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: http://www.cottongen.org/icgi/elections

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!

JCR| The effect of time and type of stress moderators on yield and yield components of cotton on conventional and double-cropping systems under saline conditions

[Background] Today, stress moderators are employed to mitigate crop loss due to the adverse effects of environmental stress. The current research aimed to investigate the impacts of time and stress moderator types on agro-physiological responses of cotton on conventional and double-cropping systems during 2017 and 2018 under saline conditions. A split-plot factorial experiment was carried out in a randomized complete block design with three replications. Cultivation system [conventional (recommended planting date) and double-cropping systems (sowing after harvest of wheat)] were considered as the main plots, and stress moderator type at four levels [water control, 2 mmol·L–1 Salicylic acid (SA), 100 mmol·L–1 Glycine betaine (GB), and 100 μmol·L–1 sodium nitroprusside (SNP)] and application time (flowering and flowering + bolling stages) were regarded as subplots.

[Result] Plant height, reproductive branch number, the number of bolls, 10-boll weight, 1 000-seed weight, biological yield, seed cotton yield, lint yield, chlorophyll a, chlorophyll b, carotenoids, total chlorophyll, sodium, potassium, and proline content were less in double-cropping system comparing with conventional system. Spraying with the stress moderators alleviated soil salinity effects on yield, yield components, and biochemical traits of cotton. SNP spraying led to maximum plant height, branch number, the number of bolls per plant, 10-boll weight and seed cotton yield. SA spraying yielded the highest 1 000-seed weight, biological yield, lint percentage and lint yield. The highest chlorophyll a, chlorophyll b, carotenoids, and total chlorophyll content resulted from SNP spraying. Yield, yield components, and biochemical traits did not respond to the stress moderator types in double-cropping system. However, the highest chlorophyll a, carotenoids, proline content, the number of bolls per plant, and seed cotton yield resulted from SNP spraying in conventional system. No statistically significant differences were observed between spraying with SNP and SA in most studied traits.

[Conclusion] The results suggest that the optimum cotton planting time and SNP spraying could be recommended for producing the most suitable yield under saline conditions.

[Title] The effect of time and type of stress moderators on yield and yield components of cotton on conventional and double-cropping systems under saline conditions

[Authors] BORZOUYI Zeinab, ARMIN Mohammad & MARVI Hamid

Journal of Cotton Research 2021, 428

https://doi.org/10.1186/s42397-021-00103-6

JCR| Knockdown of 60S ribosomal protein L14-2 reveals their potential regulatory roles to enhance drought and salt tolerance in cotton

[Background] Cotton is a valuable economic crop and the main significant source of natural fiber for textile industries globally. The effects of drought and salt stress pose a challenge to strong fiber and large-scale production due to the ever-changing climatic conditions. However, plants have evolved a number of survival strategies, among them is the induction of various stress-responsive genes such as the ribosomal protein large (RPL) gene. The RPL gene families encode critical proteins, which alleviate the effects of drought and salt stress in plants. In this study, comprehensive and functional analysis of the cotton RPL genes was carried out under drought and salt stresses.

[Result] Based on the genome-wide evaluation, 26, 8, and 5 proteins containing the RPL14B domain were identified in Gossypium hirsutumG. raimondii, and G. arboreum, respectively. Furthermore, through bioinformatics analysis, key cis-regulatory elements related to RPL14B genes were discovered. The Myb binding sites (MBS), abscisic acid-responsive element (ABRE), CAAT-box, TATA box, TGACG-motif, and CGTCA-motif responsive to methyl jasmonate, as well as the TCA-motif responsive to salicylic acid, were identified. Expression analysis revealed a key gene, Gh_D01G0234 (RPL14B), with significantly higher induction levels was further evaluated through a reverse genetic approach. The knockdown of Gh_D01G0234 (RPL14B) significantly affected the performance of cotton seedlings under drought/salt stress conditions, as evidenced by a substantial reduction in various morphological and physiological traits. Moreover, the level of the antioxidant enzyme was significantly reduced in VIGS-plants, while oxidant enzyme levels increased significantly, as demonstrated by the higher malondialdehyde concentration level.

