New ICGI co-chairs have been elected

International Cotton Genome Initiative (ICGI) has completed 2015 election process, and as a result, six new co-chairs for overall chairing and ICGI work groups have been elected for 2017-2019 terms:

ICGI Overall – Dr. John Yu (USA)

Breeding and Applied Genomics – Dr. Jodi Scheffler (USA)

Comparative Genomics and Bioinformatics – Dr. Ibrokhim Abdurakhmonov (Uzbekistan)

Functional Genomics – Dr. Guoli Song ( China)

Germplasm & Genetic Stocks – Dr. Xiongming Du (China)

Structural Genomics – Dr. Wangzhen Guo (China)

Moreover, per election results, 95-97% voters approved new Workgroup structure of ICGI and uses of ICGI funds.

Congratulations for successful election process to ICGI and its new co-chairs!

Details of ICGI election results can be fount at:

Cotton Research enters to a period of “golden” opportunities

With the recent completion of draft sequencing of diploid cotton Gossypium raimondii and G. arboreum genomes published in Nature Genetics, and the first “gold-standard” version of G. raimondii genome published in Nature, cotton research community enjoyed the pick of many seminal research results that have provided a glorious opportunity to study orthologous and paralogous genes and gene families in allotetraploid cotton.

These successes and great achievements in ancestral diploid genome sequencing further resulted in decoding of the representative genome of widely grown allotetraploid Upland (G. hirsutum L.) cotton, Texas Marker-1.

Two independent research papers published in Nature Biotechnology by Zhang et al. and Li et al. in this week issue described the complex allotetraploid TM-1 genome that further entered cotton research to an era of “golden” opportunities providing the first insights into allotetraploid cotton genome structure, genome rearrangements, gene evolution, cotton fiber biology and biotechnology that will help to rapidly translate the genomics “knowledge” to an “economic impact”!

Congratulation to all cotton community with these latest achievements, high impact journal seminal publications, and hard work to foster cotton research!

Genome-wide identification and expression analysis of DNA demethylase family in cotton

Journal of Cotton Research

[Background] DNA methylation is an important epigenetic factor that maintains and regulates gene expression. The mode and level of DNA methylation depend on the roles of DNA methyltransferase and demethylase, while DNA demethylase plays a key role in the process of DNA demethylation. The results showed that the plant’s DNA demethylase all contained conserved DNA glycosidase domain. This study identified the cotton DNA demethylase gene family and analyzed it using bioinformatics methods to lay the foundation for further study of cotton demethylase gene function.

[Results] This study used genomic information from diploid Gossypium raimondii JGI (D), Gossypium arboreum L. CRI (A), Gossypium hirsutum L. JGI (AD1) and Gossypium barbadebse L. NAU (AD2) to Arabidopsis thaliana. Using DNA demethylase genes sequence of Arabidopsis as reference, 25 DNA demethylase genes were identified in cotton by BLAST analysis. There are 4 genes in the genome D, 5 genes in the genome A, 10 genes in the genome AD1, and 6 genes in the genome AD2. The gene structure and evolution were analyzed by bioinformatics, and the expression patterns of DNA demethylase gene family in Gossypium hirsutum L. were analyzed. From the phylogenetic tree analysis, the DNA demethylase gene family of cotton can be divided into four subfamilies: REPRESSOR of SILENCING 1 (ROS1), DEMETER (DME), DEMETER-LIKE 2 (DML2), and DEMETER-LIKE3 (DML3). The sequence similarity of DNA demethylase genes in the same species was higher, and the genetic relationship was also relatively close. Analysis of the gene structure revealed that the DNA demethylase gene family members of the four subfamilies varied greatly. Among them, the number of introns of ROS1 and DME subfamily was larger, and the gene structure was more complex. For the analysis of the conserved domain, it was known that the DNA demethylase family gene member has an endonuclease III (ENDO3c) domain.

