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!

Membrane lipid raft organization during cotton fiber development

Journal of Cotton Research

[Background] Cotton fiber is a single-celled seed trichome that originates from the ovule epidermis. It is an excellent model for studying cell elongation. Along with the elongation of cotton fiber cell, the plasma membrane is also extremely expanded. Despite progress in understanding cotton fiber cell elongation, knowledge regarding the relationship of plasma membrane in cotton fiber cell development remains elusive.

[Methods] The plasma membrane of cotton fiber cells was marked with a low toxic fluorescent dye, di-4-ANEPPDHQ, at different stages of development. Fluorescence images were obtained using a confocal laser scanning microscopy. Subsequently, we investigated the relationship between lipid raft activity and cotton fiber development by calculating generalized polarization (GP values) and dual-channel ratio imaging.

[Results] We demonstrated that the optimum dyeing conditions were treatment with 3 μmol·L− 1 di-4-ANEPPDHQ for 5 min at room temperature, and the optimal fluorescence images were obtained with 488 nm excitation and 500–580 nm and 620–720 nm dual channel emission. First, we examined lipid raft organization in the course of fiber development. The GP values were high in the fiber elongation stage (5–10 DPA, days past anthesis) and relatively low in the initial (0 DPA), secondary cell wall synthesis (20 DPA), and stable synthesis (30 DPA) stages. The GP value peaked in the 10 DPA fiber, and the value in 30 DPA fiber was the lowest. Furthermore, we examined the differences in lipid raft activity in fiber cells between the short fiber cotton mutant, Li-1, and its wild-type. The GP values of the Li-1mutant fiber were lower than those of the wild type fiber at the elongation stage, and the GP values of 10 DPA fibers were lower than those of 5 DPA fibers in the Li-1 mutant.

[Conclusions] We established a system for examining membrane lipid raft activity in cotton fiber cells. We verified that lipid raft activity exhibited a low-high-low change regularity during the development of cotton fiber cell, and the pattern was disrupted in the short lint fiber Li-1 mutant, suggesting that membrane lipid order and lipid raft activity are closely linked to fiber cell development.

[Title] Membrane lipid raft organization during cotton fiber development

[Authors] XU Fan, SUO Xiaodong, LI Fang, BAO Chaoya, HE Shengyang, HUANG Li & LUO Ming

Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway

Journal of Cotton Research

[Background] Verticillium wilt, caused by the soil-borne fungus of Verticillium dahliae Kleb., is one of the most devastating diseases of cotton. The complex mechanism underlying cotton resistance to Verticillium wilt remains uncharacterized. Identifying an endogenous resistance gene may be helpful to control this disease. Previous studies revealed that succinate dehydrogenase (SDH) is involved in reactive oxygen species (ROS)-induced stress signaling pathway that is likely to be triggered by salicylic acid (SA). Here, through the metabolomics and differential expression analyses in wilt-inoculated cotton (Gossypium hirsutum), we noticed that GhSDH1–1gene in cotton may play an important role in the resistance to V. dahlia. Then we reported GhSDH1–1 gene and its functional analysis in relation to the resistance of cotton to V. dahliae.

[Results] The GhSDH1–1 gene in cotton root was significantly up-regulated after V. dahlia inoculation, and its expression level peaked at 12 and 24 h post-infection. SA can also induce the up-regulation of GhSDH1–1. Additionally, the functional analysis showed that GhSDH1–1-silenced cotton was more susceptible to V. dahliae than the control because of the significant decrease in abundance of immune-related molecules and severe damage to the SA-signaling pathway. In Arabidopsis thaliana, high expression of GhSDH1–1 conferred high resistance to V. dahliaeArabidopsis that overexpressed GhSDH1–1 had higher resistance to V. dahliae infection compared with the wild-type.

[Conclusions] Our findings provide new insights into the role of GhSDH1–1; it positively regulates cotton resistance to Verticillium wilt. The regulatory mechanism of GhSDH1–1 is closely related to SA-related signaling pathway.

