Cotton fiber is not only the most important raw material for textile industry, but also an ideal model for studying plant cell differentiation, elongation, and cell wall synthesis. The differentiation and development of cotton fiber is regulated by a complex and interrelated regulatory network. Transcription factors, functional genes, plant hormones, non-coding RNAs, and epigenetic modifications all play important regulatory roles during cotton fiber development. With the assembly, resequencing, and association analysis of different cotton genomes, more and more key factors regulating cotton fiber development have been uncovered, which is of great significance for further elucidating the molecular regulation mechanism of cotton fiber development and helping cotton biological breeding.

A new Bt gene expression cassette cry1Aa gene expression cassette was identified from transgenic insect-resistance cotton "Nannong 6 F₁" in this study. The difference was found located at the connection region between Bt gene and 7S UTR terminator while being compared with the cry1Ac gene and cry1Ab/Ac gene expression cassettes reported previous. Primer pair cry1Aa-F/cry1Aa-R was designed and construct-specific detection method of cry1Ab/Aa gene expression cassette was established based on the difference. Eight of eighteen cotton varieties from Jiangsu province were identified to have cry1Aa gene expression cassette using this methods. The method established was useful for identification Bt gene expression cassette and analysis of transgenic lineages.

[Objective] Deficit irrigation is an effective irrigation method used in water-saving agriculture. This study aims to quantitatively analyze the influence on cotton yield and irrigation water productivity under deficit irrigation in China, and to provide the reference for further application of deficit irrigation in China. [Method] A meta-analysis was used to quantitatively evaluate the influence of different factors on cotton yield and irrigation water productivity under deficit irrigation in China by integrating 53 literatures published from 2010 to 2022. [Result] The result showed that compared with full irrigation, the average yield of seed cotton under deficit irrigation was decreased by 16.2%, while the irrigation water productivity was increased by 32.2% on average. The subgroup analysis showed that the highest increase of irrigation water productivity was observed in Northwest China under deficit irrigation, particularly in Xinjiang which had the best effect with less yield reduction. Field plantation and areas with relatively low precipitation had increased efficiency of water productivity under irrigation deficit condition. In areas with the annual average temperature ≥ 10 ℃, adopting the planting method of dry sowing and wet emergence, and moderately increasing irrigation frequency can effectively reduce the risk of yield reduction under deficit irrigation condition. Under the condition of soil bulk density <1.5 kg·cm^-3, the risk of seed cotton yield reduction was lower than that of the high soil bulk density under deficit irrigation condition. The application of 80%-100% of full irrigation, and application rate of 200-300 kg·hm^-2 nitrogen, 100-150 kg·hm^-2 potassium and 150-200 kg·hm^-2 phosphorus can effectively promote water utilization rate and reduce the risk of yield reduction under deficit irrigation condition. [Conclusion] It is suggested that the planting method of dry sowing and wet emergence is suitable to conserve water and stabilize yield under mild deficit irrigation condition in the Northwest China arid region with relatively high temperature. And appropriate increase of irrigation frequency and moderate fertilizer application rate can reduce the influence of deficit irrigation on cotton production.

In the present study, a WRKY gene, GhWRKY4, was cloned from cotton(Gossypium hirsutum L.). The full-length cDNA of GhWRKY4 was 1281 bp long and contained a 1083-bp open reading frame (ORF) encoding a putative group-IIc WRKY protein of 360 amino acids. Bioinformatic analysis of the GhWRKY4 gene revealed that GhWRKY4 consists of three exons and two introns. A subcellular localization assay confirmed that the protein product was targeted in onion epidermal cell nuclei. Quantitative RT-PCR indicated that GhWRKY4 is constitutively expressed in cotton roots, stems, leaves, and flowers. The 5' flanking region of GhWRKY4 was obtained by genome walking. Bioinformatic analysis revealed that GhWRKY4 contains a series of putative cis-acting elements involved in stress regulation. Further stress treatments combined with gene expression analysis indicated that GhWRKY4 is involved in regulation of salt and cold stress.

Advance of Agrobacterium-mediated transformation and regeneration system of cotton（Gossypium hirsutum L.） is summarized. Genotype-dependent, long transformation period, low frequency of embryogenesis, and high rates of abnormal embryos are main bottlenecks of Agrobacterium-mediated transformation of cotton via somatic embryogenesis. To solve these problems, the researchers optimized traditional transformation systems, expanded recipient genotypes, screened high-frequency regeneration lines, selected different organs or tissues as recipient explants, and established new methods of Agrobacterium-mediated cotton transformation which is tissue culture- and genotypes-independent.

