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The ZF2001 vaccine, which contains a dimeric form of the receptor-binding domain of severe acute respiratory syndrome coronavirus 2 and aluminum hydroxide as an adjuvant, was shown to be safe, with an acceptable side-effect profile, and immunogenic in adults in phase 1 and 2 clinical trials.We conducted a randomized, double-blind, placebo-controlled, phase 3 trial to investigate the efficacy and confirm the safety of ZF2001. The trial was performed at 31 clinical centers across Uzbekistan, Indonesia, Pakistan, and Ecuador; an additional center in China was included in the safety analysis only. Adult participants (≥18 years of age) were randomly assigned in a 1:1 ratio to receive a total of three 25-μg doses (30 days apart) of ZF2001 or placebo. The primary end point was the occurrence of symptomatic coronavirus disease 2019 (Covid-19), as confirmed on polymerase-chain-reaction assay, at least 7 days after receipt of the third dose. A key secondary efficacy end point was the occurrence of severe-to-critical Covid-19 (including Covid-19-related death) at least 7 days after receipt of the third dose.Between December 12, 2020, and December 15, 2021, a total of 28,873 participants received at least one dose of ZF2001 or placebo and were included in the safety analysis; 25,193 participants who had completed the three-dose regimen, for whom there were approximately 6 months of follow-up data, were included in the updated primary efficacy analysis that was conducted at the second data cutoff date of December 15, 2021. In the updated analysis, primary end-point cases were reported in 158 of 12,625 participants in the ZF2001 group and in 580 of 12,568 participants in the placebo group, for a vaccine efficacy of 75.7% (95% confidence interval [CI], 71.0 to 79.8). Severe-to-critical Covid-19 occurred in 6 participants in the ZF2001 group and in 43 in the placebo group, for a vaccine efficacy of 87.6% (95% CI, 70.6 to 95.7); Covid-19-related death occurred in 2 and 12 participants, respectively, for a vaccine efficacy of 86.5% (95% CI, 38.9 to 98.5). The incidence of adverse events and serious adverse events was balanced in the two groups, and there were no vaccine-related deaths. Most adverse reactions (98.5%) were of grade 1 or 2.In a large cohort of adults, the ZF2001 vaccine was shown to be safe and effective against symptomatic and severe-to-critical Covid-19 for at least 6 months after full vaccination. (Funded by the National Science and Technology Major Project and others; ClinicalTrials.gov number, NCT04646590.).

The coronavirus pandemic showed the need for urgently improvement of different sectors in Uzbekistan, especially, the healthcare system and the biopharma industries. Uzbekistan government and private sectors have taken comprehensive measures to control the spread of infection in the country and tried to mitigate the impact of the pandemic. In this chapter, we discussed the primary measures taken to combat the coronavirus pandemic and the details of developing a local reverse transcription real-time PCR (RT-qPCR) detection kit as well as the experience of conducting the phase III clinical trials of the recombinant Uzbek-Chinese vaccine-ZF-UZ-Vac2001 against coronavirus infection. Finally, information is given on the mass vaccination campaign in the country, the difficulties encountered and the achievements made. The developed RT-qPCR detection kit was successfully implemented into production and have widely used for pathogen diagnosis. A total of 6965 volunteers over 18 years old participated in the clinical trials of ZF2001 and the vaccine had an efficacy level of 84.8%. More than 67.6 million doses were administered using seven types of anti-COVID vaccines in the country. The pandemics urged the country to establish a scientific and technical base that aimed at quickly responding to potential future challenges and emergencies.

Global climate change manifested in average annual temperature rise and imbalance of most natural factors, such as changes in annual mean rainfall, air humidity, average temperature of cold and warm months, soil quality, etc., lead to climatic zones displacement. All these have a significant impact on agricultural production in total, including cotton growing. Cotton is one of the most important technical crops in the world. However, it is very sensitive to environmental changes. The influence of abiotic stresses (high temperature, changes in the mean rainfall and soil salinity) causes a dramatic decrease yield of this crop. Moreover, temperature anomalies and climatic zones displacement cause a change in the area of pathogens and pests distribution, which also reduces the cotton yield. One of the possible ways to increase the cotton yield under the influence of abiotic and biotic stresses is the development of new resistant varieties, using both classical breeding methods and genetic engineering achievements.