[Title] Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway
[Authors] ZHANG Xiangyue, FENG Zili, ZHAO Lihong, LIU Shichao, WEI Feng, SHI Yongqiang, FENG Hongjie & ZHU Heqin

Screening and evaluation of reliable traits of upland cotton (Gossypium hirsutum L.) genotypes for salt tolerance at the seedling growth stage

Journal of Cotton Research

[Background] Salt stress significantly inhibits the growth, development, and productivity of cotton because of osmotic, ionic, and oxidative stresses. Therefore, the screening and development of salt tolerant cotton cultivars is a key issue towards sustainable agriculture. This study subjected 11 upland cotton genotypes at the seedling growth stage to five different salt concentrations and evaluated their salt tolerance and reliable traits.

[Results] Several morpho-physiological traits were measured after 10 days of salinity treatment and the salt tolerance performance varied significantly among the tested cotton genotypes. The optimal NaCl concentration for the evaluation of salt tolerance was 200 mmol·L 1. Membership function value and salt tolerance index were used to identify the most consistent salt tolerance traits. Leaf relative water content and photosynthesis were identified as reliable indicators for salt tolerance at the seedling stage. All considered traits related to salt tolerance indices were significantly and positively correlated with each other except for malondialdehyde. Cluster heat map analysis based on the morpho-physiological salt tolerance-indices clearly discriminated the 11 cotton genotypes into three different salt tolerance clusters. Cluster I represented the salt-tolerant genotypes (Z9807, Z0228, and Z7526) whereas clusters II (Z0710, Z7514, Z1910, and Z7516) and III (Z0102, Z7780, Z9648, and Z9612) represented moderately salt-tolerant and salt-sensitive genotypes, respectively.

[Conclusions] A hydroponic screening system was established. Leaf relative water content and photosynthesis were identified as two reliable traits that adequately represented the salt tolerance of cotton genotypes at the seedling growth stage. Furthermore, three salt-tolerant genotypes were identified, which might be used as genetic resources for the salt-tolerance breeding of cotton.

[Title] Screening and evaluation of reliable traits of upland cotton (Gossypium hirsutum L.) genotypes for salt tolerance at the seedling growth stage
[Authors] SIKDER Ripon Kumar, WANG Xiangru, JIN Dingsha, ZHANG Hengheng, GUI Huiping, DONG Qiang,  PANG Nianchang, ZHANG Xiling & SONG Meizhen

Stability, variation, and application of AFIS fiber length distributions

Journal of Cotton Research

[Background] Fiber length is one of the primary quality parameters for the cotton industry when considering the textile performance and end-use quality of cotton. Currently, many decisions regarding cotton fiber length utilize the industry standard measurement device, i.e., the High Volume Instrument (HVI). However, it is documented that complete fiber length distributions hold more information than the currently reported HVI length parameters, i.e., upper half mean length (UHML) and uniformity index (UI). An alternative measurement device, the Advanced Fiber Information System (AFIS), is able to capture additional information about fiber length distribution. What is currently not known is how much additional information the AFIS length distribution holds.

[Results] The stability of differences in within-sample variation in fiber length captured by the AFIS length distribution by number characterizing differences between samples was deemed stable across the extended testing period. A diverse breeding population was evaluated and four significant sources of within sample variation in length were identified. A comparison of the ability between HVI length parameters and AFIS fiber length distribution to correctly categorize breeding lines to their family was performed. In all cases, the AFIS fiber length distribution more accurately identified germplasm families.

[Conclusions] The long-term stability test of the AFIS fiber length distribution by number shows that the measurement is stable and can be used to assess differences across samples. However, more information about within-sample variation in fiber length than that can be captured by length parameters is needed to assess differences across samples in many applications. Four length parameters outperform two length parameters when trying to identify the familial background of the samples in this set. These parameters characterize distributional shape differences that are not captured by the standard AFIS length parameters, UQL and short fiber content by number (SFCn). These findings suggest that additional types of variation in cotton fiber length are not captured and are therefore not currently used in most cotton breeding programs.
[Title] Stability, variation, and application of AFIS fiber length distributions

[Authors]  HINDS Zachary, KELLY Brendan Robert & HEQUET Eric Francois

GbAt11 gene cloned from Gossypium barbadense mediates resistance to Verticillium wilt in Gossypium hirsutum

Journal of Cotton Research

[Background] Gossypium hirsutum is highly susceptible to Verticillium wilt, and once infected Verticillium wilt, its yield is greatly reduced. But G. barbadense is highly resistant to Verticillium wilt. It is possible that transferring some disease-resistant genes from G. barbadense to G. hirsutummay contribute to G. hirsutum resistance to Verticillium wilt.