[Conclusions] The genes of the DNA demethylase family are distributed differently in different cotton species, and the gene structure is very different. High expression of ROS1 genes in cotton were under abiotic stress. The expression levels of ROS1 genes were higher during the formation of cotton ovule. The transcription levels of ROS1 family genes were higher during cotton fiber development.

[Title]Genome-wide identification and expression analysis of DNA demethylase family in cotton

[Authors] YANG Xiaomin, LU Xuke, CHEN Xiugui, WANG Delong, WANG Junjuan, WANG Shuai, GUO Lixue, CHEN Chao, WANG Xiaoge, WANG Xinlei & YE Wuwei *

Journal of Cotton Research. 2019, 2: 16

An isopentyl transferase gene driven by the senescence-inducible SAG12 promoter improves salinity stress tolerance in cotton

Journal of Cotton Research

[Background] Soil salinity seriously affects cotton growth, leading to the reduction of yield and fiber quality. Recently, genetic engineering has become an efficient tool to increase abiotic stress tolerance in crops.

[Results] In this study, isopentyl transferase (IPT), a key enzyme involved in cytokinin (CTK) biosynthesis from Agrobacterium tumefaciens, was selected to generate transgenic cotton via Agrobacterium-mediated transformation. A senescence-inducible SAG12promoter from Arabidopsis was fused with the IPT gene. Ectopic-expression of SAG12::IPT significantly promoted seed germination or seedling tolerance to salt stress. Two IPTtransgenic lines, OE3 as a tolerant line during seed germination, and OE8 as a tolerant line at seedling stage, were selected for further physiological analysis. The data showed that ectopic-expression of SAG12::IPT induced the accumulation of CTKs not only in leaves and roots, but also in germinating seeds. Moreover, ectopic-expressing IPT increased the activity of antioxidant enzymes, which was associated with the less reactive oxygen species (ROS) accumulation compared with control plants. Also, ectopic-expression of IPT produced higher K+/Na+ ratio in cotton shoot and root.

[Conclusions] The senescence-induced CTK accumulation in cotton seeds and seedlings positively regulates salt stress partially by elevating ROS scavenging capability.

[TitleAn isopentyl transferase gene driven by the senescence-inducible SAG12 promoter improves salinity stress tolerance in cotton

[Authors] SHAN Yi, ZHAO Peng, LIU Zhao, LI Fangjun* & TIAN Xiaoli

Journal of Cotton Research. 2019, 2: 15

World Cotton Day

07 October 2019 has been announced as World Cotton Day by WTO. Cotton community will celebrate this day across the globe. The WTO Secretariat is organizing the event at WTO Headquarters Geneva in collaboration with the Secretariats of the United Nations Food and Agriculture Organization (FAO), the United Nations Conference on Trade and Development (UNCTAD), the International Trade Centre (ITC) and the International Cotton Advisory Committee (ICAC). This event stems from the Cotton-4’s official application for the recognition of a World Cotton Day by the United Nations General Assembly, reflecting the importance of cotton as a global commodity.

For detail

Genetic analysis of yield and fiber quality traits in upland cotton (Gossypium hirsutum L.) cultivated in different ecological regions of China

Journal of Cotton Research

[Background] Cotton is an important fiber crop worldwide. The yield potential of current genotypes of cotton can be exploited through hybridization. However, to develop superior hybrids with high yield and fiber quality traits, information of genetic control of traits is prerequisite. Therefore, genetic analysis plays pivotal role in plant breeding.

[Results] In present study, North Carolina II mating design was used to cross 5 female parents with 6 male parents to produce 30 intraspecific F1 cotton hybrids. All plant materials were tested in three different ecological regions of China during the year of 2016–2017. Additive-dominance-environment (ADE) genetic model was used to estimate the genetic effects and genotypic and phenotypic correlation of yield and fiber quality traits. Results showed that yield traits except lint percentage were mainly controlled by genetic and environment interaction effects, whereas lint percentage and fiber quality traits were determined by main genetic effects. Moreover, dominant and additive-environment interaction effects had more influence on yield traits, whereas additive and dominance-environment interaction effects were found to be predominant for fiber traits. Broad-sense and its interaction heritability were significant for all yield and most of fiber quality traits. Narrow-sense and its interaction heritability were non-significant for boll number and seed cotton yield. Correlation analysis indicated that seed cotton yield had significant positive correlation with other yield attributes and non-significant with fiber quality traits. All fiber quality traits had significant positive correlation with each other except micronaire.

