic pathway. Furthermore, our results showed that root applied negatively charged C-CDs demonstrated higher leaf fluorescence than did positively charged P-CDs in both cucumber (8.09 ± 0.99 vs 3.75 ± 0.23) and cotton (7.27 ± 1.06 vs 3.23 ± 0.22), indicating that negatively charged CDs have a higher translocation efficiency from root to leaf than do positively charged CDs. It should be noted that CDs do not affect root cell activities, ROS level, and photosynthetic performance in cucumber and cotton, showing its good biocompatibility. Overall, this study not only figured out that root applied negatively charged CDs employed both symplastic and apoplastic pathways to do the transportation in roots compared with mainly the employment of apoplastic pathway for positively charge CDs, but also found that negatively charge CDs could be more efficiently translocated from root to leaf than positively charged CDs, indicating that imparting negative charge to NPs, at least CDs, matters for its efficient delivery in crops.

Phosphorus application under continuous wheat-cotton straw retention enhanced cotton root productivity and seedcotton yield by improving the carbohydrate metabolism of root

ContextStraw retention could reduce phosphorus (P) application without decreasing seedcotton yield but related physiological mechanisms were unclear. Cotton root is the first organ to sense the changes in soil environment, and its growth and development, especially carbohydrate metabolism, significantly affected the formation of seedcotton yield. Therefore, it is necessary to explore the responses of cotton root carbohydrate metabolism to straw retention combined with P application. ObjectiveThis study was to investigate the effects of straw retention combined with P application on root carbohydrate metabolism and its relationship with seedcotton yield. MethodsA field experiment (2020–2022) was conducted to evaluate the changes in seedcotton yield, cotton canopy apparent photosynthesis rate (CAP), biomass, root productivity, root carbohydrate contents and related enzyme activities under different straw management [removal (S0), retention (S1)] and P rates (0, 100, 200 kg P2O5 ha−1). ResultsStraw retention and P application both increased seedcotton yield and had a significant interaction effect on it. In the 5th-7th year of straw retention, straw retention reduced 24 %-26 % P application to reach a similar yield of S0 with 100 kg P2O5 ha−1. Analyzing the reasons: (1) Straw retention combined with P application increased cotton CAP, providing adequate assimilates for cotton development; (2) Straw retention combined with P application promoted the utilization of root carbohydrates, thereby increasing root productivity and seedcotton yield. Specifically, compared with S0 without P, S1 combined with P application increased the enzyme activities related to carbohydrate metabolism, especially sucrose synthase (7.6 %-59.4 %) and acid invertase (3.9 %-58.6 %), which reduced sucrose (3.3 %-32.2 %) and starch (4.3 %-28.7 %) contents at the peak boll setting stage. Efficient utilization of sucrose and starch enhanced root productivity, the ratio of root to shoot (R/S) reduced by 2.7 %-21.6 %, while the boll loading of root system (BLR) and boll capacity of root system (BCR) increased by 0.6 %-39.2 % and 3.1 %-50.6 % at the boll opening stage, respectively, favoring the formation of seedcotton yield. Furthermore, when the R/S, BLR, and BCR reached 0.12, 0.81 boll g−1, and 4.33 g g−1, cotton harvested the maximum theoretical yield of 3780, 3774, and 4069 kg ha−1, respectively. ConclusionsStraw retention combined with P application increased root productivity and seedcotton yield by promoting the utilization of root carbohydrates. ImplicationsThis study revealed the internal mechanism for straw retention combined with P application to affect seedcotton yield from the angle of root carbohydrate metabolism and provided a theoretical basis for rationally reducing P fertilizer under straw retention.

Chitinase Gene FoChi20 in Fusarium oxysporum Reduces Its Pathogenicity and Improves Disease Resistance in Cotton.