This article discusses problems in the breeding programs of the seedless grapes, the way of introducing of the biotechnology and gene technology skills to resolve its issues, and the advantages of molecular markers to select seedlessness among the hybrid progeny of grapes. Uzbekistan is famous for its seedless grapes, but on the other hand, the grape breeding is oriented on the conventional breeding method. In other words, seedless grapes have a recessive character, a male form is using only as a pollinator, and all these factors limit to create new seedless varieties and forms. Nowadays the word grape breeders, especially seedless grape breeders use advantages of the biotechnology and gene technology skills to resolve above listed issues. As a result, except for obtaining hybrid progeny by crossing between ♂seedless × seeded ♀ that was an unchangeable algorithm of the cross combination in the traditional grape breeding. But today, researchers argued that crossing between ♂seedless × seedless ♀ is also possible to obtain a hybrid progeny through “embryo rescue technique”. Thus introducing this novel breeding program directly to grape breeding of Uzbekistan leads to an increase the diversity of the new seedless grape varieties and also for increasing the export potential of the grape industry. KEYWORDS: Seedless grape varieties, variety, cross combination, embryo culture, molecular markers, DNA.

Due to rapid mutations in the coronavirus genome over time and re-emergence of multiple novel variants of concerns (VOC), there is a continuous need for a periodic genome sequencing of SARS-CoV-2 genotypes of particular region. This is for on-time development of diagnostics, monitoring and therapeutic tools against virus in the global pandemics condition. Toward this goal, we have generated 18 high-quality whole-genome sequence data from 32 SARS-CoV-2 genotypes of PCR-positive COVID-19 patients, sampled from the Tashkent region of Uzbekistan. The nucleotide polymorphisms in the sequenced sample genomes were determined, including nonsynonymous (missense) and synonymous mutations in coding regions of coronavirus genome. Phylogenetic analysis grouped fourteen whole genome sample sequences (1, 2, 4, 5, 8, 10-15, 17, 32) into the G clade (or GR sub-clade) and four whole genome sample sequences (3, 6, 25, 27) into the S clade. A total of 128 mutations were identified, consisting of 45 shared and 83 unique mutations. Collectively, nucleotide changes represented one unique frameshift mutation, four upstream region mutations, six downstream region mutations, 50 synonymous mutations, and 67 missense mutations. The sequence data, presented herein, is the first coronavirus genomic sequence data from the Republic of Uzbekistan, which should contribute to enrich the global coronavirus sequence database, helping in future comparative studies. More importantly, the sequenced genomic data of coronavirus genotypes of this study should be useful for comparisons, diagnostics, monitoring, and therapeutics of COVID-19 disease in local and regional levels.

Genetic approaches often lead to the most cost-effective and efficient means to improve crops, especially those grown widely. But for most crops, cotton included, genetic improvement efforts have focused far more on above-ground plant attributes than on root systems. Root system establishment is crucial to cotton seedling success, subsequent development, crop performance and sustainability. As a first step toward genetic enhancement of cotton root systems, significant heritable phenotypic variation must be found or created. The overall objective of this research was to study the effect of substituted chromosomes or chromosome segments from the donor tetraploid species Gossypium barbadense, G. mustelinum, and G. tomentosum on the selected traits of the stem, leaf, and especially root in CS lines. Twenty-seven chromosome substitution (CS) lines, containing different pairs or short segments of chromosomes from G. barbadense (CS-B lines), G. mustelinum (CS-M lines), and G. tomentosum (CS-T lines) and two parents, TM-1, parent quasi-isogenic to the CS lines and G. barbadense 3-79, the donor parent to all CS-B lines, were analyzed. Goals were to determine if CS lines significantly affect any of 17 morphological shoot and root traits. Indeed, significant line-based variation occurred for several root and shoot phenotypes. Comparisons of means and two-way hierarchical cluster analysis revealed several CS lines simultaneously affected multiple shoot and/or root traits, positively or negatively. Pairwise correlations of traits and the cluster analysis showed strong relationships among certain traits. The high correlation among several root traits suggests that easier-to-screen traits might be leveraged strategically to devise breeding-friendly methods for phenotypically evaluating root system morphology. Most importantly, this research identifies CS lines with prospectively novel individual trait effects and others with multi-trait effects that can be further dissected and used to improve our knowledge of cotton root systems, their development, genetic control and genetic improvement.

