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Soil microbes are crucial in shaping the root-associated microbial communities. In this study, we analyzed the effect of the soil–root niche gradient on the diversity, composition, and assembly of the bacterial community and co-occurrence network of two cotton varieties. The results revealed that the bacterial communities in cotton soil–root compartment niches exhibited a skewed species abundance distribution, dominated by abundant taxa showing a strong spatial specificity. The assembly processes of the rhizosphere bacterial communities were mainly driven by stochastic processes, dominated by the enrichment pattern and supplemented by the depletion pattern to recruit bacteria from the bulk soil, resulting in a more stable bacterial community. The assembly processes of the endosphere bacterial communities were determined by processes dominated by the depletion pattern and supplemented by the enrichment pattern to recruit species from the rhizosphere, resulting in a decrease in the stability and complexity of the community co-occurrence network. The compartment niche shaped the diversity of the bacterial communities, and the cotton variety genotype was an important source of diversity in bacterial communities within the compartment niche. We suggest that the moderate taxa contribute to significantly more changes in the diversity of the bacterial community than the rare and abundant taxa during the succession of bacterial communities in the cotton root–soil continuum. [ABSTRACT FROM AUTHOR]

Key message: Two regions located at chromosome A05 and D04 were found to be significantly associated with 0–0.5 mm and 0.5–2 mm diameter roots, respectively, and two candidate genes related to root development were identified. Roots absorb water and nutrients, and play an important role in plant growth. However, there are few genetic developmental studies on cotton root structural traits. In this study, we used 200 upland cotton (Gossypium hirsutum L.) varieties to analyze the phenotypic variation of 43 traits. A total of 2001 related single-nucleotide polymorphism (SNP) sites located within or near 1046 genes were detected through a genome-wide association study (GWAS). The 32 root traits were linked to SNPs that corresponded to 317 nonrepetitive genes. For SNPs associated with root length and 0–0.5 mm diameter root traits, a significant peak appeared on chromosome A05 (between 21.91 and 22.24 Mb). For SNPs associated with root surface area, root volume and 0.5–2 mm diameter root traits, a significant peak appeared on chromosome D04 (between 7.35 and 7.70 Mb). Within these two key regions, SNPs were detected in the promoter and coding regions of two candidate genes, GhTRL1-A05 and GhPIN8-D04. The expression levels of these two genes also changed significantly according to transcriptome sequencing and quantitative real-time PCR (qRT–PCR). After silencing the GhTRL1 and GhPIN8 genes via virus-induced gene silencing (VIGS), we found that the plants expressing TRV2::GhTRL1 and TRV2::GhPIN8 had a reduced root length, surface area. Moreover, the contents of cis-12-oxo-phytodienoic acid (cis-OPDA), isopentenyl adenosine (iPR) and cis-zeatin (cZ) in the roots of the plants expressing TRV2::GhTRL1 decreased. This study contributes to the cultivation and improvement of cotton varieties. [ABSTRACT FROM AUTHOR]

Cold stress is a major environmental factor affecting plant growth and development. Although some plants have developed resistance to cold stress, the molecular mechanisms underlying this process are poorly understood. Using genome-wide association mapping with 200 cotton accessions collected from different regions, we identified variations in the short chain alcohol dehydrogenase gene, GhSAD1 , that responds to cold stress. Virus-induced gene silencing and overexpression in Arabidopsis revealed that GhSAD1 fulfils important roles in cold stress responses. Ectopic expression of a haploid genotype of GhSAD1 (GhSAD1 HapB ) in Arabidopsis increased cold tolerance. Silencing of GhSAD1 HapB resulted in a decrease in abscisic acid (ABA) content. Conversely, overexpression of GhSAD1 HapB increased ABA content. GhSAD1 HapB regulates cold stress responses in cotton through modulation of C-repeat binding factor activity, which regulates ABA signalling. GhSAD1 HapB induces the expression of COLD - REGULATED (COR) genes and increases the amount of metabolites associated with cold stress tolerance. Overexpression of GhSAD1 HapB partially complements the phenotype of the Arabidopsis ABA2 mutant, aba2-1. Collectively, these findings increase our understanding of the mechanisms underlying GhSAD1 -mediated cold stress responses in cotton. [ABSTRACT FROM AUTHOR]