Chitinase genes, as a class of cell wall hydrolases, are essential for the development and pathogenesis of Fusarium oxysporum f.sp. vasinfectum (F. ox) in cotton, but related research focused on chitinase genes are limited. This study explored two island cotton root secretions from the highly resistant cultivar Xinhai 41 and sensitive cultivar Xinhai 14 to investigate their interaction with F. ox by a weighted correlation network analysis (WGCNA). As a result, two modules that related to the fungal pathogenicity emerged. Additionally, a total of twenty-five chitinase genes were identified. Finally, host-induced gene silencing (HIGS) of FoChi20 was conducted, and the cotton plants showed noticeably milder disease with a significantly lower disease index than the control. This study illuminated that chitinase genes play crucial roles in the pathogenicity of cotton wilt fungi, and the FoChi20 gene could participate in the pathogenesis of F. ox and host-pathogen interactions, which establishes a theoretical framework for disease control in Sea Island cotton.

Pioneering Nit Gene Exploitation to Develop Molecular Diagnostic Assay forRapid Detection ofCotton Root Rot Incitant, Macrophomina phaseolina (Tassi) Goid, in Field Soil.

Cotton root rot caused by Macrophomina phaseolina pose a significant threat to cotton production, leading to substantial yield and quality losses. Early and accurate diagnosis of this pathogen in soil is crucial for effective disease management. Thisstudy presents a pioneering investigation into the utilization of the nit gene encoding nitrilase for the development of a molecular diagnostic assay aimed at the rapid detection of M. phaseolina in field soils. The methodology involved the design and validation of primers targeting the Nit gene sequence, followed by the optimization of PCR conditions for efficient amplification. Leveraging state-of-the-art molecular techniques, the assay offers a novel protocol to accurately identify the presence of M. phaseolina in soil with high sensitivity and specificity. The specificity of the designed primers was confirmed through PCR amplification using DNA from M. phaseolina and other related fungi. Sensitivity tests demonstrated that the PCR assay reliably detected M. phaseolina DNA at concentrations as low as 1 ng. Furthermore, the performance of the diagnostic assay was rigorously evaluated using field soil samples with a known status of M. phaseolina infection, demonstrating its reliability and efficacy in real-world scenarios. This study introduces a novel molecular marker for the detection of M. phaseolina and offers a rapid and efficient means for screening M. phaseolina in large soil samples with minimal time and manpower.

Effects of Drip Irrigation Flow Rate and Layout Designs on Soil Salt Leaching and Cotton Growth under Limited Irrigation

Optimal drip irrigation management in shallow groundwater areas needs to clarify the effects of flow rate and layout designs on the soil moisture, salt distribution, cotton root length density, plant height, leaf area, and yield. In this study, a one-year field experiment was conducted from April to October 2018 in the fifth company of the 16th Regiment in Alar City, Xinjiang, to investigate the effects of various drip flow rates and layout designs of cotton growth. Two drip flow rates (2.8 and 5.6 L·h−1) and two layout designs (one film, two drip tapes, and six rows; one film, three drip tapes, and six rows) were applied to explore the optimal combination, resulting in a total of four treatments that were irrigated three times in the whole growth period. Soil moisture, salt distribution, cotton root length density, plant height, and leaf area were measured. The main results were as follows: (1) Under the same layout designs, the soil moisture content was higher and the soil salinity was lower when the drip flow rate was 5.6 L·h−1, and the cotton root length density, plant height, leaf area, and yield were significantly higher than that of 2.8 L·h−1. (2) Under the same drip flow rate, the soil desalination rate, cotton growth indexes, and yield under the three-tapes treatment were significantly higher than the values of the two-tapes treatment. The actual yield of treatment D was 21.56%, 19.23%, and 11.71% higher than that of treatments A, B, and C, respectively. (3) The crop evapotranspiration of cotton during the two irrigation cycles showed an increasing trend, and the groundwater contribution showed a smaller and then increasing trend. Overall, the combination of three tapes and a drip flow rate of 5.6 L·h−1 had the highest cotton yield and net income, which were 6211.36 kg·hm−2 and 4820.21 kg·hm−2 for the theoretical and actual yields. The results of this study can provide a reference for the management of limited irrigation leaching soil salinity and cotton cultivation in shallow groundwater areas.

Positive roles of the Ca2+ sensors GbCML45 and GbCML50 in improving cotton Verticillium wilt resistance.