The main task of plant breeding is creating of high-yield, resistant to biotic and abiotic stresses crop varieties with high product quality. The using of traditional breeding methods is limited by the duration of the new crop varieties creation with the required agronomic traits. This depends not only on the duration of growing season and reaching of mature stage of plants (especially the long-period growth plants, e.g. trees), as well as is associated with applying of multiple stages of crossing, selection and testing in breeding process. In addition, conventional methods of chemical and physical mutagenesis do not allow targeting effect to genome. However, the introduction of modern DNA-technology methods, such as genome editing, has opened in a new era in plant breeding. These methods allow to carry out precise and efficient targeted genome modifications, significantly reducing the time required to get plants with desirable features to create new crop varieties in perspective. This review provides the knowledge about application of genome editing methods to increase crop yields and product quality, as well as crop resistance to biotic and abiotic stresses. In addition, future prospects for integrating these technologies into crop breeding strategies are also discussed.

Background Recently, putative pre-miRNAs locations have been identified in the introns of plant genes, raising the question whether such genes can show a dual functionality by having both correct maturation of the host gene pre-mRNA and maturation of the miRNAs from the intron. Here, we demonstrated that such dual functionality is indeed possible, using as host gene the firefly luciferase gene with intron (ffgLUC), and different artificial intronic miRNAs (aimiRNA) placed within the intron of ffgLUC. Results The miRNAs were based on the structure of the natural miR319a. Luciferase (LUC) activity in planta was used to evaluate a correct splicing of the ffgLUC mRNA. Different target sequences were inserted into the aimiRNA to monitor efficiency of silencing of different target mRNAs. After adjusting the insertion cloning strategy, the ffgLUCaimiR-319a gene showed dual functionality with correct splicing of ffgLUC and efficient silencing of TEOSINTE BRANCHED1/CYCLOIDEA/PROLIFERATING CELL FACTOR1 transcription factor genes targeted in-trans by aimiR-319a or targeting the transgene ffLUC in-cis by an aimiR-LUC. Silencing of endogenous target genes by aimiRNA or amiRNA is efficient both in transient assays and stable transformants. A behave as strong phenotype the PHYTOCHROME B (PHYB) gene was also targeted by ffgLUCaimiR-PHYB. The lack of silencing of the PHYB target was most likely due to an insensitive target site within the PHYB mRNA which can potentially form a double stranded stem structure. Conclusion The combination of an overexpression construct with an artificial intronic microRNA allows for a simultaneous dual function in plants. The concept therefore adds new options to engineering of plant traits that require multiple gene manipulations.

A chromosome substitution line, CS-B25, was developed by the substitution of chromosome pair 25 of Gossypium hirsutum TM-1 with the homologous pair of chromosome 25 from G. barbadense, a double haploid Pima 3-79 line. CS-B25 has improved fiber traits compared to its parent TM-1. To explore the molecule mechanisms underlying improved fiber traits, deep sequencing of total RNA was used to compare gene expression in fibers of CS-B25 and TM-1 at 10 days post anthesis (10-DPA). A total of 1872 differentially expressed genes (DEGs) were detected between the two lines, with 1175 up-regulated and 697 down-regulated in CS-B25. Gene Ontology (GO) enrichment analysis of the expression data by Generally Applicable Gene-set Enrichment (GAGE) and ReviGO indicated that the most prevalent Biological Process GO terms associated with DEGs included DNA-templated transcription, response to oxidative stress, and cellulose biosynthesis. Enriched Molecular Function GO terms included structural constituents of cytoskeleton, peroxidase activity, cellulose synthase (UDP-forming) activity, and transcription regulatory region sequence-specific DNA binding factors. GAGE was also used to find enriched KEGG pathways, and the highly represented pathways were Biosynthesis of Amino Acids, Starch and Sucrose Metabolism, Phenylpropanoid Biosynthesis, Protein Processing in Endoplasmic Reticulum, and Plant Hormone Signal Transduction. Many of the identified DEGs are involved in cytoskeleton and cell wall metabolism. The results of gene expression data have provided new insight into the molecular mechanisms of fiber development during the fiber elongation stage and would offer novel candidate genes that may be utilized in cotton fiber quality improvement.