Roots play an important role in the response to nitrogen stress in cotton. To better understand the molecular and physiological mechanisms underlying the adaptation of cotton roots to nitrogen stress, the responses of genes in roots to nitrogen changes were analysed by RNA sequencing (RNA‐seq), and morphological and physiological indicators were measured for verification. This study revealed that lack of nitrogen stress (LN, 0 mm) and excess nitrogen stress (HN, 8 mm) inhibited root growth. Moderate nitrogen (MN, 4 mm) resulted in the largest values for root length, projected area and volume. Nitrogen stress regulated root growth via two mechanisms. Nitrogen stress decreased root growth by regulating cell wall growth via alterations in the cell wall composition and the expression of cell wall‐related genes. Under LN and HN, the contents of cellular polysaccharide and glucan reached their lowest levels, whereas the contents of lignin and cellulose reached their highest levels. Lower expression of EXPA17, EXLB1 and PME3 as well as higher expression of EXLA1, WAT1, CESA1, CESA3, CAD6, COMT1, SAMS, LAC4 and NAC081 were obtained under nitrogen stress compared to MN, indicating that nitrogen stress increases lignin and cellulose synthesis and promotes root ageing. Nitrogen stress also decreased root growth by affecting the contents and regulation of salicylic acid (SA), jasmonic acid (JA) and abscisic acid (ABA). Nitrogen significantly upregulated the expression of PAD4, ALD1, WRKY70, WAKL10, MYB44, FER, LHY and BHLH112 as well as significantly downregulated that of TGA6, BT1, BT2 and PYL4. The changes in the expression of these genes under nitrogen stress resulted in significant increases in the SA, JA and ABA contents in roots. Our results suggested that nitrogen stress inhibits the growth of the cotton root system by affecting cell wall growth and hormone regulation. These results contribute to our understanding of how nitrogen regulates cotton root growth at the genetic and physiological levels, and they provide a theoretical basis for the efficient utilization of nitrogen resources. [ABSTRACT FROM AUTHOR]

Cotton yield is affected by drought stress. We performed widely targeted metabolomics to explore metabolic changes under drought stress in the roots and leaves of two cotton varieties differing in drought tolerance—XLZ8 as sensitive and G95079 as tolerant variety. A total of 537 metabolites were detected at different stages of drought stress. Abscisic acid (ABA) was significantly enriched in all stages of drought stress in both roots and leaves of XLZ8. Amino acids showed enrichment in leaves of G95079 in the early stage of drought stress. Flavonoids were significantly enriched in the leaves of the two varieties in the late stage of drought stress. In roots, nucleotides and their derivatives were highly enriched in XLZ8 in the late stage of drought stress. The biosynthetic pathways of kynurenine and polyamine and glycerophospholipid metabolism may play an important role in cotton drought tolerance by scavenging reactive oxygen species (ROS) and reconstructing cell membranes. Spraying appropriate concentrations of proline, kynurenine, S‐adenosylmethionine, glucose and 1‐oleoyl‐2‐hydroxy‐sn‐glycero‐3‐phosphocholine (lyso PC18:1) significantly increased the survival rate of cotton seedlings under drought stress. We speculated that ABA‐dependent and ABA‐independent metabolic changes may lead to differences in drought tolerance among cotton varieties. [ABSTRACT FROM AUTHOR]

Gossypium hirsutum L., is a widely cultivated cotton species around the world, but its production is seriously threatened by its susceptibility to chilling stress. Low temperature affects its germination, and the underlying molecular mechanisms are rarely known, particularly from a transcriptional perspective. In this study, transcriptomic profiles were analyzed and compared between two cotton varieties, the cold-tolerant variety KN27-3 and susceptible variety XLZ38. A total of 7535 differentially expressed genes (DEGs) were identified. Among them, the transcripts involved in energy metabolism were significantly enriched during germination based on analysis of Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways, such as glycolysis/gluconeogenesis, tricarboxylic acid cycle (TCA cycle), and glyoxylate cycle (GAC). Results from further GO enrichment analysis show the earlier appearance of DNA integration, meristem growth, cotyledon morphogenesis, and other biological processes in KN27-3 compared with XLZ38 under chilling conditions. The synthesis of asparagine, GDP-mannose, and trehalose and the catabolic process of raffinose were activated. DEGs encoding antioxidants (spermidine) and antioxidase (CAT1, GPX4, DHAR2, and APX1) were much more up-regulated in embryos of KN27-3. The content of auxin (IAA), cis-zeatin riboside (cZR), and trans-zeatin riboside (tZR) in KN27-3 are higher than that in XLZ38 at five stages (from 12 h to 54 h). GA3 was expressed at a higher level in KN27-3 from 18 h to 54 h post imbibition compared to that in XLZ38. And abscisic acid (ABA) content of KN27-3 is lower than that in XLZ38 at five stages. Results from hormone content measurements and the related gene expression analysis indicated that IAA, CTK, and GA3 may promote germination of the cold-tolerant variety, while ABA inhibits it. These results expand the understanding of cottonseed germination and physiological regulations under chilling conditions by multiple pathways. [ABSTRACT FROM AUTHOR]

