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!

WCRC-7 WEBINAR on ‘Cotton and Climate Change’ 4 November 2020

COTTON WEBINARS
WCRC-7 Plenary Lecture Series

The ICAC and ICRA are delighted to announce the second COTTON WEBINAR to be held at 7.30 to 9.30 AM (Eastern Time, Washington DC) on 4 November 2020. The webinar lectures will feature two presentations (30 min) each day by eminent globally renowned experts followed by a Q& A session. The lectures will be translated simultaneously into French and Spanish. Zoom-Pro has a provision for language preference options which are easy to access. 
COTTON AND CLIMATE CHANGE 
Time & Date: 7.30 to 9.30 AM (Eastern time, Washington DC) 4 November 2020

Dr. K. Raja ReddyProfessor, Environmental Plant Physiology, Mississippi State University, USA
Topic: Clime Change -Physiological implications and Challenges

Dr. Michael Bange, Former Chief Scientist, CSIRO Australia
Topic: Climate Change -Management Implications and Challenges

Please find the first flyer of the event attached herewith
Link to join the meeting, ID and password are provided below
Best Regards
Keshav Kranthi


Join Zoom Meeting
https://us02web.zoom.us/j/84140126878?pwd=SWV2MmljS0sxdjJnMFVBZHY1ZlBUdz09

Meeting ID: 841 4012 6878
Passcode: 819742

History under writing

The content of this post is a replication of a message I have just sent. You can react to my message by commenting this post.

This is to attract your attention to the fact that some of you have taken over the challenge of embarking to write of the history of cotton research. Click on wiki after logging in and discover what has been started for the State of Gujarat, as a chapter of the history of cotton research in India. This chapter will be enriched as additional materials are provided.

The supply of some materials related to the cotton history in Sudan gave me the idea of starting a book dedicated to the tools, implements and devices in cotton production. I believe that many research teams have carried out specific tools for the implementation of their experiments and they could be useful to research fellows in other countries if not to cotton growers producing on small scale. I hope that many of you could contribute to this book.

I do hope that we could actually achieve  a collaborative approach in writing our Gossybooks in our Gossypedia. This means that every one could free to contribute to books under process.

The Gossypedia functionality of our website is well adapted to the collaborative process in the sense that books, chapters or pages are “viewable” by ICRA members only when we decide to. This means that, as long as the writing of a page is not over, it can remain hidden and only viewable to and editable by those endowed with the relevant rights.

Even when some of you volunteer for a book or a chapter, they have been reluctant so far to take command of the Gossypedia tool and play the editor’s role. By default, I am playing this role.Although I understand the hesitation to invest in mastering a web tool, the current way is not sustainable as I should be quitting my position soon.

 

A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

[Background] Cotton is the world’s largest and most important source of renewable natural fiber. BEL1-like homeodomain (BLH) genes are ubiquitous in plants and have been reported to contribute to plant development. However, there is no comprehensive characterization of this gene family in cotton. In this study, 32, 16, and 18 BLH genes were identified from the G. hirsutumG. arboreum, and G. raimondii genome, respectively. In addition, we also studied the phylogenetic relationships, chromosomal location, gene structure, and gene expression patterns of the BLH genes.

[Result] The results indicated that these BLH proteins were divided into seven distinct groups by phylogenetic analysis. Among them, 25 members were assigned to 15 chromosomes. Furthermore, gene structure, chromosomal location, conserved motifs, and expression level of BLH genes were investigated in G. hirsutum. Expression profiles analysis showed that four genes (GhBLH1_3GhBLH1_4GhBLH1_5, and GhBLH1_6) from BLH1 subfamily were highly expressed during the fiber cell elongation period. The expression levels of these genes were significantly induced by gibberellic acid and brassinosteroid, but not auxin. Exogenous application of gibberellic acid significantly enhanced GhBLH1_3GhBLH1_4, and GhBLH1_5transcripts. Expression levels of GhBLH1_3 and GhBLH1_4 genes were significantly increased under brassinosteroid treatment.

[Conclusion] The BLH gene family plays a very important role in many biological processes during plant growth and development. This study deepens our understanding of the role of the GhBLH1gene involved in fiber development and will help us in breeding better cotton varieties in the future.

[Title] A genome-wide identification of the BLH gene family reveals BLH1 involved in cotton fiber development

[Authors] LIU Cuixia, LI Zhifang, DOU Lingling, Yi YUAN, ZOU Changsong, SHANG Haihong, CUI Langjun & XIAO  Guanghui

Journal of Cotton Research 2020, 326

https://doi.org/10.1186/s42397-020-00068-y

Cotton research history?

World Cotton Day

As we have been recently recalled, ICAC has launched the initiative of declaring October 7 as the World Cotton Day. Hopefully, in a couple of days, it will become the new UN World Cotton Day and give us some pride in working on cotton.

For sure, the World Cotton Day will be celebrated at various cotton research organizations all over the world, along celebrations initiated by other stakeholders of the cotton industry.

World Cotton Research History?

I nevertheless wonder how we, cotton scientists or professionals, could more specifically celebrate cotton.