Silencing phytochrome A1 gene (PHYA1) by RNA interference in Upland cotton (Gossypium hirsutum L. cv. Coker 312) had generated PHYA1 RNAi lines with improved fiber quality (longer, stronger and finer fiber). To reveal molecular mechanisms that govern fiber development with positive fiber traits, a study of global gene expression profiling of 10-DPA fibers in a PHYA1 RNAi line and its parent Coker 312 was conducted by high-throughput RNA sequencing. A comparative analysis of transcriptomes between the two lines had identified 142 genes that were differentially expressed in the 10-DPA fiber of the RNAi line. Gene Ontology analysis showed that these differentially expressed genes were mainly involved in metabolic pathways, heterocyclic/organic cyclic compound binding and multiple enzyme activities, and cell structures which were reported to play important roles in fiber development. Twenty-eight KEGG pathways were mapped for the 142 genes, and the pathways related to glycolysis/gluconeogenesis and pyruvate metabolism were the most abundant and followed by cytochrome P450-involved pathways, suggesting that fiber improvement could be through the regulation of proteins involved in cytochrome P450 pathways. Genes encoding WRKY transcription factors, sucrose synthase, xyloglucan endotransglucosylase hydrolase, udp-glucuronate: xylan alpha-glucuronosyltransferase, and genes involved in lipid metabolism and ABA/brassinosteroid signal transduction pathways were found differentially expressed in the RNAi line. These genes have direct impacts on cotton fiber quality. The results of this study elucidate molecular signatures and possible mechanisms of fiber improvement in the background of PHYA1 RNAi in cotton and should help for future fine-tuning and programming of cotton fiber development.

The importance of the cytoplasmic genome for many economically important traits is well documented in several crop species, including cotton. There is no report on application of cotton chloroplast specific SSR markers as a diagnostic tool to study genetic diversity among improved Upland cotton lines. The complete plastome sequence information in GenBank provided us an opportunity to report on 17 chloroplast specific SSR markers using a cost-effective data mining strategy. Here we report the comparative analysis of genetic diversity among a set of 42 improved Upland cotton lines using SSR markers specific to chloroplast and nuclear genome, respectively. Our results revealed that low to moderate level of genetic diversity existed in both nuclear and cytoplasm genome among this set of cotton lines. However, the specific estimation suggested that genetic diversity is lower in cytoplasmic genome compared to the nuclear genome among this set of Upland cotton lines. In summary, this research is important from several perspectives. We detected a set of cytoplasm genome specific SSR primer pairs by using a cost-effective data mining strategy. We reported for the first time the genetic diversity in the cytoplasmic genome within a set of improved Upland cotton accessions. Results revealed that the genetic diversity in cytoplasmic genome is narrow, compared to the nuclear genome within this set of Upland cotton accessions. Our results suggested that most of these polymorphic chloroplast SSRs would be a valuable complementary tool in addition to the nuclear SSR in the study of evolution, gene flow and genetic diversity in Upland cotton.

The chewing insect boll weevil larvae (Anthonomus grandis) and phloem feeding insect Bemisia tabaci cause the loss of diverse cotton products. The pink cotton bollworm Pectinophora gossypiella is a model organism for insect responses to Bacillus thuringiensis (Bt) toxins, but the molecular mechanism of its tolerance was studied to a lesser extent. The increased quantity of secondary metabolites, namely, natural insecticides in plants is associated with abiotic stresses such as treatment with NaCl. The role of plants in mediating the interaction between herbivores and natural enemies of herbivores was demonstrated to be a critically dynamic phenomenon. To better control the insects, a subunit of mitochondrial complex I NDUFV2 that catalyzes NADH dehydrogenation in respiratory chain was suppressed by double-stranded RNA (dsRNA). The novel transcriptome approaches as vital applications in insect research should be very helpful to shed light on details of the molecular signatures and their interactions during insect-plant interaction.

To illustrate the differences in the strategy of risk assessment for the cis and transgenic organisms, it is worth considering the assessments in terms of the new generation of genome modification tools such as RNAi. A procedure of risk assessment of allergenicity of genetically modified (GM) plants and novel GM foods, including Cry-based crops, is based on tested and reliable protocols set forth by diverse safety agencies. Despite the absence of a single universal test for an accurate estimation of allergenicity level risk, every developed protocol begins with a description of the allergic potential of transgenic source, specifically, the potential allergenicity of the donor. The assessments of possible risks of RNAi-based IR cultivars are challenged by the phenomena of preand post-RNAi development. In the preliminary development of RNAi-based IR crops, an important step is to design a dsRNA fragment for insertion into a hairpin structure.