[Results] Here, we described a new gene in G. barbadense encoding AXMN Toxin Induced Protein-11, GbAt11, which is specifically induced by Verticillium dahliae in G. barbadense and enhances Verticillium wilt resistance in G. hirsutum. Overexpression in G. hirsutum not only significantly improves resistance to Verticillium wilt, but also increases the boll number per plant. Transcriptome analysis and real-time polymerase chain reaction showed that GbAt11overexpression can simultaneously activate FLS2BAK1 and other genes, which are involved in ETI and PTI pathways in G. hirsutum.

[Conclusions] These data suggest that GbAt11 plays a very important role in resistance to Verticillium wilt in cotton. And it is significant for improving resistance to Verticillium wilt and breeding high-yield cotton cultivars.

[Title] GbAt11 gene cloned from Gossypium barbadense mediates resistance to Verticillium wilt in Gossypium hirsutum

[Authors] QIU Tingting, WANG Yanjun, JIANG Juan, ZHAO Jia, WANG Yanqing & QI Junsheng

Towards complete deconstruction of cotton transcriptional landscape

Journal of Cotton Research

Abstract: Recently, Wang et al. systematically explored the transcription landscape in diploid cotton Gossypium arboreum. In the study, they integrated four high-throughput sequencing techniques, including Pacbio sequencing, strand-specific RNA sequencing (ssRNA-seq), Cap analysis gene expression sequencing (CAGE-seq), and PolyA sequencing (PolyA-seq) to profile the RNA transcriptome of G. arboreum. They developed a pipeline, IGIA to construct accurate gene structure annotation based on the updated genome of G. arboreum and the multi-strategic RNA-seq data. Their study revealed some intriguing phenomena and potential novel mechanisms in the regulation of RNA transcription in plants, and also provided valuable resources for further functional genomic research in cotton.

[Title] Towards complete deconstruction of cotton transcriptional landscape

[Author] LI Fuguang

Extrafloral nectary–the sleeping beauty of plant science

Journal of Cotton Research

Abstract: Cotton is one of the most important cash crops, its growth season coincides with a high incidence of diverse groups of pests, leading to heavy use of pesticides. Recent identification of a signaling protein as a candidate regulator of cotton extrafloral nectary provides a new insight into the formation of sophisticated defense mechanisms in plants.

[Title] Extrafloral nectary–the sleeping beauty of plant science

[Author] CHEN Xiaoya

QTL mapping for plant height and fruit branch number based on RIL population of upland cotton

Journal of Cotton Research

[Background] Plant height (PH) and fruit branch number (FBN) are important traits for improving yield and mechanical harvesting of cotton. In order to identify genes of PH and FBN in cotton germplasms to develop superior cultivars, quantitative trait loci (QTLs) for these traits were detected based on the phenotypic evaluation data in nine environments across four locations and 4 years and a previously reported genetic linkage map of an recombinant inbred line (RIL) population of upland cotton.

[Results] In total, 53 QTLs of PH and FBN, were identified on 21 chromosomes of the cotton genome except chromosomes c02, c09-c11, and c22. For PH, 27 QTLs explaining 3.81%–8.54% proportions of phenotypic variance were identified on 18 chromosomes except c02, c08-c12, c15, and c22. For FBN, 26 QTLs explaining 3.23%–11.00% proportions of phenotypic variance were identified on 16 chromosomes except c02-c03, c06, c09-c11, c17, c22-c23, and c25. Eight QTLs were simultaneously identified in at least two environments. Three QTL clusters containing seven QTLs were identified on three chromosomes (c01, c18 and c21). Eleven QTLs were the same as previously reported ones, while the rest were newly identified.

[Conclusions] The QTLs and QTL clusters identified in the current study will be helpful to further understand the genetic mechanism of PH and FBN development of cotton and will enhance the development of excellent cultivars for mechanical managements in cotton production.