In order to detect and exploit the QTLs related to superior fiber qualities in upland cotton (Gossypium hirsutum) accession NM 03102，we constructed an F₂ and its corresponding F_2:3 populations by crossing Lumianyan 21 to NM 03102 and employed 7892 simple sequence repeats (SSR) primer pairs to screen the polymorphism between the two parents, 222 polymorphic primer pairs were obtained for genotyping the 195 individual plants of F2 population, and 242 loci were obtained. The linkage test indicated that 182 loci could be mapped to 37 linkage groups, 35 of them could be assigned to 20 chromosomes. The linkage map covered 1661.6 cM , about 37.34% of the whole genome, and the average distance between two loci was 9.1 cM.  20 QTLs were detected based on Composite Interval Mapping (CIM) method, 4 for fiber length, 4 for fiber strength, 5 for fiber micronaire value, 4 for fiber uniformity ration and 3 for fiber elongation, respectively. These QTLs could explain 5.10%~ 28.49% of the corresponding phenotypic variations. QTLs qFS-5-1 and qFU-24-1 were consistent with previous reports in different mapping populations. And 2 QTLs (qFS-5-1 and qFMIC-1-1) could be detected in both F₂ and F_2:3 generations. These stable QTL might be utilized to improve the fiber qualities in the molecular markers assisted selection(MAS) breeding programs.

There have been enormous economical losses in agriculture caused by devastating insect pests, such as cotton bollworm Helicoverpa armigera (Hübner) and diamondback moth Plutella xylostella (L.), etc. The pests could be effectively controlled by insecticides, however many kinds of the pests have showed serious resistance to different insecticides. Studies have proved that insect resistance related to the detoxification enzymes or receptors including cytochrome P450 enzymes, esterases and cadherin proteins, etc. Knockout of genes related with resistance in insect pests has been carried out by RNA interference (RNAi) recently, which is a powerful tool in molecular biology for researches on functional genes and genomes. This review focuses on the mechanisms of RNAi and its applications in silencing resistance-related genes in insects in vivo, aiming at providing novel ideas and approaches for insect controlling and resistant management in agricultural pests.

Population structure and LD（Linkage disequilibrium）of 204 upland cotton accessions were analyzed with 79 SSR (Simple sequence repeat) markers located on nine chromosomes.  Analysis of population genetic structure based on SSR data revealed that this population could be divided into three groups, two out of which were composed of three subgroups, respectively. 47% of the SSR loci pairs showed LD at significant level of P≤0.05. The maximum genetic distance of LD could be observed extended to 120 cM. The LD average decay distance was 29.7 cM at r²≤0.05. Genome wide LD reduced to 3.4 cM at r²≥0.1, providing evidence of the potential for association mapping of important traits in cotton breeding program.

microRNAs(miRNAs) are 21-24 nt non-protein-coding small RNAs (sRNAs) that regulate plant gene expression by directing target mRNA cleavage or translational inhibition. In this study, four miRNA libraries from Zaoshuchangrong-7 and Nandanbadidahua exposed to 200 mmol·L^-1 NaCl for 4 h were constructed and sequenced. Compared with the D5 genome (Gossypium raimondii L.) and the salt stress transcriptome sequences of upland cotton(Gossypium hirsutum L.) from our library, 360 miRNAs including 308 conserved miRNAs and 52 novel miRNAs were identified. A total of 94 differentially expressed miRNAs were detected in the two lines and they could be divided into two expression types. Of these, 20 candidate miRNAs were selected. Kyoto Encyclopedia of Genes and Genomes(KEGG) analysis indicated that the target genes of differentially expressed conserved miRNAs were significantly enriched in antigen processing and presentation pathway in salt-tolerant line, but in isoquinoline alkaloid biosynthesis in salt-sensitive line.

In this review, we elucidated the role of cell-wall-degrading enzymes, proteases, phytotoxins produced by Verticillium dahliae Kleb in pathogenicity and the mechanism of microsclerotial development. Recent advances in fungi functional genomics technologies such as genomics methods, RNA interference（RNAi） and Agrobacterium tumefaciens-mediated transformation（ATMT）applied for researching on the pathogenisis molecular mechanism of V. dahliae were also reviewed.