Genes for host-plant resistant do exist in cotton (Gossypium spp.) but improvement of cotton cultivars with resistance is difficult due to intensive breeding. Identifying molecular-genetic mechanisms associated with disease resistance can offer a new way to combat a serious threat such as Fusarium oxysporum f. sp. vasinfectum (FOV). Here, we captured and annotated “top-layer” of abundantly and specifically expressed cotton root small RNA (sRNA) including microRNA (miR) sequences during FOV pathogenesis using size-directed and adenylated linker-based sRNA cloning strategy. A total of 4116 candidate sRNA sequences with 16 to 30 nucleotide (nt) length were identified from four complementary DNA (cDNA) libraries of noninfected and FOV race 3-infected roots of susceptible (“11970”) versus resistant (“Mebane B-1”) cotton genotypes (G. hirsutum L.). The highest numbers of sRNA signatures were those with 19–24 nt long in all libraries, and interestingly, the number of sRNAs substantially increased during FOV infection in a resistant genotype, while it sharply decreased in a susceptible genotype. In BLAST analysis, more than 73 % of sRNAs matched Gossypium (G. arboretum L., G. hirsutum, and G. barbadense L.) ESTs. A small percentage of sRNAs matched A. thaliana (1.68 %), T. cacao (1.26 %), fungal (2 %), and other organism (21.33 %) ESTs. mirBase comparisons showed that 4 % of sRNAs were homologous to previously reported plant miRs, among which we predicted novel cotton Ghr-miR-160 that was not registered in the cotton miR database. These major representative sRNA signatures targeted proteins associated with the key biological processes and molecular functions, explaining the molecular mechanisms of the host defense response during the FOV pathogenesis in cotton.

The primary gene pool for tetraploid cotton species includes Gossypium hirsutum L., as well as the other four 2n = 52 species of Gossypium (G. barbadense, G. mustellinum, G. tomentosum and G. darwinii). To help overcome barriers to effective introgression, we have developed a number of alien chromosome substitution (CS) lines from G. barbadense, G. mustellinum and G. tomentosum, most of which are nearly isogenic to the inbred ‘Texas Marker-1’, a genetic standard. At the time CS line development was initiated, molecular markers did not exist for some CS lines, and most of these lines were developed based on cytological analysis without using any marker-based testing. Here we report on tests with SSR markers from one ore more linkage maps specific to the substituted chromosome or chromosome segment from one or more linkage maps to assess the constitution and genetic identity of the CS lines. The specific objective of this paper is to report on the genetic identity of the CS lines using SSR markers and some special characteristics associated with some of the CS lines. We used chromosome-specific SSR markers following standard methods of DNA extraction, PCR and according to manufacturer’s protocol on ABI Genetic Analyzer 3130xl to confirm the identity of the introgressed alien chromosome or chromosome segments in the CS lines. For most CS lines and most mapped markers, the observed SSR profiles were concordant with expectations as per the results of cytological analysis. For a minority of markers and lines, however, the results were discordant; these markers, linkage groups, and CS lines will be further investigated to understand and define their genetic identity for use as breeding resources. Interspecific germplasm introgression can be useful for genetic improvement of Upland cotton. However, such efforts are constrained by genetic incompatibilities between the species. Our results document for the first time the development of CS lines from G. tomentosum and G. mustelinum. These CS lines will open a new paradigm in cotton breeding program by providing a tool for introgression of useful genes from wild and unadapted species in the genetic improvement of Upland cotton.