[Conclusion] The results revealed the potential role of the RPL14B gene in promoting the induction of antioxidant enzymes, which are key in oxidizing the various oxidants. The key pathways need to be investigated and even as we exploit these genes in the developing of more stress-resilient cotton germplasms.

[Title] Knockdown of 60S ribosomal protein L14-2 reveals their potential regulatory roles to enhance drought and salt tolerance in cotton

[Authors] SHIRAKU Margaret Linyerera, MAGWANGA Richard Odongo, CAI Xiaoyan, KIRUNGU Joy Nyangasi, XU Yanchao, MEHARI Teame Gereziher, HOU Yuqing, WANG Yuhong, WANG Kunbo, PENG Renhai, ZHOU Zhongli & LIU Fang

Journal of Cotton Research 2021, 427

https://doi.org/10.1186/s42397-021-00102-7

JCR | Tolerance of Pima and Upland cotton to trifloxysulfuron (Envoke) herbicide under field conditions

[Abstract] Trifloxysulfuron (Envoke) is an acetolactate synthase-inhibitor herbicide and can be used to control many broadleaf weeds and nutsedges in cotton production. However, there is a lack of information on genotypic variation in response to the herbicide. In this field study, 60 Pima (Gossypium barbadense L.) lines, 122 Upland (G. hirsutum L.) lines, and 9 Upland × Pima segregating populations were divided into five tests (18A, 18B, 18G, 18RB, and 18HQ) to evaluate trifloxysulfuron tolerance at the 7-true leaf stage (42 days after planting) under the same field conditions in 2018. Across the five tests, Pima cotton genotypes tested in this study did not show any visual crop injury based on percentage of plants with chlorosis at 6 days after treatment (DAT), indicating consistent and high levels of trifloxysulfuron tolerance. However, the response to trifloxysulfuron within Upland cotton is highly variable. While Upland cotton is overall more sensitive to trifloxysulfuron with crop injury up to 80% than Pima cotton, 19 lines had injury below 5% including one line with no visual injury, and 19 lines had injury between 5% and 10%. In test 18HQ with 15 transgenic Upland cultivars and 17 non-transgenic Upland lines, the analysis of variance detected a significant genotypic difference. The broad-sense heritability estimates for trifloxysulfuron tolerance based on crop injury at 6 DAT was 0.555, suggesting that trifloxysulfuron tolerance in Upland cotton is moderately heritable. This study represents the first report that Pima cotton and many Upland cotton lines are highly tolerant to trifloxysulfuron with no or little crop injury.

[Title] Tolerance of Pima and Upland cotton to trifloxysulfuron (Envoke) herbicide under field conditions

[Authors] ZHANG Jinfa, ABDELRAHEEM Abdelraheem & WEDEGAERTNER Tom

Journal of Cotton Research 2021, 426

https://doi.org/10.1186/s42397-021-00101-8

JCR | Current advances in pathogen-plant interaction between Verticillium dahliae and cotton provide new insight in the disease management

[Abstract] Verticillium wilt is the second serious vascular wilt caused by the phytopathogenic fungus Verticillium dahliae Kleb. It has distributed worldwide, causing serious yield losses and fiber quality reduction in cotton production. The pathogen has developed different mechanisms like the production of cell wall degrading enzymes, activation of virulence genes and protein effectors to succeed in its infection. Cotton plant has also evolved multiple mechanisms in response to the fungus infection, including a strong production of lignin and callose deposition to strengthen the cell wall, burst of reactive oxygen species, accumulation of defene hormones, expression of defense-related genes, and target-directed strategies like cross-kingdom RNAi for specific virulent gene silencing. This review summarizes the recent progress made over the past two decades in understanding the interactions between cotton plant and the pathogen Verticillium dahliae during the infection process. The review also discusses the achievements in the control practices of cotton verticillium wilt in recent years, including cultivation practices, biological control, and molecular breeding strategies. These studies reveal that effective management strategies are needed to control the disease, while cultural practices and biological control approaches show promising results in the future. Furthermore, the biological control approaches developed in recent years, including antagonistic fungi, endophytic bacteria, and host induced gene silencing strategies provide efficient choices for integrated disease management.