As a universal second messenger, cytosolic calcium (Ca2+) functions in multifaceted intracellular processes, including growth, development and responses to biotic/abiotic stresses in plant. The plant-specific Ca2+ sensors, calmodulin and calmodulin-like (CML) proteins, function as members of the second-messenger system to transfer Ca2+ signal into downstream responses. However, the functions of CMLs in the responses of cotton (Gossypium spp.) after Verticillium dahliae infection, which causes the serious vascular disease Verticillium wilt, remain elusive. Here, we discovered that the expression level of GbCML45 was promoted after V. dahliae infection in roots of cotton, suggesting its potential role in Verticillium wilt resistance. We found that knockdown of GbCML45 in cotton plants decreased resistance while overexpression of GbCML45 in Arabidopsis thaliana plants enhanced resistance to V. dahliae infection. Furthermore, there was physiological interaction between GbCML45 and its close homologue GbCML50 by using yeast two-hybrid and bimolecular fluorescence assays, and both proteins enhanced cotton resistance to V. dahliae infection in a Ca2+-dependent way in a knockdown study. Detailed investigations indicated that several defence-related pathways, including salicylic acid, ethylene, reactive oxygen species and nitric oxide signalling pathways, as well as accumulations of lignin and callose, are responsible for GbCML45- and GbCML50-modulated V. dahliae resistance in cotton. These results collectively indicated that GbCML45 and GbCML50 act as positive regulators to improve cotton Verticillium wilt resistance, providing potential targets for exploitation of improved Verticillium wilt-tolerant cotton cultivars by genetic engineering and molecular breeding.

Optimum Plant Density Improved Cotton (Gossypium hirsutum L.) Root Production Capacity and Photosynthesis for High Cotton Yield under Plastic Film Mulching

Optimum Plant Density Improved Cotton (Gossypium hirsutum L.) Root Production Capacity and Photosynthesis for High Cotton Yield under Plastic Film Mulching

Characterizing the Diversity of Oomycetes Associated with Diseased Cotton Seedlings in Alabama.

Many oomycete species are associated with the seedlings of crops, including upland cotton (Gossypium hirsutum L.), which leads to annual threats. The diversity of oomycete species in Alabama needs to be better understood since the last survey of oomycetes associated with cotton in Alabama was 20 years ago-before significant updates to taxonomy and improvements in identification of oomycetes using molecular tools. Our current study aimed to identify oomycetes associated with Alabama cotton seedlings, correlate diversity with soil edaphic factors, and assess virulence toward cotton seed. Thirty symptomatic cotton seedlings were collected independently from 25 fields in 2021 and 2022 2 to 4 weeks after planting. Oomycetes were isolated by plating root sections onto a semiselective medium. The internal transcribed spacer (ITS) region was sequenced to identify the resulting isolates. A seed virulence assay was conducted in vitro to verify pathogenicity, and 347 oomycete isolates were obtained representing 36 species. Northern Alabama soils had the richest oomycete communities and a greater silt and clay concentration than sandier soils in the central and southern coastal plains. Globisporangium irregulare and Phytophthora nicotianae were consistently recovered from cotton roots in both years. Globisporangium irregulare was pathogenic and recovered from all Alabama regions, whereas P. nicotianae was pathogenic but recovered primarily in areas with lower sand content in northern Alabama. Many oomycete species have not been previously reported in Alabama or the southeastern United States. Altogether, this knowledge will help facilitate effective management strategies for cotton seedling diseases caused by oomycetes in Alabama and the United States.

Cotton adapts to Na2SO4 stress by regulating the metabolic intensity and distribution of metabolites in roots and leaves