Fusarium wilt [Fusarium oxysporum f.sp. vasinfectum (FOV) Atk. Sny & Hans] represents a serious threat to cotton (Gossypium spp.) production. For the last few decades, the FOV pathogen has become a significant problem in Uzbekistan causing severe wilt disease and yield losses of G. hirsutum L. cultivars. We present the first genetic analyses of FOV race 3 resistance on Uzbek Cotton Germplasm with a series of field and greenhouse artificial inoculation-evaluations and inheritance studies. The field experiments were conducted in two different sites: the experimental station in Zangiota region-Environment (Env) 1 and the Institute of Cotton Breeding (Env-2, Tashkent province). The Env-1 was known to be free of FOV while the Env-2 was known to be a heavily FOV infested soil. In both (Env-1 and Env-2) of these sites, field soil was inoculated with FOV race 3. F2 and an F3 Upland populations ("Mebane B1" × "11970") were observed with a large phenotypic variance for plant survival and FOV disease severity within populations and among control or check Upland accessions. Wilt symptoms among studied F2 individuals and F3 families significantly differed depending on test type and evaluation site. Distribution of Mendelian rations of susceptible (S) and resistant (R) phenotypes were 1S:1R field Env-1 and 3S:1R field Env-2 in the F2 population, and 1S:3R greenhouse site in the F3 population. The different segregation distribution of the Uzbek populations may be explained by differences in FOV inoculum level and environmental conditions during assays. However, genetic analysis indicated a recessive single gene action under high inoculum levels or disease pressure for FOV race 3 resistance. Uzbek germplasm may be more susceptible than expected to FOV race 3, and sources of resistance to FOV may be limited under the FOV inoculum levels present in highly-infested fields making the breeding process more complex.

Global food demand is expected to nearly double by 2050 due to an increase in the world's population. The Green Revolution has played a key role in the past century by increasing agricultural productivity worldwide, however, limited availability and continued depletion of natural resources such as arable land and water will continue to pose a serious challenge for global food security in the coming decades. High yielding varieties with proven tolerance to biotic and abiotic stresses, superior nutritional profiles, and the ability to adapt to the changing environment are needed for continued agricultural sustainability. The narrow genetic base of modern cultivars is becoming a major bottleneck for crop improvement efforts and, therefore, the use of crop wild relatives (CWRs) is a promising approach to enhance genetic diversity of cultivated crops. This article provides a review of the efforts to date on the exploration of CWRs as a source of tolerance to multiple biotic and abiotic stresses in four global crops of importance; maize, rice, cotton, and soybean. In addition to the overview of the repertoire and geographical spread of CWRs in each of the respective crops, we have provided a comprehensive discussion on the morphological and/or genetic basis of the traits along with some examples, when available, of the research in the transfer of traits from CWRs to cultivated varieties. The emergence of modern molecular and genomic technologies has not only accelerated the pace of dissecting the genetics underlying the traits found in CWRs, but also enabled rapid and efficient trait transfer and genome manipulation. The potential and promise of these technologies has also been highlighted in this review.

In crop research programs that implement transgene-based strategies for trait improvement it is necessary to distinguish between transgene homozygous and hemizygous individuals in segregating populations. Direct methods for determining transgene zygosity are technically challenging, expensive, and require specialized equipment. In this report, we describe a standard PCR-based protocol coupled with capillary electrophoresis that can identify transgene homozygous and hemizygous individuals in a segregating population without knowledge of transgene insertion site. PCR primers were designed to amplify conserved T-DNA segments of the 35S promoter, OCS terminator, and NPTII kanamycin resistance gene in the pHellsgate-8 RNAi construct for the Gossypium hirsutum phytochrome A1 gene. Using an optimized multiplexed reaction mixture and an amplification program of only 10 cycles we could discriminate between transgene homozygous and hemizygous cotton control DNA samples based on PCR product peak characteristics gathered by capillary electrophoresis. The protocol was refined by evaluating segregating transgenic progeny from nine BC1S1 populations derived from crosses between the transgenic cotton parent ‘E-1-7-6’ and other cotton cultivars. OCS PCR product peak height and peak area, normalized by amplification of the native cotton gene GhUBC1, revealed clear bimodal distributions of OCS product characteristics for each BC1S1 population indicating the presence of homozygous and hemizygous clusters which was further confirmed via K-means clustering. BC1S1 plants identified as homozygous or hemizygous were self-fertilized to produce BC1S2 progeny. For the homozygous class, 19/20 BC1S2 families confirmed the homozygous BC1S1 prediction while 21/21 BC1S2 families confirmed the hemizygous prediction of the original parent. This relatively simple protocol provides a reliable, rapid, and high-throughput way of evaluating segregating transgenic populations using methods and equipment common to crop molecular breeding labs.