[Conclusions] Results of current study provide important information about genetic control of yield and fiber quality traits. Further, this study identified that parental lines, e.g., SJ48–1, ZB-1, 851–2, and DT-8 can be utilized to improve yield and fiber quality traits in cotton.

[Title] Genetic analysis of yield and fiber quality traits in upland cotton (Gossypium hirsutum L.) cultivated in different ecological regions of China

[Authors] SHAHZAD Kashif+, LI Xue+, QI Tingxiang, GUO Liping, TANG Huini, ZHANG Xuexian, WANG Hailin, ZHANG Meng, ZHANG Bingbing, QIAO Xiuqin, XING Chaozhu* & WU Jianyong*

Journal of Cotton Research. 2019, 2: 14

JCR-QTL mapping for fiber quality and yield-related traits across multiple generations in segregating population of CCRI 70

Journal of Cotton Reseach

[Background] Cotton is a significant economic crop that plays an indispensable role in many domains. Gossypium hirsutum L. is the most important fiber crop worldwide and contributes to more than 95% of global cotton production. Identifying stable quantitative trait locus (QTLs) controlling fiber quality and yield related traits are necessary prerequisites for marker-assisted selection (MAS).

[Results] A genetic linkage map was constructed with 312 simple sequence repeat (SSR) loci and 35 linkage groups using JoinMap 4.0; the map spanned 1 929.9 cM, with an average interval between two markers of 6.19 cM, and covered approximately 43.37% of the cotton genome. A total of 74 QTLs controlling fiber quality and 41 QTLs controlling yield-related traits were identified in 4 segregating generations. These QTLs were distributed across 20 chromosomes and collectively explained 1.01%~27.80% of the observed phenotypic variations. In particular, 35 stable QTLs could be identified in multiple generations, 25 common QTLs were consistent with those in previous studies, and 15 QTL clusters were found in 11 chromosome segments.

[Conclusion] These studies provide a theoretical basis for improving cotton yield and fiber quality for molecular marker-assisted selection.

[Title] QTL mapping for fiber quality and yield-related traits across multiple generations in segregating population of CCRI 70

[Authors] DENG Xiaoying, GONG Juwu, LIU Aiying, SHI Yuzhen, GONG Wankui, GE Qun, LI Junwen, SHANG Haihong, WU Yuxiang & YUAN Youlu

Journal of Cotton Research. 2019, 2:13

Determination of manganese content in cottonseed meal using near-infrared spectrometry and multivariate calibration

[Background] Manganese (Mn) is an essential microelement in cottonseeds, which is usually determined by the techniques relied on hazardous reagents and complex pretreatment procedures. Therefore a rapid, low-cost, and reagent-free analytical way is demanded to substitute the traditional analytical method.

[Results] The Mn content in cottonseed meal was investigated by near-infrared spectroscopy (NIRS) and chemometrics techniques. Standard normal variate (SNV) combined with first derivatives (FD) was the optimal spectra pre-treatment method. Monte Carlo uninformative variable elimination (MCUVE) and successive projections algorithm method (SPA) were employed to extract the informative variables from the full NIR spectra. The linear and nonlinear calibration models for cottonseed Mn content were developed. Finally, the optimal model for cottonseed Mn content was obtained by MCUVE-SPA-LSSVM, with root mean squares error of prediction (RMSEP) of 1.994 6, coefficient of determination (R2) of 0.949 3, and the residual predictive deviation (RPD) of 4.370 5, respectively.

[Conclusions] The MCUVE-SPA-LSSVM model is accuracy enough to measure the Mn content in cottonseed meal, which can be used as an alternative way to substitute for traditional analytical method.