[Title] QTL mapping for plant height and fruit branch number based on RIL population of upland cotton

[Authors] LIU Ruixian, XIAO Xianghui, GONG Juwu, LI Junwen, ZHANG Zhen, LIU Aiying, LU Quanwei, SHANG Haihong, SHI Yuzhen, GE Qun, IQBAL Muhammad Sajid, CHEN Quanjia, YUAN Youlu & GONG Wankui

The GhREV transcription factor regulate the development of shoot apical meristem in cotton (Gossypium hirsutum)

Journal of Cotton Research

[Background] Manual topping is a routine agronomic practice for balancing the vegetative and reproductive growth of cotton (Gossypium hirsutum) in China, but its cost-effectiveness has decreased over time. Therefore, there is an urgent need to replace manual topping with new approaches, such as biological topping. In this study, we examined the function of GhREV transcription factors (a class III homeodomain-leucine zipper family, HD-ZIP III) in regulating the development of shoot apical meristem (SAM) in cotton with the purpose of providing candidate genes for biological topping of cotton in the future.

[Results] We cloned four orthologous genes of AtREV in cotton, namely GhREV1GhREV2GhREV3, and GhREV4. All the GhREVs expressed in roots, stem, leaves, and SAM. Compared with GhREV1 and GhREV3, the expression level of GhREV2 and GhREV4 was higher in the SAM. However, only GhREV2 had transcriptional activity. GhREV2 is localized in the nucleus; and silencing it via virus-induced gene silencing (VIGS) produced an abnormal SAM. Two key genes, GhWUSA10 and GhSTM, which involved in regulating the development of plant SAM, showed about 50% reduction in their transcripts in VIGS-GhREV2 plants.

[Conclusion] GhREV2 positively regulates the development of cotton SAM by regulating GhWUSA10 and GhSTM potentially.

[Title] The GhREV transcription factor regulate the development of shoot apical meristem in cotton (Gossypium hirsutum)

[Authors] YANG Doudou, AN Jing, LI Fangjun, ENEJI A. Agrinya, TIAN Xiaoli & LI Zhaohu

Identification of QTLs and candidate genes for physiological traits associated with drought tolerance in cotton

Journal of Cotton Research

[Background] Cotton is mainly grown for its natural fiber and edible oil. The fiber obtained from cotton is the indispensable raw material for the textile industries. The ever changing climatic condition, threatens cotton production due to a lack of sufficient water for its cultivation. Effects of drought stress are estimated to affect more than 50% of the cotton growing regions. To elucidate the drought tolerance phenomenon in cotton, a backcross population was developed from G. tomentosum, a drought tolerant donor parent and G. hirsutum which is highly susceptible to drought stress.

[Results] A genetic map of 10 888 SNP markers was developed from 200 BC2F2 populations. The map spanned 4 191.3 centi-Morgan (cM), with an average distance of 0.104 7 cM, covering 51% and 49% of At and Dt sub genomes, respectively. Thirty stable Quantitative trait loci (QTLs) were detected, in which more than a half were detected in the At subgenome. Eighty-nine candidate genes were mined within the QTL regions for three traits: cell membrane stability (CMS), saturated leaf weight (SLW) and chlorophyll content. The genes had varied physiochemical properties. A majority of the genes were interrupted by introns, and only 15 genes were intronless, accounting for 17% of the mined genes. The genes were found to be involved molecular function (MF), cellular component (CC) and biological process (BP), which are the main gene ontological (GO) functions. A number of miRNAs were detected, such as miR164, which is associated with NAC and MYB genes, with a profound role in enhancing drought tolerance in plants. Through RT-qPCR analysis, 5 genes were found to be the key genes involved in enhancing drought tolerance in cotton. Wild cotton harbors a number of favorable alleles, which can be exploited to aid in improving the narrow genetic base of the elite cotton cultivars. The detection of 30 stable QTLs and 89 candidate genes found to be contributed by the donor parent, G. tomentosum, showed the significant genes harbored by the wild progenitors which can be exploited in developing more robust cotton genotypes with diverse tolerance levels to various environmental stresses.

[Conclusion] This was the first study involving genome wide association mapping for drought tolerance traits in semi wild cotton genotypes. It offers an opportunity for future exploration of these genes in developing highly tolerant cotton cultivars to boost cotton production.

[Title] Identification of QTLs and candidate genes for physiological traits associated with drought tolerance in cotton

[Authors] MAGWANGA Richard Odongo, LU Pu, KIRUNGU Joy Nyangasi, CAI Xiaoyan, ZHOU Zhongli, AGONG Stephen Gaya, WANG Kunbo & LIU Fang