Background: Appropriate plant architecture can improve the amount of cotton boll opening and allow increased planting density, thus increasing the level of cotton mechanical harvesting and cotton yields. The internodes of cotton fruiting branches are an important part of cotton plant architecture. Thus, studying the molecular mechanism of internode elongation in cotton fruiting branches is highly important. Results: In this study, we selected internodes of cotton fruiting branches at three different stages from two cultivars whose internode lengths differed significantly. A total of 76,331 genes were detected by transcriptome sequencing. By KEGG pathway analysis, we found that DEGs were significantly enriched in the plant hormone signal transduction pathway. The transcriptional data and qRT-PCR results showed that members of the GH3 gene family, which are involved in auxin signal transduction, and CKX enzymes, which can reduce the level of CKs, were highly expressed in the cultivar XLZ77, which has relatively short internodes. Genes related to ethylene synthase (ACS), EIN2/3 and ERF in the ethylene signal transduction pathway and genes related to JAR1, COI1 and MYC2 in the JA signal transduction pathway were also highly expressed in XLZ77. Plant hormone determination results showed that the IAA and CK contents significantly decreased in cultivar XLZ77 compared with those in cultivar L28, while the ACC (the precursor of ethylene) and JA contents significantly increased. GO enrichment analysis revealed that the GO categories associated with promoting cell elongation, such as cell division, the cell cycle process and cell wall organization, were significantly enriched, and related genes were highly expressed in L28. However, genes related to the sphingolipid metabolic process and lignin biosynthetic process, whose expression can affect cell elongation, were highly expressed in XLZ77. In addition, 2067 TFs were differentially expressed. The WRKY, ERF and bHLH TF families were the top three largest families whose members were active in the two varieties, and the expression levels of most of the genes encoding these TFs were upregulated in XLZ77. Conclusions: Auxin and CK are positive regulators of internode elongation in cotton branches. In contrast, ethylene and JA may act as negative regulators of internode elongation in cotton branches. Furthermore, the WRKY, ERF and bHLH TFs were identified as important inhibitors of internode elongation in cotton. In XLZ77(a short-internode variety), the mass synthesis of ethylene and amino acid conjugation of auxin led to the inhibition of plant cell elongation, while an increase in JA content and degradation of CKs led to a slow rate of cell division, which eventually resulted in a phenotype that presented relatively short internodes on the fruiting branches. The results of this study not only provide gene resources for the genetic improvement of cotton plant architecture but also lay a foundation for improved understanding of the molecular mechanism of the internode elongation of cotton branches. [ABSTRACT FROM AUTHOR]

(1) Background: Upland cotton (Gossypium hirsutum L.) is the most important natural fiber worldwide, and it is extensively planted and plentifully used in the textile industry. Major cotton planting regions are frequently affected by abiotic stress, especially drought stress. Drought resistance is a complex, quantitative trait. A genome-wide association study (GWAS) constitutes an efficient method for dissecting the genetic architecture of complex traits. In this study, the drought resistance of a population of 316 upland cotton accessions was studied via GWAS. (2) Methods: GWAS methodology was employed to identify relationships between molecular markers or candidate genes and phenotypes of interest. (3) Results: A total of 8, 3, and 6 SNPs were associated with the euphylla wilting score (EWS), cotyledon wilting score (CWS), and leaf temperature (LT), respectively, based on a general linear model and a factored spectrally transformed linear mixed model. For these traits, 7 QTLs were found, of which 2 each were located on chromosomes A05, A11, and D03, and of which 1 was located on chromosome A01. Importantly, in the candidate regions WRKY70, GhCIPK6, SnRK2.6, and NET1A, which are involved in the response to abscisic acid (ABA), the mitogen-activated protein kinase (MAPK) signaling pathway and the calcium transduction pathway were identified in upland cotton at the seedling stage under drought stress according to annotation information and linkage disequilibrium (LD) block analysis. Moreover, RNA sequencing analysis showed that WRKY70, GhCIPK6, SnRK2.6, and NET1A were induced by drought stress, and the expression of these genes was significantly different between normal and drought stress conditions. (4) Conclusions: The present study should provide some genomic resources for drought resistance in upland cotton. Moreover, the germplasm of the different phenotypes, the detected SNPs and, the potential candidate genes will be helpful for molecular marker-assisted breeding studies about increased drought resistance in upland cotton. [ABSTRACT FROM AUTHOR]