In order to study the gene regulatory network underlining the cotton fiber initiation, a yeast one hybrid cDNA library of the Gossypium barbadence L. ovule at the stage of flowering(0 DPA, 0 days post anthesis) was constructed and used to screen the potential upstream genes of GbPDF2, an important gene related to fiber initiation, using the Matchmaker Gold Yeast One-Hybrid Library Screening System developed by the Clonetech company. The promoter region of GbPDF2 was cloned and inserted into the vector pAbAi. The recombination bait vector and the cDNA library within the pGADT7-Rec fusion expression vectors were co-transformed into the yeast Y1HGold. The estimated cDNA library storage capacity is almost 2.23 × 10⁶, recombinant rate is 95.8 % and inserted PCR fragments sizes are 300 bp～2000 bp, of which the fragment length of 109 positive insertion clones are larger than 1000 bp. The positive yeast colonies were harvested and cultured for extracting the plasmid, followed by PCR and sequencing analysis. Several transcription factors are screened out such as WRKY7 transcription factor, WD-repeat protein 40, IAA responsible transcription factors. This research has laid the fundament in applying yeast one hybrid method to study signal transduction pathway of fiber initiation in cotton.

In this paper, a Fosmid library of G. raimondii chloroplast genome was constructed. The chloroplast DNA was isolated by high ionic strength and low pH buffer method. The DNA was randomly sheared and cloned into pCC1FOS vector. Recombinant DNA was packaged with the Lambda Packaging Extracts, then transfected into E. coli strain EPI300. The best sheared parameter employed in the study was 18 times with middle speed using a 1 mL injector. The library of chloroplast genome (titer: 1×10⁴ cfu·mL^-1) was obtained in which the average inserted DNA fragment was 38 kb. Thirty-nine clones covering 9.2 fold the chloroplast genome were selected by selection marker to be further analyzed. Six clones, F66, F46, F28, F8, F55, and F3, which could span G. raimondii complete genome, were screened out by cotton chloroplast markers. The library would be a valuable resource for study on genome structure and functional genes investigation in cotton.

RNA editing is one of the post-transcriptional regulation mechanisms of gene expression in the chloroplast of land plants. Recently, studies have shown that albino or yellow phenotype of high plants may be relevant to chloroplast RNA editing. In this paper, we investigated the RNA editing sites of 10 plasmid protein-coding genes from cotyledons and leaves of virescent mutant V1, Gossypium hirsutum, using PCR, RT-PCR and sequencing methods. There were 34 editing sites in both of them, but the editing efficiency was different in 6 sites of 34. Compared all editing sites between V1 and Coker310FR, we found that V1 had 5 novelty editing sites in accD-109, accD-468, ndhD-347, rpoA-69, and rpoA-279. Analyzed all the editing sites by using bioinformatics, the results showed that 13 sites, accD-109, clpP-187, ndhB-50, ndhB-196, ndhD-128, ndhD-225 and so on, would affect their protein secondary structures or three-dimensional structures. All the results indicate that the above-mentioned sites may play important roles in proteins assemble correctly and execute their function effectively.

The cotton root distribution characteristics under different amounts of drip irrigation was studied using root ecological niche index(RENI) which was compared with root parameters(root length, root dry weight, root volume, root surface area) ahead. And the results surely will be contributed to describing root distribution traits and root research methodology. The results showed: (1) RENI was well correlated with other root parameters and so can reflect root distribution characteristics. The contribution rate of root dry weight to RENI was of maximum under sufficient irrigation, and was of minimum under insufficient irrigation. However, root volume was the least influence factor of RENI under sufficient irrigation, and was the most important influence factor under insufficient irrigation. (2)Shown as skewed normal distribution, the RENI of cotton in the upper layer  soil above 40 cm depth accounted for 86.8% of the total RENI. (3) Roots developed in film-uncovered land were centrally impacted by the distance to the cotton plant，i.e., the closer of the distance，the higher of the RENI.