Most wild and semi-wild species of the genus Gossypium are exhibit photoperiod-sensitive flowering. The wild germplasm cotton is a valuable source of genes for genetic improvement of modern cotton cultivars. A bi-parental cotton population segregating for photoperiodic flowering was developed by crossing a photoperiod insensitive irradiation mutant line with its pre-mutagenesis photoperiodic wild-type G. darwinii Watt genotype. Individuals from the F2 and F3 generations were grown with their parental lines and F1 hybrid progeny in the long day and short night summer condition (natural day-length) of Uzbekistan to evaluate photoperiod sensitivity, i.e., flowering-time during the seasons 2008-2009. Through genotyping the individuals of this bi-parental population segregating for flowering-time, linkage maps were constructed using 212 simple-sequence repeat (SSR) and three cleaved amplified polymorphic sequence (CAPS) markers. Six QTLs directly associated with flowering-time and photoperiodic flowering were discovered in the F2 population, whereas eight QTLs were identified in the F3 population. Two QTLs controlling photoperiodic flowering and duration of flowering were common in both populations. In silico annotations of the flanking DNA sequences of mapped SSRs from sequenced cotton (G. hirsutum L.) genome database has identified several potential 'candidate' genes that are known to be associated with regulation of flowering characteristics of plants. The outcome of this research will expand our understanding of the genetic and molecular mechanisms of photoperiodic flowering. Identified markers should be useful for marker-assisted selection in cotton breeding to improve early flowering characteristics.

The emergence of genome manipulation methods promises a real revolution in biotechnology and genetic engineering. Targeted editing of the genomes of living organisms not only permits investigations into the understanding of the fundamental basis of biological systems but also allows addressing a wide range of goals towards improving productivity and quality of crops. This includes the creation of plants with valuable compositional properties and with traits that confer resistance to various biotic and abiotic stresses. During the past few years, several novel genome editing systems have been developed; these include zinc finger nucleases (ZFNs), transcription activator-like effector nucleases (TALENs), and clustered regularly interspaced short palindromic repeats/Cas9 (CRISPR/Cas9). These exciting new methods, briefly reviewed herein, have proved themselves as effective and reliable tools for the genetic improvement of plants.

Allele specific (AS) SNP primers were developed for rapid detection of Fusarium oxysporum f.sp. vasinfectum (FOV) race 3. These primers were designed based on single nucleotide polymorphisms of partial sequence alignment of the β-tubulin (BT) gene from several FOV races. The primers showed high specificity for FOV race 3, and exclusively amplified PCR products from FOV race 3 DNAs and total genomic DNAs of FOV race 3-infected plant tissues. These primers did not produce any amplification products for races 1, 2, 4, 6, 7 and 8 of FOV or other FOV and Fusarium species from infected plant tissues. The assay is useful for specific and rapid detection of Fusarium oxysporum f. sp. vasinfectum race 3.

A global analysis of cotton (Gossypium spp.) genetic diversity is the first step to understanding its geographical distribution, dissemination, genetic relatedness, and population structure. To assess the genetic diversity and population structure in Gossypium species, 111 cotton accessions representing five allotetraploids (AD1–AD5genomes), 23 Asiatic diploids of the Old World (A1and A2genomes), and 82 diploids of the New World subgenus Houzingenia (D1–D11genomes) species were assessed using simple sequence repeats (SSR) markers with wide genome coverage. The mean genetic distance (GD) between the two most important New World tetraploid cottons (Upland (Gossypium hirsutum L.) and Pima (Gossypium barbadense L.)) was 0.39. Among the three shrub type sections (Houzingenia, Integrifolia, and Caducibracteolata) and three arborescent sections (Erioxylum, Selera, and Austroamericana), the GD ranged between 0.19 and 0.41. Phylogenetic analyses clustered all species into distinct phylogenetic groups, which were consistent with genomic origin, evolutionary history, and geographic distribution or ecotypes of these accessions, suggesting the existence of clear structured strata. With all of the genomes, the highest statistical analysis of Structure test through measurements of ad hoc (ΔK) occurred at K = 2, with group Q1 with the Old World diploid A genomes and with group Q2 with all the New World diploids of the D genome. AD genome accessions shared nearly equal alleles from both Q1 and Q2 groups. With all of the diploids of the New World D genomes, the highest value of ΔK occurred at K = 5. These results are consistent with the fundamental knowledge of tetraploid AD-genome formation and the rapid radiation of the American diploid cotton linage that took place somewhere in southwestern Mexico, followed by a differentiation–speciation during angiosperm evolution. In addition, SSR markers provide an alternative solution for distinguishing phylogenetic relationships between accessions of different ecotypes and for elucidating population structure of cottons of the New World.