The objective of this study was to investigate the root growth compensatory effects and cotton yield under drought stress. The results indicate that the root dry weight, boll weight, and cotton yield increased in both the drought-resistant cultivar (CCRI-45) and the drought-sensitive cultivar (CCRI-60). Compensation effects were exhibited under the three-day drought stress treatment at a soil relative water content (SRWC) of 60% and 45% during the seedling stage, and flowering and boll-forming stage over two years. The yield of the drought-resistant cultivar (CCRI-45) was higher than the control, however, following the six-day 45% SRWC drought treatments, the yield of the drought-sensitive cultivar (CCRI-60) was lower than the control. The soluble sugar content, proline content, superoxide dismutase (SOD) activity, and peroxidase (POD) activity of the roots increased under drought stress and then decreased after re-watering, although the values remained higher than those of the controls for a short period. These physiological measures may represent stress reactions and thus may not indicate factors that result in compensation effects. However, catalase (CAT) activity and gibberellic acid (GA) content of the roots decreased under drought stress. After re-watering, the CAT activity and the GA content increased and were significantly higher than those of the controls under the six-day 60% SRWC and 45% SRWC drought treatments. The abscisic acid (ABA) content of the roots increased under drought stress. After re-watering, the ABA content decreased to a lower level under the three and six-day 60% SRWC and 45% SRWC drought treatments than in the controls. According to an analysis of various indicators, the interaction between ABA and GA signals may play an important role in root growth compensatory effects. In summary, the results demonstrate that moderate drought stress is beneficial to root growth and yield. This conclusion is of great significance to improving our understanding of the maximum utilization of limited water resources. [ABSTRACT FROM AUTHOR]

The MYB transcription factor (TF) family is among the largest TF families and plays an important role in plant growth and stress response. However, few studies have investigated the role of the MYB gene in drought resistance in cotton. In this study, we analysed the drought transcriptomic data of cotton and identified that the GhMYB102 gene was significantly upregulated in upland cotton during the early stages of drought stress. Bioinformatics analysis showed that the amino acid sequence encoded by GhMYB102 contained two highly conserved MYB binding domains belonging to R2R3-MYB TFs. GhMYB102 was most closely related to AtMYB102. GhMYB102 is mainly expressed in roots and is induced by abiotic stresses and abscisic acid (ABA); it is localised in the nucleus and has transcriptional activation activity. Silencing of GhMYB102 decreased plant drought resistance. In addition, dual-luciferase assays and yeast single hybridisation analysis showed that GhMYB102 could directly bind the MYB motif elements in the promoter regions of GhNCED1 and GhZAT10. These results indicate that GhMYB102 plays a positive role in drought tolerance by regulating the expression of GhNCED1 and GhZAT10. Thus, GhMYB102 enhances drought resistance by participating in ABA biosynthesis or regulating the expression of drought-responsive genes. • Drought resistance transcription factors were screened from drought transcriptome. • Functional validation of MYB transcription factors under drought stress in plants. • MYB transcription factors regulates plant drought tolerance by regulating ABA synthesis. • Drought-responsive genes regulated by MYB transcription factors. [ABSTRACT FROM AUTHOR]

Cotton is an important economic crop worldwide, which is mainly distributed in the tropics and subtropics; therefore, it is highly sensitive to low temperatures. ZAT and CBF play important roles in plant growth and stress responses. However, few studies have investigated the role of these genes in freezing tolerance of cotton, and the interaction between these two remains unclear. In this study, KN27–3 cotton with strong freezing tolerance was selected from 17 cotton varieties. RNA-sequencing analysis showed that KN27–3 cotton presented 6747 differentially expressed genes (DEGs), which were mostly upregulated at the early time points after the treatments. Weighted gene co-expression network analysis and Gene Ontology enrichment analysis showed that various DEGs were involved in plant abiotic stress resistance, including SRK2I , ELF3 , WRKY70 , and TPS6. Moreover, 31 early upregulated transcription factors, including CBF and ZAT, were identified after 15 min of freezing treatment. Such significant upregulation at the early stage suggested that GhCBF4 (Gh_A12G2357) and GhZAT10 (Gh_D05G2011) play important roles in cotton freezing stress. Virus-induced gene silencing indicated that GhCBF4 - and GhZAT10 -silenced plants exhibit significant freezing-sensitive phenotypes. Biofilm interferometry and dual luciferase experiments showed that GhCBF4 regulated transcription by directly binding to a CRT/DRE motif within the GhZAT10 promoter. In summary, GhZAT10 and GhCBF4 regulated plant freezing tolerance, and GhZAT10 expression was at least partially regulated by CBF. These findings expand our current understanding of the mechanisms underlying GhZAT10 - and GhCBF4 -mediated freezing stress reactions in cotton, thereby establishing a foundation for further research on the molecular mechanisms underlying cotton freezing tolerance. ● Cotton is a very important economic crop which sensitive to low temperatures. ● A cotton material, KN27-3, with strong freezing tolerance was selected in the study. ● Weighted gene co-expression network analysis (WGCNA) and Gene ontology (GO) enrichment found that a variety of genes including SRK2I , ELF3 , WRKY70 and TPS6 were involved in freezing response. ● GhCBF4 can binding promoter of GhZAT10 and both regulates freezing tolerance. [ABSTRACT FROM AUTHOR]