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!

The impact of plant density and spatial arrangement on light interception on cotton crop and seed cotton yield: an overview

[Abstract] Light attenuation within a row of crops such as cotton is influenced by canopy architecture, which is defined by size, shape and orientation of shoot components. Level of light interception causes an array of morpho-anatomical, physiological and biochemical changes. Physiological determinants of growth include light interception, light use efficiency, dry matter accumulation, duration of growth and dry matter partitioning. Maximum light utilization in cotton production can be attained by adopting cultural practices that yields optimum plant populations as they affect canopy arrangement by modifying the plant canopy components. This paper highlights the extent to which spatial arrangement and density affect light interception in cotton crops. The cotton crop branches tend to grow into the inter-row space to avoid shade. The modification of canopy components suggests a shade avoidance and competition for light. Maximum leaf area index is obtained especially at flowering stage with higher populations which depicts better yields in cotton production.
[Keywords] Light interception, Plant populations, Spatial arrangement, Canopy architecture

[Title] The impact of plant density and spatial arrangement on light interception on cotton crop and seed cotton yield: an overview

[Authors] CHAPEPA Blessing, MUDADA Nhamo & MAPURANGA Rangarirai

Journal of Cotton Research 2020, 318

Unraveling the puzzle of the origin and evolution of cotton A-genome

[Abstract] Gossypium hirsutum, the most widely planted cotton species, its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species. To better understand the genetic component of cotton, Huang et al. recently sequenced and assembled the first A1-genome G. herbaceum, and updated the A2-genome G. arboreum and (AD)1-genome G. hirsutum. On the basis of the three reference genomes, they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome.

[Title] Unraveling the puzzle of the origin and evolution of cotton A-genome

[Authors] MA Zhiying

Journal of Cotton Research 3, Article number: 17 (2020)

Applying plant-based irrigation scheduling to assess water use efficiency of cotton following a high-biomass rye cover crop

[Background] This study addressed the potential of combining a high biomass rye winter cover crop with predawn leaf water potential (ΨPD) irrigation thresholds to increase agricultural water use efficiency (WUE) in cotton. To this end, a study was conducted near Tifton, Georgia under a manually-controlled, variable-rate lateral irrigation system using a Scholander pressure chamber approach to measure leaf water potential and impose varying irrigation scheduling treatments during the growing season. ΨPD thresholds were − 0.4 MPa (T1), − 0.5 MPa (T2), and − 0.7 MPa (T3). A winter rye cover crop or conventional tillage were utilized for T1-T3 as well.

[Results] Reductions in irrigation of up to 10% were noted in this study for the driest threshold (− 0.7 MPa) with no reduction in lint yield relative to the − 0.4 MPa and − 0.5 MPa thresholds. Drier conditions during flowering (2014) limited plant growth and node production, hastened cutout, and decreased yield and WUE relative to 2015.

[Conclusions] We conclude that ΨPD irrigation thresholds between − 0.5 MPa and − 0.7 MPa appear to be viable for use in a ΨPD scheduling system with adequate yield and WUE for cotton production in the southeastern U.S. Rye cover positively impacted water potential at certain points throughout the growing season but not yield or WUE indicating the potential for rye cover crops to improve water use efficiency should be tested under longer-term production scenarios.

[Title] Applying plant-based irrigation scheduling to assess water use efficiency of cotton following a high-biomass rye cover crop

[Authors] MEEKS Calvin D., SNIDER John L., CULPEPPER Stanley and HAWKINS Gary
Journal of Cotton Research 3, Article number: 16 (2020)

Genotypic variance in 13C-photosynthate partitioning and within-plant boll distribution in cotton

[Background] Photosynthate partitioning and within-plant boll distribution play an important role in yield formation of cotton; however, if and how they interact to mediate yield remains unclear. The objective of this study was to investigate the genotypic variance in photosynthate partitioning and within-plant boll distribution, with a focus on their interactions with regard to yield and yield components. A field experiment was conducted in the Yellow River region in China in 2017 and 2018 using a randomized complete block design with three replicates. Photosynthate partitioning of three commercial cultivars (DP 99B, Lumianyan 21 and Jimian 169), varying in yield potential, to different organs (including bolls) at early flowering, peak flowering, and peak boll-setting stages, as well as within-plant boll distribution at harvest, and their effects on yield formation were examined.

[Results] Lint yield of Jimian 169 was the highest, followed by Lumianyan 21 and DP 99B. Similar differences were observed in the number of inner bolls and boll weight among the three cultivars. J169 partitioned significantly more photosynthate to the fruit and fiber than Lumianyan 21 and DP 99B and allocated over 80% of assimilates to the inner bolls. Additionally, Lumianyan 21 allocated a higher proportion of photosynthate to bolls and fiber, with 12.5%–17.6% more assimilates observed in the inner bolls, than DP 99B.

[Conclusions] Genotypic variance in lint yield can be attributed to differences in the number of inner bolls and boll weight, which are affected by photosynthate partitioning. Therefore, the partitioning of photosynthate to fiber and inner bolls can be used as an important reference for cotton breeding and cultivation.

[Title] Genotypic variance in 13C-photosynthate partitioning and within-plant boll distribution in cotton

[Authors] NIE Junjun, QIN Dulin, MAO Lili, LIU Yanhui, DONG Hezhong, SONG Xianliang and SUN Xuezhen

Journal of Cotton Research 3, Article number: 15 (2020)

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