Significant Na2SO4 stress severely restricts cotton production in Xinjiang. However, the tolerance mechanism of cotton to Na2SO4 stress is not yet fully understood. This study set up two treatments, normal soil (control, CK) and Na2SO4 stress (Na2SO4, SS), to explore the effects of Na2SO4 stress on the physiological metabolism of cotton leaves and roots. Compared with CK, the total biomass and net photosynthetic stress rate decreased significantly (P < 0.05) by 49.0 and 14.7%, respectively. Additionally, the relative conductivity, malondialdehyde content, superoxide dismutase, peroxidase, and catalase activities of leaves increased significantly by 114.5, 99.8, 160, 16.8, and 117%, respectively. A tandem mass tag (TMT) proteomics analysis identified 319 and 583 differentially expressed proteins in roots and leaves, respectively. They mainly participate in amino acid metabolism, such as alanine, aspartic acid, and glutamate metabolism; histidine metabolism; tyrosine metabolism; tryptophan metabolism; energy metabolism, such as glycolysis; the tricarboxylic acid cycle; phosphorus oxide metabolism; lipid metabolism, such as fatty acid biosynthesis; glycerol phospholipid metabolism; steroid biosynthesis; and steroid hormone biosynthesis. Metabolomic data also showed significant changes in amino acid metabolism, organic acid metabolism, and carbohydrate metabolism in the roots and leaves. Na2SO4 stress inhibited metabolism in cotton roots but promoted metabolism in cotton leaves. Under Na2SO4 stress, cotton may prioritize the use of limited photosynthetic products to maintain the health and life activities of its leaves, while also transporting some organic matter from the leaves to the roots to maintain normal metabolic activity of the roots.

The trade-off between root growth redundancy and premature senescence under different straw returning modes affects boll formation and seedcotton yield

The indeterminate growth habit of cotton (Gossypium hirsutum L.) makes a coordinated rootshoot relationship critical for increasing yield, which requires comprehensive consideration of root growth redundancy and premature senescence. Although recent evidence suggests that straw management affects root growth and thus seedcotton yield, there is limited documentation on the dynamics of root physiological activity and the rootshoot relationship of cotton under different straw returning modes. The present study compared four treatments: straw removal (CK), straw mulching (SM), straw incorporation (SI), and strawderived biochar incorporation (SBI) in an 8year field experiment. The growth dynamics of roots, shoots and reproductive organs, root physiological activity and seedcotton yield were investigated. The results showed that longterm straw application significantly enhanced seedcotton yield, but the effect varied significantly with straw returning modes. The seedcotton yield increased by 30.5%, 17.8% and 1.8% under SBI, SI and SM respectively in the 8th year of straw management, compared to CK. SBI and SI significantly enhanced the biomass of cotton roots and shoots while had higher growth rate of shoots relative to roots from peak squaring stage to peak bollsetting stage. This reduced root growth redundancy and increased the boll loading and boll capacity of root system. Besides, SBI increased the root activity, soluble protein content and antioxidant enzyme activities, and reduced the root malondialdehyde content from peak bollsetting stage to boll opening stage. These resulted in the greatest increase in boll number (53.862.1%) and boll biomass (39.480.4%) at the boll opening stage under SBI compared to CK. Overall, strawderived biochar improved the boll retention capacity of cotton roots by balancing the growth redundancy and premature senescence of the root system, and was a more suitable straw returning strategy to promote boll formation and increase cotton yield.

Water and nitrogen supply at spatially distinct locations improves cotton water productivity and nitrogen use efficiency and yield under drip irrigation

The location of water and fertilizer supply directly affects the distribution of soil moisture and nutrients, thereby affecting crop yield and fertilizer use efficiency. However, the impact of water and nitrogen (N) supply location on cotton water and N use efficiency and yield is not yet clear, especially under drip irrigation conditions. A field experiment was conducted in 2022 and 2023. Four water and N supply patterns were set as: water and N supply at the same location (narrow row (PN) or wide row (PW)), water and N supply at spatially distinct (SD) and spatially and temporally distinct locations (STD). Soil water and N leaching, cotton root growth, water productivity (WP) and recovery efficiency of N (REN), and yield were quantified. The soil moisture and NO3--N vertical distribution range (0–60 cm) were deeper at the same location for water and N supply than at spatially distinct locations for water and N supply (0–40 cm). Compared to water and N supply at the same location, supply at spatially distinct locations significantly increased cotton root weight, root length density, and root surface area. In addition, water and NO3--N leaching of water and N supply at spatially distinct (SD and STD) were 12%-50% and 32%-59% lower, respectively, than those from the same location (PN and PW), while the yield and WP increased significantly by 7%-11% and 7%-10%, respectively. The REN of water and N supply at spatially and temporally distinct locations was the highest. Therefore, water and N supply at spatially distinct or spatially and temporally distinct locations can improve water productivity, recovery efficiency of N, and yield of cotton, and reduce soil water and N leaching loss under drip irrigation.