I believe that many of you would concur with me that research has contribute a lot to what cotton industry has become in all producing countries. However, is there any track of that? Has the history of cotton research ever been written and updated anywhere? Would it be relevant to initiate the writing of such histories in producing countries so as to compose the World History of Cotton Research?

Answers and challenges are yours! And quite difficult.

More modestly and realistically, would you have ideas of particular research outputs, maybe associated to particular researchers, that you think have been crucial breakthroughs in the development of the cotton industry in your country?

 

Global identification of genes associated with xylan biosynthesis in cotton fiber

[Background] Mature cotton fiber secondary cell wall comprises largely of cellulose (> 90%) and small amounts of xylan and lignin. Little is known about the cotton fiber xylan biosynthesis by far.

[Result] To comprehensively survey xylan biosynthetic genes in cotton fiber, we identified five IRX9, five IRX10, one IRX14, six IRX15, two FRA8, one PARVUS, eight GUX, four GXM, two RWA, two AXY9, 13 TBL genes by using phylogenetic analysis coupled with expression profile analysis and co-expression analyses. In addition, we also identified two GT61 members, two GT47 members, and two DUF579 family members whose homologs in Arabidopsis were not functionally characterized. These 55 genes were regarded as the most probable genes to be involved in fiber xylan biosynthesis. Further complementation analysis indicated that one IRX10 like and two FRA8 related genes were able to partially recover the irregular xylem phenotype conferred by the xylan deficiency in their respective Arabidopsis mutant. We conclude that these genes are functional orthologs of respective genes that are implicated in GX biosynthesis.

[Conclusion] The list of 55 cotton genes presented here provides not only a solid basis to uncover the biosynthesis of xylan in cotton fiber, but also a genetic resource potentially useful for future studies aiming at fiber improvement via biotechnological approaches.

[Title] Global identification of genes associated with xylan biosynthesis in cotton fiber

[Authors] CHEN Feng, GUO Yanjun, CHEN Li, GAN Xinli, LIU Min, LI Juan & XU Wenliang

Journal of Cotton Research 2020, 325

https://doi.org/10.1186/s42397-020-00063-3

Development and application of perfect SSR markers in cotton

[Background] This study aimed to develop a set of perfect simple sequence repeat (SSR) markers with a single copy in the cotton genome, to construct a DNA fingerprint database suitable for authentication of cotton cultivars. We optimized the polymerase chain reaction (PCR) system for multi-platform compatibility and improving detection efficiency. Based on the reference genome of upland cotton and 10× resequencing data of 48 basic cotton germplasm lines, single-copy polymorphic SSR sites were identified and developed as diploidization SSR markers. The SSR markers were detected by denaturing polyacrylamide gel electrophoresis (PAGE) for initial screening, then fluorescence capillary electrophoresis for secondary screening. The final perfect SSR markers were evaluated and verified using 210 lines from different sources among Chinese cotton regional trials.

[Result] Using bioinformatics techniques, 1 246 SSR markers were designed from 26 626 single-copy SSR loci. Adopting a stepwise (primary and secondary) screening strategy, a set of 60 perfect SSR markers was selected with high amplification efficiency and stability, easy interpretation of peak type, multiple allelic variations, high polymorphism information content (PIC) value, uniform chromosome distribution, and single-copy characteristics. A multiplex PCR system was established with ten SSR markers using capillary electrophoresis detection.

[Conclusion] A set of perfect SSR markers of cotton was developed and a high-throughput SSR marker detection system was established. This study lays a foundation for large-scale and standardized construction of a cotton DNA fingerprint database for authentication of cotton varieties.

[Title] Development and application of perfect SSR markers in cotton

[Authors] WU Yuzhen, HUANG Longyu, ZHOU Dayun, FU Xiaoqiong, LI Chao, WEI Shoujun, PENG Jun & KUANG Meng

Journal of Cotton Research 2020, 321

https://doi.org/10.1186/s42397-020-00066-0

Toward the efficient use of Beauveria bassiana in integrated cotton insect pest management

[Background] For controlling the resistance to insects, in particular carpophagous and phyllophagous caterpillars, using chemical pesticides has led to contamination of cotton area in Benin. Facing this problem, alternative methods including the use of entomopathogenic fungi as biopesticide could be a sound measure to preserve the environment, biodiversity and ensure good quality of crops. Previous studies have revealed the insecticidal potential of the entomopathogenic Beauveria bassiana on some insect pest species. However, little is known about its effectiveness on cotton Lepidopteran pests. This review is done to learn more about B. bassina for its application in controlling cotton insect pests, especially Lepidopteran species.

