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!

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

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

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

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

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

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

COTTON WEBINAR 9th Edition 8.00AM To 10.00AM (ET) 2 June 2021


Slider-2-June 2021

Better Together -International Partnerships Can Solve Threats to Cotton Production

Speaker: Dr. Jodi Scheffler. Research Geneticist Plants. USDA-ARS. Stoneville, Mississippi, United States

When the seed breaks, when the fibre sticks… Some contaminants of cotton

Speakers: Dr Bruno Bachelier. Assistant Unit Director, Cotton Supply Chain Correspondent, CIRAD France. & Dr Jean-Paul Gourlot. Co-leader of the Cotton Sector Group, CIRAD, France.

Genome-wide association study of micronaire using a natural population of representative upland cotton (Gossypium hirsutum L.)

[Background] Micronaire is a comprehensive index reflecting the fineness and maturity of cotton fiber. Micronaire is one of the important internal quality indicators of the cotton fiber and is closely related to the value of the cotton fiber. Understanding the genetic basis of micronaire is required for the genetic improvement of the trait. However, the genetic architecture of micronaire at the genomic level is unclear. The present genome-wide association study (GWAS) aimed to identify the genetic mechanism of the micronaire trait in 83 representative upland cotton lines grown in multiple environments.

[Results] GWAS of micronaire used 83 upland cotton accessions assayed by a Cotton 63 K Illumina Infinium single nucleotide polymorphism (SNP) array. A total of 11 quantitative trait loci (QTLs) for micronaire were detected on 10 chromosomes. These 11 QTLs included 27 identified genes with specific expression patterns. A novel QTL, qFM-A12–1, included 12 significant SNPs, and GhFLA9 was identified as a candidate gene based on haplotype block analysis and on strong and direct linkage disequilibrium between the significantly related SNPs and gene. GhFLA9 was expressed at a high level during secondary wall thickening at 2025 days post-anthesis. The expression level of GhFLA9 was significantly higher in the low micronaire line (Msco-12) than that in the high micronaire line (Chuangyou-9).

[Conclusion] This study provides a genetic reference for genetic improvement of cotton fiber micronaire and a foundation for verification of the functions of GhFLA9.

[Title] Genome-wide association study of micronaire using a natural population of representative upland cotton (Gossypium hirsutum L.)

[Authors] SONG Jikun, PEI Wenfeng, MA Jianjiang, YANG Shuxian, JIA Bing, BIAN Yingying, XIN Yue, WU Luyao, ZANG Xinshan, QU Yanying, ZHANG Jinfa, WU Man & YU Jiwen

Journal of Cotton Research 2021, 414

Increasing plant density increases Bt toxin concentration of boll wall in cotton by decreasing boll setting speed

[Background] In order to uncover the mechanism of significantly reduced insect resistance at the late developmental stage in cotton (Gossypium hirsutum L.), the relationship between boll setting rate under different planting densities and Bacillus thuringiensis (Bt) insecticidal concentrations in the boll wall were investigated in the present study. Two studies were arranged at Yangzhou, China during the 2017–2018 cotton growth seasons. Five planting densities (15 000, 25 000, 45 000, 60 000 and 75 000 plants per hectare) and the flower-removal treatment were imposed separately on Bt cotton cultivar Sikang3 to arrange different boll setting rates, and the boll setting rates and Bt toxin content were compared.

[Results] Higher boll setting rate together with lower Bt toxin contents in boll wall was observed under low planting density, whereas lower boll setting rate and higher Bt toxin contents were found under high planting density. Also, higher Bt protein concentration was associated with higher soluble protein content, glutamic-pyruvic transaminase (GPT), and glutamic oxaloacetate transaminase (GOT) activities, but lower amino acid content, and protease and peptidase activities. It was further confirmed that a higher boll setting rate with lower Bt protein content under flower-removal.

[Conclusion] This study demonstrated that the insecticidal efficacy of boll walls was significantly impacted by boll formation. Reduced protein synthesis and enhanced protein degradation were related to the reduced Bt toxin concentration.

[Title] Increasing plant density increases Bt toxin concentration of boll wall in cotton by decreasing boll setting speed

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

Journal of Cotton Research 2021, 412