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.

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.

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 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.

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.

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.

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 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.

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.

According to published EST sequences, an new pepc(Phosphoenolpyruvate carboxylase) gene was cloned from Gossypium barbadense L. cultivar 7124 by the utilization of the RACE and genome walking technology. The gene was named Gb.pepc3. It consists of 3259 bps, contains an open reading frame for 2910 bps, and encodes 969 amino acids with a deduced molecular weight of 110.7 kd and an isoelectric point of 6.08 I. Homology and phylogenetic trees analysis showed high similarity between Gb.pepc3 and pepcs in other reported plants, and all belong to C₃ type pepc. The result of the fluorescence quantitative PCR displayed that Gb.pepc3 existed in all tissues of cotton. It expressed highly in the embryo but low in fiber. The expression quantity of Gb.pepc3 varied in different stages of the development of cotton. The expression of Gb.pepc3 reached the highest level at 15 days after blossoming for Gossypium barbadense L. while 20 days after blossoming for G. hirsutum, and there was significant difference in the expression quantities between two species.

The cDNA encoding the full length of a receptor-like protein kinase of cotton was cloned through degenerate primers amplification, genome walking and RT-PCR. Sequence analysis showed that introns were absent in the gene. It contains a 2964 bp open reading frame, encodes a deduced protein of 988 amino acid residues, and shows 60% homology to HAESA-like2, which regulates floral organ abscission in Arabidopsis. This gene was tentatively designated as GRLK5.  GRLK5 expresses higher in seed, stem bark, root, and fibre than in other organs. The ABA treatment induce the expression of GRLK5. The over expression vector was constructed by inserting GRLK5 into the pCAMBIA2301, tobacco plants were transformed by co-cultivating leaves method via Agrobacterium mediation．The object gene was verified to have been integrated into the genome of tobacco by PCR.

A series of stable polymorphism SSR primers in Xiangzamian series cultivars were used to construct various primer combinations according to the difference of their amplified band’s size for multiplex PCR amplification of cotton. Eighty percent of double PCR amplified normally based on the principle of amplified fragments size difference under the same conditions as their single PCR reactions. Besides, triplex and quadruple PCR were also amplified normally using primers of double PCR with good results. So we proposed a simplified protocol of multiplex PCR assay in cotton. The multiplex PCR technology was used to detect the purity of hybrid cotton seeds which clearly identified impurity and blend of female parent seeds and also other hybrid cotton seeds. It can be used as a reference for the rapid and accurate identification of cotton hybrids.

Artificial disease nursery, severe disease field and greenhouse were jointly used for Verticillium wilt disease resistance identification of a transgenic cotton line 61217-1 into which chitinase and glucanase genes were transferred. Results showed that transgenic line 61217-1 exhibited high resistant level to Verticillium wilt disease in artificial nursery during successive three years. Average disease index of line 61217-1 was 17.9, which was significantly lower than that of the acceptor CCRI 24. In 2009, in the severe disease fields, the average disease indexes of this transgenic line were 18.7, 18.1 and 16.7 in Anyang, Henan Province, Dafeng, Jiangsu Province, and Shihezi, Xinjiang, respectively. These indexes were obviously lower than those of the acceptor CCRI 24, respectively. Furthermore, this chitinase-glucanase transgenic cotton line 61217-1 also showed higher resistant to strong virulent defoliating Verticillium dahliae, which was isolated from Hebei, Hubei and Xinjiang, respectively. And their average disease indexes were 16.4, 16.8 and 15.6, which were significantly lower than that of CCRI 24, respectively. The results indicated that the transgenic cotton line 61217-1 (Chi+Glu) exhibited excellent and stable resistance to Verticillium wilt disease.

By setting the alternative furrow irrigation, conventional furrow irrigation, and fixed every-other furrow irrigation, the amount of nitrogen and irrigation design using two general rotation experiment conducted to study the regulation effect of water and nitrogen on cotton yield and water use efficiency. The results showed that: cotton yield was significantly positively correlative, with nitrogen applied amount in the range of 56.2 ~ 95.2 kg·hm^-2, and same as cotton yield and water within 37.52 ~ 160.00 mm; Cotton yield was not significant different under the same water and nitrogen treatments between alternative furrow irrigation and conventional furrow irrigation, cotton yield of conventional furrow irrigation was higher on average than the fixed every-other furrow irrigation by 9.15%. Cotton water use efficiency and nitrogen within 56.2 ~ 122.8 kg·hm^-2 was a significant positive correlation, and was significantly negatively correlated with irrigation within 37.52 ~160.00 mm. Cotton water use efficiency was no significant difference under the same water and nitrogen treatments between conventional furrow irrigation and alternative furrow irrigation, and conventional furrow irrigation was higher on average than the fixed every-other furrow irrigation in cotton water use efficiency by 9.01%. Therefore, alternative furrow irrigation can increase the cotton yield and water use efficiency.

GZFP, derived from Gossypium hirsutum L, belongs to the SUPERMAN-like zinc finger protein. To further analyze the function of GZFP, the promoter region of GZFP was obtained by genome walking. The recombination vector pBI-pGZFP-5::GUS containing the promoter was constructed and transformed to Arabidopsis by Agrobacterium-mediated method. GUS staining showed GZFP promoter driven GUS activity was specifically detected in roots and flowers and the activity was very low in leaves. In addition, the GUS activity in roots was very strong throughout the whole growth period. By semi-quantitative RT-PCR, we have found the expression of GZFP was induced by ABA, drought and salt. The over expression vector was constructed by inserting GZFP into the pCAMBIA2301, tobacco plants were transformed by co-cultivating leaves method via Agrobacterium mediation．The object gene was verified to have been integrated into the genome of tobacco by PCR. The phenotype of transgenic plants was normal compared to the wild type, but the expression of NtOPBP1 and NtERD10 was relatively higher than the wild type. As the two genes involved in the stress reaction, GZFP may have some relevance to the plant stress reaction.

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.