[Title]Current advances in pathogen-plant interaction between Verticillium dahliae and cotton provide new insight in the disease management

[Authors] PALANGA Koffi Kibalou, LIU Ruixian, GE Qun, GONG Juwu, LI Junwen, LU Quanwei, LI Pengtao, YUAN Youlu & GONG Wankui

Journal of Cotton Research 2021, 425

https://doi.org/10.1186/s42397-021-00100-9

JCR | Zinc finger transcription factor ZAT family genes confer multi-tolerances in Gossypium hirsutum L.

[Abstract] ZAT (Zinc Finger of Arabidopsis thaliana) proteins are composed of a plant-specific transcription factor family, which play an important role in plant growth, development, and stress resistance. To study the potential function of ZAT family in cotton, the whole genome identification, expression, and structure analysis of ZAT gene family were carried out. In this study, our analysis revealed the presence of 115, 56, 59, and 115 ZAT genes in Gossypium hirsutumG. raimondiiG. arboreum and G. barbadense, respectively. According to the number of domains and phylogenetic characteristics, we divided ZAT genes of four Gossypium species into 4 different clades, and further divided them into 11 subfamilies. The results of collinearity analysis showed that segmental duplication was the main method to amplify the cotton ZAT genes family. Analysis of cis-elements of promoters indicated that most GhZAT genes contained cis-elements related to plant hormones and abiotic stress. According to heatmap analysis, the expression patterns of GhZAT genes under different stresses indicated that GhZAT genes were significantly involved in the response to cold, heat, salt, and PEG stress, possibly through different mechanisms. Among the highly expressed genes, we cloned a G. hirsutum gene GhZAT67. Through virus-induced gene silencing (VIGS), we found that its expression level decreased significantly after being silenced. Under alkaline treatment, the wilting degree of silenced plants was even greater than the wild type, which proved that GhZAT67 gene was involved in the response to alkaline stress.

[Title] Zinc finger transcription factor ZAT family genes confer multi-tolerances in Gossypium hirsutum L.

[Authors] FAN Yapeng, ZHANG Yuexin, RUI Cun, XU Nan, ZHANG Hong, WANG Jing, MALIK Waqar Afzal, HAN Mingge, ZHAO Lanjie, LU Xuke, CHEN Xiugui, CHEN Chao & YE Wuwei

Journal of Cotton Research 2021, 424

https://doi.org/10.1186/s42397-021-00098-0

JCR | Improved Gossypium raimondii genome using a Hi-C-based proximity-guided assembly

[Introduction] Genome sequence plays an important role in both basic and applied studies. Gossypium raimondii, the putative contributor of the D subgenome of upland cotton (G. hirsutum), highlights the need to improve the genome quality rapidly and efficiently.

[Methods] We performed Hi-C sequencing of G. raimondii and reassembled its genome based on a set of new Hi-C data and previously published scaffolds. We also compared the reassembled genome sequence with the previously published G. raimondii genomes for gene and genome sequence collinearity.

[Result] A total of 98.42% of scaffold sequences were clustered successfully, among which 99.72% of the clustered sequences were ordered and 99.92% of the ordered sequences were oriented with high-quality. Further evaluation of results by heat-map and collinearity analysis revealed that the current reassembled genome is significantly improved than the previous one (Nat Genet 44:98–1103, 2012).

[Conclusion] This improvement in G. raimondii genome not only provides a better reference to increase study efficiency but also offers a new way to assemble cotton genomes. Furthermore, Hi-C data of G. raimondii may be used for 3D structure research or regulating analysis.