 [Title] Determination of manganese content in cottonseed meal using near-infrared spectrometry and multivariate calibration

[Authors] En YU, Rubing ZHAO, Yunfei CAI, Jieqiong HUANG, Cheng LI, Cong LI, Lei MEI, Lisheng BAO, Jinhong CHEN & Shuijin ZHU

Journal of Cotton Research. 2019, 2: 12

Genome-wide identification of OSCA gene family and their potential function in the regulation of dehydration and salt stress in Gossypium hirsutum

[Background] Cotton (Gossypium hirsutum) provides the largest natural fiber for the textile manufacturing industries, but its production is on the decline due to the effects of salinity. Soil salt-alkalization leads to damage in cotton growth and a decrease in yields. Hyperosmolality-gated calcium-permeable channels (OSCA) have been found to be involved in the detection of extracellular changes which trigger an increase in cytosolic free calcium concentration. Hyperosmolality-induced calcium ion increases have been widely speculated to be playing a role in osmosensing in plants. However, the molecular nature of the corresponding calcium ion channels remains unclearly. In this research work, we describe the OSCAgenes and their putative function in osmosensing in plants by carrying out genome-wide identification, characterization and functional analysis of the significantly up-regulated OSCA gene, GhOSCA1.1 through reverse genetics.

[Results] A total of 35, 21 and 22 OSCA genes were identified in G. hirsutum, G. arboreum, and G. raimondii genomes, respectively, and were classified into four different clades according to their gene structure and phylogenetic relationship. Gene and protein structure analysis indicated that 35 GhOSCA genes contained a conserved RSN1_7TM (PF02714) domain. Moreover, the cis-regulatory element analysis indicated that the OSCA genes were involved in response to abiotic stress. Furthermore, the knockdown of one of the highly up-regulated genes, Gh_OSCA1.1showed that the virus-induced gene silenced (VIGS) plants were highly sensitive to dehydration and salinity stresses compared with the none VIGS plants as evident with higher concentration levels of oxidant enzymes compared with the antioxidant enzymes on the leaves of the stressed plants.

[Conclusions] This study provides the first systematic analysis of the OSCA gene family and will be important for understanding the putative functions of the proteins encoded by the OSCA genes in cotton. These results provide a new insight of defense responses in general and lay the foundation for further investigation of the molecular role played by the OSCA genes, thereby providing suitable approaches to improve crop performance under salinity and drought stress conditions.

[Title] Genome-wide identification of OSCA gene family and their potential function in the regulation of dehydration and salt stress in Gossypium hirsutum 

[Authors] Xiu YANG, Yanchao XU, Fangfang YANG, Richard Odongo MAGWANGA, Xiaoyan CAI, Xingxing WANG, Yuhong WANG, Yuqing HOU, Kunbo WANG, Fang LIU & Zhongli ZHOU

Journal of Cotton Research. 2019; 2:11

Effects of mepiquat chloride on yield and main properties of cottonseed under different plant densities

[Background] Cottonseed oil and protein content as well as germination traits are major indicators of seed quality. However, the responses of these indicators to plant density and mepiquat chloride (MC) are still uncertain. To investigate plant density and MC effects on cottonseed yield and main quality parameters, we conducted a two-year field experiment including four plant densities (1.35, 2.55, 3.75 and 4.95 plants·m− 2) and two doses of MC (0 and 135 g·hm− 2) in Dafeng, Jiangsu Province, in 2013 and 2014.

[Results] The application of MC reduced plant height, fruit branch length and fruiting branch number under different plant densities, resulting in a lower and more compact plant canopy. Cottonseed yield showed a nonlinear increase as plant density increasing and achieved the highest value at 3.75 plants·m− 2, regardless of MC application. No significant interactions were found between plant density and MC for cottonseed yield and quality parameters. The 100-seed weight, cottonseed oil content and vigor index significantly decreased as plant density increased, while these parameters significantly increased with MC applying under different plant densities. Seed vigor index was positively correlated with 100-seed weight and seed oil content across different plant densities and MC treatments.