[Main body] Different sections of the current review deal with the related description and action modes of B. bassiana against insects, multi-trophic interactions between B. bassiana and plants, arthropods, soil and other microbes, and biological control programs including B. bassiana during last decade. Advantages and constraints in applying B. bassiana and challenges in commercialization of B. bassiana-based biopesticide have been addressed. In this review, emphasis is put on the application methods and targeted insects in various studies with regard to their applicability in cotton

[Conclusion] This review helps us to identify the knowledge gaps related to application of B. bassiana on cotton pest in general and especially in Lepidopteran species in Benin. This work should be supported by complementary laboratory bioassays, station and/or fields experiments for effective management of cotton Lepidopteran pests in Benin.
[Title] Toward the efficient use of Beauveria bassiana in integrated cotton insect pest management

[Authors] DANNON H. Fabrice, DANNON A. Elie, DOURO-KPINDOU O. Kobi, ZINSOU A. Valerien, HOUNDETE A. Thomas, TOFFA-MEHINTO Joëlle, ELEGBEDE I. A. T. Maurille, OLOU B. Dénis & TAMÒ Manuele

Journal of Cotton Research 2020, 324

https://doi.org/10.1186/s42397-020-00061-5

Heritability and correlation analysis of morphological and yield traits in genetically modified cotton

[Background] Cotton is known for fiber extraction and it is grown in tropical and sub-tropical areas of the world due to having hot weather. Cotton crop has a significant role in GDP of Pakistan. Therefore, the two-years research was conducted to estimate heritability and association among various yield contributing parameters of cotton, i.e., plant height, number of bolls per plant, number of sympodial branches per plant, seed cotton yield, boll weight, seed index, ginning outturn (GOT), fiber length, fiber strength, and fiber fineness.

[Result] Association analysis revealed that seed cotton yield had a significant positive correlation with plant height, number of bolls per plant, number of sympodial branches per plant, GOT, staple length and fiber strength. Staple length and fiber strength were negatively linked with each other. Estimates of heritability were high for all of the traits except the number of sympodial branches per plant and boll weight.

[Conclusion] The parent IUB-222 was found to be the best for plant height, the number of bolls per plant, boll weight, GOT, seed cotton yield, and seed index. The genotypes namely, NIAB-414 and VH-367 were identified as the best parents for fiber length, strength, and fineness. Among the crosses NIAB-414 × IUB-222 was the best for the number of bolls per plant, seed index, seed cotton yield and fiber fineness, whereas, the cross of NIAB-414 × CIM-632 was good for plant height. The combination of A555 × CIM-632 was the best for the number of sympodial branches per plant, boll weight, fiber length, and strength, and VH-367 × CIM-632 proved the best for GOT.
[Title] Heritability and correlation analysis of morphological and yield traits in genetically modified cotton

[Authors] REHMAN Abdul, MUSTAFA Nida, DU Xiongming & AZHAR Muhammad Tehsee

Journal of Cotton Research 2020, 323

https://doi.org/10.1186/s42397-020-00067-z

QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

[Background] Genetic improvement in fiber quality is one of the main challenges for cotton breeders. Quantitative trait loci (QTL) mapping provides a powerful approach to dissect the molecular mechanism in fiber quality traits. In present study, F14recombinant inbred line (RIL) population was backcrossed to paternal parent for a paternal backcross (BC/P) population, deriving from one upland cotton hybrid. Three repetitive BC/P field trials and one maternal backcross (BC/M) field trial were performed including both two BC populations and the original RIL population.

[Result] In total, 24 novel QTLs are detected for fiber quality traits and among which 13 QTLs validated previous results. Thirty-five QTLs in BC/P populations explain 5.01%–22.09% of phenotype variation (PV). Among the 35 QTLs, 23 QTLs are detected in BC/P population alone. Present study provides novel alleles of male parent for fiber quality traits with positive genetic effects. Particularly, qFS-Chr3–1 explains 22.09% of PV in BC/P population, which increaseds 0.48 cN·tex− 1 for fiber strength. A total of 7, 2, 8, 2 and 6 QTLs explain over 10.00% of PV for fiber length, fiber uniformity, fiber strength, fiber elongation and fiber micronaire, respectively. In RIL population, six common QTLs are detected in more than one environment: qFL-Chr1–2qFS-Chr5–1qFS-Chr9–1qFS-Chr21–1qFM-Chr9–1 and qFM-Chr9–2. Two common QTLs of qFE-Chr2–2(TMB2386-SWU12343) and qFM-Chr9–1 (NAU2873-CGR6771) explain 22.42% and 21.91% of PV. The region between NAU4034 and TMB1296 harbor 30 genes (379 kb) in A05 and 42 genes (49 kb) in D05 for fiber length along the QTL qFL-Chr5–1 in BC/P population, respectively. In addition, a total of 142 and 46 epistatic QTLs and QTL × environments (E-QTLs and QQEs) are identified in recombinant inbred lines in paternal backcross (RIL-P) and paternal backcross (BC/P) populations, respectively.

[Conclusion] The present studies provide informative basis for improving cotton fiber quality in different populations.
[Title] QTL and genetic analysis controlling fiber quality traits using paternal backcross population in upland cotton

[Authors] MA LingLing, SU Ying, NIE Hushuai, CUI Yupeng, CHENG Cheng, IJAZ Babar & HUA  Jinping

Journal of Cotton Research 2020, 322

https://doi.org/10.1186/s42397-020-00060-6