[Title] Improved Gossypium raimondii genome using a Hi-C-based proximity-guided assembly

[Authors] YANG Qiuhong, ZUO Dongyun, CHENG Hailiang, ZHANG Youping, WANG Qiaolian, JAVARIA Ashraf, FENG Xiaoxu, LI Simin, CHEN Xiaoqin, LIU Shang & SONG Guoli

Journal of Cotton Research 2021, 423

https://doi.org/10.1186/s42397-021-00096-2

JCR | Research progress in the population differentiation and geographical adaptation of cotton

[Abstract] Recently, Du and his team revealed the genomic basis of population differentiation and geographical distribution of Chinese cultivated G. hirsutum(upland cotton). Our previous study showed that the large-scale inversions on chromosome A08 are widely distributed in a core collection of upland cotton and have driven population differentiation in G. hirsutum. With 3248 tetraploid cotton germplasms, He et al. identified new inversions on chromosome A06, and found these inversions together with those in chromosome A08 caused subpopulation differentiation Chinese cultivars that were highly consistent with their corresponding geographical distributions. This work provides new perspectives to further understand environmental adaptation of Chinese upland cotton germplasms.

[Title] Research progress in the population differentiation and geographical adaptation of cotton

[Authors] LI Fuguang

Journal of Cotton Research 2021, 421

https://doi.org/10.1186/s42397-021-00095-3

JCR | Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development

[Background] Pectin is a key substance involved in cell wall development, and the galacturonosyltransferases (GAUTs) gene family is a critical participant in the pectin synthesis pathway. Systematic and comprehensive research on GAUTshas not been performed in cotton. Analysis of the evolution and expression patterns of the GAUT gene family in different cotton species is needed to increase knowledge of the function of pectin in cotton fiber development.

[Results] In this study, we have identified 131 GAUT genes in the genomes of four Gossypium species (G. raimondiiG. barbadenseG. hirsutum, and G. arboreum), and classified them as GAUT-AGAUT-B and GAUT-C, which coding probable galacturonosyltransferases. Among them, the GAUT genes encode proteins GAUT1 to GAUT15. All GAUT proteins except for GAUT7 contain a conserved glycosyl transferase family 8 domain (H-DN-A-SVV-S-V-H-T-F). The conserved sequence of GAUT7 is PLN (phospholamban) 02769 domain. According to cis-elemet analysis, GAUT genes transcript levels may be regulated by hormones such as JA, GA, SA, ABA, Me-JA, and IAA. The evolution and transcription patterns of the GAUT gene family in different cotton species and the transcript levels in upland cotton lines with different fiber strength were analyzed. Peak transcript level of GhGAUT genes have been observed before 15 DPA. In the six materials with high fiber strength, the transcription of GhGAUT genes were concentrated from 10 to 15 DPA; while the highest transcript levels in low fiber strength materials were detected between 5 and 10 DPA. These results lays the foundation for future research on gene function during cotton fiber development.

[Conclusion] The GAUT gene family may affect cotton fiber development, including fiber elongation and fiber thickening. In the low strength fiber lines, GAUTs mainly participate in fiber elongation, whereas their major effect on cotton with high strength fiber is related to both elongation and thickening.

[Title] Evolution of pectin synthesis relevant galacturonosyltransferase gene family and its expression during cotton fiber development

[Authors] FAN Senmiao, LIU Aiying, ZOU Xianyan, ZHANG Zhen, GE Qun, GONG Wankui, LI Junwen, GONG Juwu, SHI Yuzhen, DENG Xiaoying, JIA Tingting, YUAN Youlu & SHANG Haihong

Journal of Cotton Research 2021, 422

https://doi.org/10.1186/s42397-021-00099-z

JCR | Genetic variability for yield and fiber related traits in genetically modified cotton

[Background] Cotton (Gossypium hirsutum L.) is grown for fiber and oil purposes in tropical and sub-tropical areas of the world. Pakistan is the 4th largest producer of cotton. It has a significant contribution in the GDP of Pakistan. Therefore, the present study was performed to assess the genetic variations and genetic diversity of yield and fiber quality traits in cotton and to analyze the associations present among them.