[Conclusions] Thus, application of MC could realize a win-win situation between cottonseed yield and main quality parameters under various densities; and plant density of 3.75 plants·m− 2combined with 135 g·hm− 2 of MC applying is optimal for high cottonseed yield and quality in this cotton production area.


[Title] Effects of mepiquat chloride on yield and main properties of cottonseed under different plant densities

[Authors] ZHAO Wenqing, YAN Qiang, YANG Hongkun, YANG Xiaoni, WANG Leran, CHEN Binglin, MENG Yali and ZHOU Zhiguo

Journal of Cotton Research. 2019; 2:10

Amino acids application enhances flowers insecticidal protein content in Bt cotton

[Background] Low insecticidal protein expression at reproductive organs affect insect resistance in Bt transgenic cotton. In order to enhance flower insecticidal protein expression, the conventional cultivar Sikang1 (S1) and the hybrid cultivar Sikang3 (S3) were used as experimental materials; the applications of selected 5 types of amino acids and 21 types of amino acids were sprayed on the flowers in 2016 and 2017 cotton growing seasons.

[Results] The flower Bt protein contents increased significantly under the two amino acid treatments in both cultivars, the Bt protein concentration increased by 15.2 to 25.8% compared with the control. However, no significant differences were detected between the two treatments of amino acid application. Increased amino acid and soluble protein contents, enhanced GPT, GOT, protease,and peptidase activities were observed under the amino acid application at the flowering stage.

[Conclusions] These results suggest that exterior application of the amino acids treatments could bolster the flower insecticidal protein expression.

[Authors] TAMBEL Leila. I. M., ZHOU Mingyuan, CHEN Yuan, ZHANG Xiang, CHEN Yuan  and CHEN Dehua

Journal of Cotton Research. 2019; 2:7

Feasibility assessment of phenotyping cotton fiber maturity using infrared spectroscopy and algorithms for genotyping analyses

[Background] Cotton fiber maturity is an important property that partially determines the processing and performance of cotton. Due to difficulties of obtaining fiber maturity values accurately from every plant of a genetic population, cotton geneticists often use micronaire (MIC) and/or lint percentage for classifying immature phenotypes from mature fiber phenotypes although they are complex fiber traits. The recent development of an algorithm for determining cotton fiber maturity (MIR) from Fourier transform infrared (FT-IR) spectra explores a novel way to measure fiber maturity efficiently and accurately. However, the algorithm has not been tested with a genetic population consisting of a large number of progeny plants.

[Results] The merits and limits of the MIC- or lint percentage-based phenotyping method were demonstrated by comparing the observed phenotypes with the predicted phenotypes based on their DNA marker genotypes in a genetic population consisting of 708 F2 plants with various fiber maturity. The observed MIC-based fiber phenotypes matched to the predicted phenotypes better than the observed lint percentage-based fiber phenotypes. The lint percentage was obtained from each of F2 plants, whereas the MIC values were unable to be obtained from the entire population since certain F2 plants produced insufficient fiber mass for their measurements. To test the feasibility of cotton fiber infrared maturity (MIR) as a viable phenotyping tool for genetic analyses, we measured FT-IR spectra from the second population composed of 80 F2 plants with various fiber maturities, determined MIR values using the algorithms, and compared them with their genotypes in addition to other fiber phenotypes. The results showed that MIR values were successfully obtained from each of the F2 plants, and the observed MIR-based phenotypes fit well to the predicted phenotypes based on their DNA marker genotypes as well as the observed phenotypes based on a combination of MIC and lint percentage.

[Conclusions] The MIR value obtained from FT-IR spectra of cotton fibers is able to accurately assess fiber maturity of all plants of a population in a quantitative way. The technique provides an option for cotton geneticists to determine fiber maturity rapidly and efficiently.

[Authors] KIM Hee Jin, LIU Yongliang, FANG David D. and DELHOM Christopher D.

Journal of Cotton Research2019; 2:8