Mining elite loci and candidate genes for root morphology-related traits at the seedling stage by genome-wide association studies in upland cotton (Gossypium hirsutum L.)

Root system architecture plays an essential role in water and nutrient acquisition in plants, and it is significantly involved in plant adaptations to various environmental stresses. In this study, a panel of 242 cotton accessions was collected to investigate six root morphological traits at the seedling stage, including main root length (MRL), root fresh weight (RFW), total root length (TRL), root surface area (RSA), root volume (RV), and root average diameter (AvgD). The correlation analysis of the six root morphological traits revealed strong positive correlations of TRL with RSA, as well as RV with RSA and AvgD, whereas a significant negative correlation was found between TRL and AvgD. Subsequently, a genome-wide association study (GWAS) was performed using the root phenotypic and genotypic data reported previously for the 242 accessions using 56,010 single nucleotide polymorphisms (SNPs) from the CottonSNP80K array. A total of 41 quantitative trait loci (QTLs) were identified, including nine for MRL, six for RFW, nine for TRL, 12 for RSA, 12 for RV and two for AvgD. Among them, eight QTLs were repeatedly detected in two or more traits. Integrating these results with a transcriptome analysis, we identified 17 candidate genes with high transcript values of transcripts per million (TPM)≥30 in the roots. Furthermore, we functionally verified the candidate gene GH_D05G2106, which encodes a WPP domain protein 2 in root development. A virus-induced gene silencing (VIGS) assay showed that knocking down GH_D05G2106 significantly inhibited root development in cotton, indicating its positive role in root system architecture formation. Collectively, these results provide a theoretical basis and candidate genes for future studies on cotton root developmental biology and root-related cotton breeding.

Host-induced gene silencing of the Verticillium dahliae thiamine transporter protein gene (VdThit) confers resistance to Verticillium wilt in cotton

Verticillium wilt (VW), induced by the soil-borne fungus Verticillium dahliae (Vd), poses a substantial threat to a diverse array of plant species. Employing molecular breeding technology for the development of cotton varieties with heightened resistance to VW stands out as one of the most efficacious protective measures. In this study, we successfully generated two stable transgenic lines of cotton (Gossypium hirsutum L.), VdThit-RNAi-1 and VdThit-RNAi-2, using host-induced gene silencing (HIGS) technology to introduce double-stranded RNA (dsRNA) targeting the thiamine transporter protein gene (VdThit). Southern blot analysis confirmed the presence of a single-copy insertion in each line. Microscopic examination showed marked reductions in the colonization and spread of Vd-mCherry in the roots of VdThit-RNAi cotton compared to wild type (WT). The corresponding disease index and fungal biomass of VdThit-RNAi-1/2 also exhibited significant reductions. Real-time quantitative PCR (qRT-PCR) analysis demonstrated a substantial inhibition of VdThit expression following prolonged inoculation of VdThit-RNAi cotton. Small RNA sequencing (sRNA-Seq) analysis revealed the generation of a substantial number of VdThit-specific siRNAs in the VdThit-RNAi transgenic lines. Additionally, the silencing of VdThit by the siVdThit produced by VdThit-RNAi-1/2 resulted in the elevated expression of multiple genes involved in the thiamine biosynthesis pathway in Vd. Under field conditions, VdThit-RNAi transgenic cotton exhibited significantly enhanced disease resistance and yield compared with WT. In summary, our findings underscore the efficacy of HIGS targeting VdThit in restraining the infection and spread of Vd in cotton, thereby potentially enabling the development of cotton breeding as a promising strategy for managing VW.

Identification and characterization of candidate genes for primary root length in Asiatic cotton (Gossypium arboreum L.).