[Results] Analysis of variance exhibited significant variation for all studied traits except total number of nodes and the height to node ratio. The phenotypic coefficient of variation was higher than the genotypic coefficient of variation for all studied traits. Plant height, monopodial branches, total number of bolls, lint index, seed index, and seed cotton yield displayed high heritabilities in a broad sense with maximum genetic advance. Correlation analysis revealed that seed cotton yield had a significant positive association with plant height, the number of monopodial branches, the number of sympodial branches, ginning outturn (GOT), the number of bolls, seed per boll, seed index, uniformity index, the number of sympodial branches, reflectance, and seed index at the genotypic level while a significant positive relationship was observed with plant height, the number of sympodial branches, boll number, and GOT. Plant height, monopodial branches, GOT, boll weight, seeds per boll, and short fiber index exerted direct positive effects on seed cotton yield. The first 6 principal component analysis (PCs) out of the total fourteen PCs displayed eigenvalues (> 1) and had maximum share to total variability (82.79%). The attributes that had maximum share to total divergence included plant height, uniformity index, the number of sympodial branches, seed per boll, GOT, seed cotton yield, and short fiber index.

[Conclusion] The genotype AA-802, IUB-13, FH-159, FH-458, and CIM-595 were genetically diverse for most of the yield and fiber quality traits and could be utilized for the selection of better performing genotypes for further improvement.

[Title] Genetic variability for yield and fiber related traits in genetically modified cotton

[Authors] SAHAR Adeela, ZAFAR Muhammad Mubashar, RAZZAQ Abdul, MANAN Abdul, HAROON Muhammad, SAJID Sunaina, REHMAN Abdul, MO Huijuan, ASHRAF Muhammad, REN Maozhi, SHAKEE AmirL & YUAN Youlu

Journal of Cotton Research 2021, 419

https://doi.org/10.1186/s42397-021-00094-4

JCR | Identification and expression analysis of Tubulin gene family in upland cotton

[Background] Cotton fibers are single-celled extensions of the seed epidermis, a model tissue for studying cytoskeleton. Tubulin genes play a critical role in synthesizing the microtubules (MT) as a core element of the cytoskeleton. However, there is a lack of studies concerning the systematic characterization of the tubulin gene family in cotton. Therefore, the identification and portrayal of G. hirsutum tubulin genes can provide key targets for molecular manipulation in cotton breeding.

[Results] In this study, we investigated all tubulin genes from different plant species and identified 98 tubulin genes in G. hirsutum. Phylogenetic analysis showed that tubulin family genes were classified into three subfamilies. The protein motifs and gene structure of α-, β-tubulin genes are more conserved compared with γ-tubulin genes. Most tubulin genes are located at the proximate ends of the chromosomes. Spatiotemporal expression pattern by transcriptome and qRT-PCR analysis revealed that 12 α-tubulin and 7 β-tubulin genes are specifically expressed during different fiber development stages. However, Gh.A03G027200Gh.D03G169300, and Gh.A11G258900 had differential expression patterns at distinct stages of fiber development in varieties J02508 and ZRI015.

[Conclusion] In this study, the evolutionary analysis showed that the tubulin genes were divided into three clades. The genetic structures and molecular functions were highly conserved in different plants. Three candidate genes, Gh.A03G027200Gh.D03G169300, and Gh.A11G258900 may play a key role during fiber development complementing fiber length and strength.

[Title] Identification and expression analysis of Tubulin gene family in upland cotton

[Authors] CHEN Baojun, ZHAO Junjie, FU Guoyong, PEI Xinxin, PAN Zhaoe, LI Hongge, AHMED Haris, HE Shoupu & DU Xiongming

Journal of Cotton Research 2021, 420

https://doi.org/10.1186/s42397-021-00097-1