In this study, we carried out T-DNA insertional mutagenesis to identify mutants, which are effective in pathogenicity. The highly virulent, defoliating strain was mutated through Agrobacterium tumefaciens-mediated transformation, and 5000 transformants were obtained. Pathogenicity test of randomly selected 1000 transformants found that five mutants lost their virulence on a susceptible cotton cultivar. A new mutant, d1, was unable to cause full disease on cotton. Analysis of the mutation using Thermal Asymmetric Interlaced PCR(TAIL-PCR) confirmed an insertion into a gene DVK1. The full length of DVK1 genomic DNA and cDNA sequences were obtained using TAIL-PCR and RT-PCR methods. DVK1 has an open reading frame of 3325 bp interrupted by two introns with 52 bp and 36 bp, respectively, and putatively encodes a 1079 aa protein. The reduced pathogenic phenotype of d1 was fully complemented by reintroduction of the gene, indicating DVK1 is essential for pathogenicity in V. dahliae.

Cotton genome project is being implemented and functional genomics has already played an essential role in cotton research. Great molecular progress has been made in genomic and proteomic field of cotton recently. This paper reviewed the progress of the cotton genomic and proteomics, particularly focusing on its genetic map, physical map, functional genome, proteomic techniques and cotton proteomics.

Variation of culturable soil microflora and microbial activity were investigated in continuous and rotation cropping cotton field in Xinjiang. The results showed that culturable microbial population gradually decreased with long-term continuous cropping of cotton. Compared with 5 years continous cropping, the total quantity of soil microbes in 6～8 years, 9～12 years and more than 13 years continuous cropping, decreased by 40.2%, 46.7%, 52.4%,respectively. After more than  5 years continuous cropping, the structure of the soil microbial community transformed from rich nutrition bacteria type to lower nutrition fungi type, the ratio of bacteria to fungi and actinomycetes to fungi decreased significantly. The amount of nitrogen physiological communities such as ammonifying bacteria, nitrobacteria and aerobic nitrogen-fixing bacteria decreased, while denitrifying bacteria increased. Moreover, continuous cropping resulted in soil respiration intensity and cellulolytic activity reducing. Contrary to continuous cropping, under the cotton/melilotus suavena, tomato, spring wheat or corn rotation systems were  most beneficial for increasing the total quantity of soil micro-organism, improving  the capability of soil microbial activity, adjusting the balance of microbial community. Also there was substantial increasement in the number of azotobacteria. The effects of different rotation modes were different, the benefits of cotton-tomato and cotton-melilotus suavena rotation were more obvious.

With many fungal genomes having been or currently being sequenced, identification of gene function has become a hot topic in fungal research. Gene knockout is one of several techniques used in studies of gene function. The method can be used to delete entire genes, replace an allele with another, exchange a given gene's normal promoter for a regulatable one, and label genes with epitope tags or fluorescent proteins. In this paper, we review applications of gene knockout via Agrobacterium tumefaciens-mediated transformation (ATMT) in filamentous fungus functional genomics.

A FT-like homolog was isolated from Gossypium hirsutum L. CV. Xinluzao 33 through RT-PCR and RACE, which was named GhFTL1 gene (accession number: HM631972). The 525-bp open reading frame encoded a putative protein of 174 amino acids with high similarity to FT proteins of different plants which contains two critical residues and conserved motif, both of which identified as diagnostic of true FT. GhFTL1 gene showed constitutive expression in root, stem, flower, leaf, fiber, and ovule. The levels of transcript in leaf and ovule were higher than that in other tissues. Phylogenetic analysis at the amino acid level confirmed that the isolated sequence is FT-like, and also showed that GhFTL1 had shorter genetic distance with MdFT1 compared with other 18 FT homologs confirmed to inducing early flowering from 13 different plants. Over-expression of GhFTL1 in Arabidopsis using the CaMV 35S promoter resulted in significant accelerated flowering compared with wild-type plants. Based on our results, we concluded that GhFTL1 was responsible for inducing flowering and may be one of important components for the flowering pathway in cotton.

Agrobacterium tumefaciens-mediated transformation(ATMT) has become an important tool for strain improvement, new genes' tagging and target gene's screening, isolating and cloning. The advantages of this method are simple operation, a wide host range, highly efficient transformation, and a high frequency of single inserted T-DNA. Mutant libraries of many fungi with high capacity and quality have been constructed by ATMT. The screening and identification of related functional genes will be the following research focus on the basis of these mutant libraries. This research will provide a basis for further studies on pathogenic mechanisms and will aid disease-resistance breeding.