One major gene controlling primary root length (PRL) in Gossypium arboreum is identified and this research provides a theoretical basis for root development for cotton. Primary root elongation is an essential process in plant root system structure. Here, we investigated the primary root length (PRL) of 215 diploid cotton (G. arboreum) accessions at 5, 8, 10, 15days after sowing. A Genome-wide association study was performed for the PRL, resulting in 49 significant SNPs associated with 32 putative candidate genes. The SNP with the strongest signal (Chr07_8047530) could clearly distinguish the PRLs between accessions with two haplotypes. GamurG is the only gene that showed higher relative expression in the long PRL genotypes than the short PRL genotypes, which indicated it was the most likely candidate gene for regulating PRL. Moreover, the GamurG-silenced cotton seedlings showed a shorter PRL, while the GamurG-overexpressed Arabidopsis exhibited a significantly longer PRL. Our findings provide insight into the regulation mechanism of cotton root growth and will facilitate future breeding programs to optimize the root system structure in cotton.

Climate-smart cotton (Gossypium herbaceum) crop production in Punjab: A comprehensive review of sustainable management practices

The growth and productivity of cotton (Gossypium herbaceum L.) crop are greatly influenced by major fluctuations in the local weather. The output of cotton is negatively impacted by extended periods of unfavourable weather, despite the crop's apparent relative resistance to heat and drought. Among various cotton growing states in India, Gujarat often leads as the highest cotton-producing state in the country followed by Maharashtra, Telangana, Rajasthan, Karnataka and Andhra Pradesh. These states collectively contribute more than 65% to India's cotton production. In Punjab, the optimal sowing window for cotton spans from the 1stApril to 15th May. Deviating from this recommended time frame, be it through excessively early or late sowing, correlates with compromised crop establishment and reduced productivity. Temperature thresholds dictate progression of the cotton crop's key stages. For germination, a threshold temperature of 16°C is required, while the range of 21 to 27°C is conducive to vegetative growth, and 27 to 32°C supports reproductive development. The diurnal/night time temperature for fostering cotton root growth resides within 30°C/22°C to 35°C/27°C. Elevated temperatures (40°C/32°C), even under adequate water and nutrient conditions, results in the emergence of shallow root systems. Strategic measures encompassing suitable sowing dates, precise plant spacing, favourable row orientations, judicious irrigation techniques and mulching can effectively temper the influence of climate change on cotton output. Furthermore, the application of crop simulation models and access to timely, accurate weather forecasts and agro-advisories equips decision-makers with invaluable insights for short-term operational planning.

Differences in soil bacterial community structure during the remediation of Cd-polluted cotton fields by biochar and biofertilizer in Xinjiang, China.

Heavy metal pollution is a major worldwide environmental problem. Many remediation techniques have been developed, these techniques have different performance in different environments. In this study, soil sampling was conducted in multiple cotton fields in Xinjiang, China, and found that cadmium (Cd) was the most abundant soil heavy metal. Then, to find the most suitable technique for the remediation of Cd pollution in cotton fields, a two-year study was conducted to explore the effects of cotton straw-derived biochar (BC, 3%) and Bacillus-based biofertilizer (BF, 1.5%) on cotton Cd uptake and transport and soil microbial community structure under Cd exposure conditions (soil Cd contents: 1, 2, and 4 mg·kg-1). The results showed that the bioaccumulation coefficients (Cd content of cotton organs / soil available Cd content) of cotton roots, stems, leaves, and buds/bolls reduced by 15.93%, 14.41%, 23.53%, and 20.68%, respectively after the application of BC, and reduced by 16.83%, 17.15%, 22.21%, and 26.25%, respectively after the application of BF, compared with the control (no BC and BF). Besides, the application of BC and BF reduced the transport of Cd from soil to root system, and enhanced the diversity of soil bacterial communities (dominant species: Alphaproteobacteria and Actinobacteria) and the metabolic functions related to amino acid synthesis. It was worth noting that the differential species for BF group vs BC group including Alphaproteobacteria, Gemmatimonadetes, Bacilli, and Vicinamibacteria were associated with the enrichment and transport of Cd, especially the transport of Cd from cotton roots to stems. Therefore, the application of BC and BF changed the soil bacterial diversity in Cd-polluted cotton field, and then promoted the transport of Cd in cotton, ultimately improving soil quality. This study will provide a reference for the selection of soil heavy metal pollution remediation techniques in Xinjiang, China.