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!

Effects of irrigation and planting geometry on cotton (Gossypium hirsutum L.) fiber quality and seed composition

[Background] Cotton fiber quality and seed composition play vital roles in the economics of cotton production systems and the cottonseed meal industry. This research aimed to examine the effects of different irrigation levels and planting geometries on fiber quality and seed composition of cotton (Gossypium hirsutum L.). We conducted a 2-year study in 2018 and 2019 in a warm, humid area in the Southeast United States on Dundee silt loam soil. There were three irrigation treatments in the study. The treatments included irrigating every furrow, or full irrigation (FI), every alternate furrow, or half irrigation (HI), and no irrigation, or rain-fed (RF). Planting geometries were on ridges spaced 102 cm apart and either a single-row (SR) or twin-rows (TR).

[Results] The results of high-volume instrument (HVI), advanced fiber information systems (AFIS) and near-infrared reflectance spectroscopy (NIRS) showed that irrigation and planting treatments played a significant role in fiber quality and seed composition. Across irrigation treatments, significant differences were seen in fiber properties, including fineness, maturity ratio, micronaire, neps, short fiber, strength, uniformity, upper half mean length (UHML), upper quartile length by weight (UQLw), and yellowness (+b). Irrigation and planting geometry (PG) had a significant effect on micronaire, strength, and UHML while their interaction was significant only for micronaire. The micronaire was negatively affected by irrigation as FI-SR, FI-TR, HI-SR, and HI-TR recorded 11% ~ 12% lower over the RF-SR and TR treatments. The PG played a minor role in determining fiber quality traits like micronaire and nep count. Irrigation treatments produced significantly lower (3% ~ 4%) protein content than rain-fed, while oil content increased significantly (6% ~ 10%).

[Conclusion] The study results indicate a potential for improving cotton fiber and seed qualities by managing irrigation and planting geometries in cotton production systems in the Mississippi (MS) Delta region. The HI-TR system appears promising for lint and seed quality.

[Title] Effects of irrigation and planting geometry on cotton (Gossypium hirsutum L.) fiber quality and seed composition

[Authors]  PINNAMANENI Srinivasa R., ANAPALLI Saseendran S., SUI Ruixiu, BELLALOUI Nacer & REDDY Krishna N. 

Journal of Cotton Research 2021, 42

Cotton germplasm improvement and progress in Pakistan

[Abstract] Cotton (Gossypium spp.) contributes significantly to the economy of cotton-producing countries. Pakistan is the fourth-largest producer of cotton after China, the USA and India. The average yield of cotton is about 570.99− 2 in Pakistan. Climate change and different biotic stresses are causing reduction in cotton production. Transgenic approaches have unique advantage to tackle all these problems. However, how to confer permanent resistance in cotton against insects through genetic modification, is still a big challenge to address. Development of transgenic cotton has been proven to be effective. But its effectiveness depends upon several factors, including heterogeneity, seed purity, diffusion of varieties, backcrossing and ethical concerns. Cotton biotechnology was initiated in Pakistan in 1992–1993 with a focus on acquiring cotton leaf curl virus (CLCuV)-resistant insect-resistant, and improving fiber quality. This review summarizes the use of molecular markers, QTLs, GWAS, and gene cloning for cotton germplasm improvement, particularly in Pakistan.
[Title] Cotton germplasm improvement and progress in Pakistan

[Authors] RAZZAQ Abdul, ZAFAR Muhammad Mubashar, ALI Arfan, HAFEEZ Abdul, BATOOL Wajeeha, SHI Yuzhen,  GONG Wankui & YUAN Youlu

Journal of Cotton Research 2021, 41

Decisions Taken in a Special Executive Committee Meeting held online on 08 January, 2021


8.00 to 10.00 AM Eastern Time, 8 January 2021

A special online meeting of the ICRA Executive Committee was held at 8.00 to 10.00 AM on 8 January 2021.
At the outset, the chair and the ICRA EC members unanimously recorded their deep gratitude and appreciation to Dr. Michel Fok for his commendable contributions and leadership as Chair of ICRA from 2016 to 2020.

The following decisions were taken by majority vote

  • Postponed the election of new EC members to the next WCRC-7.
  • The current Executive Committee will continue until the WCRC-7 with Dr. Mohamed Negm as the Chair
  • Eric Hequet has been unanimously elected as the vice-Chair.
  • Elections will be held at the General Body meeting to be convened at the WCRC-7


  • The ICRA newsletter will be renamed as ‘Cotton Innovations’
  • The newsletter will be published at monthly intervals
  • ICRA-EC members will take turns to act as editors of ‘Cotton Innovations’
  • Mike McCue, Communications Director, ICAC will be requested to be the chief Editor
  • Kai Hughes will be requested for permission of ICAC support (chief Editor, design and layout)
  • The ICRA Secretariat will circulate the newsletter and solicit feedback from ICRA members


COTTON WEBINAR 5th EDITION 3 February 2021

COTTON WEBINAR 5th Edition, 8.00 to 10.00 AM (Eastern Time) 3 February 2021

Prof. Jonathan F. Wendel: Topic: Genes, Jeans, and Genomes; what we now know about the Evolution of Gossypium and the Origin of the Polyploids

Dr. Edward (Ed) M. Barnes: Topic: Increasing Automation & Robotic Applications in Cotton


Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL, significant SNP and transcriptomic data

[Background] Meta-analysis of quantitative trait locus (QTL) is a computational technique to identify consensus QTL and refine QTL positions on the consensus map from multiple mapping studies. The combination of meta-QTL intervals, significant SNPs and transcriptome analysis has been widely used to identify candidate genes in various plants.

[Results] In our study, 884 QTLs associated with cotton fiber quality traits from 12 studies were used for meta-QTL analysis based on reference genome TM-1, as a result, 74 meta-QTLs were identified, including 19 meta-QTLs for fiber length; 18 meta-QTLs for fiber strength; 11 meta-QTLs for fiber uniformity; 11 meta-QTLs for fiber elongation; and 15 meta-QTLs for micronaire. Combined with 8 589 significant single nucleotide polymorphisms associated with fiber quality traits collected from 15 studies, 297 candidate genes were identified in the meta-QTL intervals, 20 of which showed high expression levels specifically in the developing fibers. According to the function annotations, some of the 20 key candidate genes are associated with the fiber development.

[Conclusion] This study provides not only stable QTLs used for marker-assisted selection, but also candidate genes to uncover the molecular mechanisms for cotton fiber development.

[Title] Identification of candidate genes controlling fiber quality traits in upland cotton through integration of meta-QTL, significant SNP and transcriptomic data
[Authors] XU Shudi, PAN Zhenyuan, YIN Feifan, YANG Qingyong, LIN Zhongxu, WEN Tianwang, ZHU Longfu, ZHANG Dawei and NIE Xinhui

Journal of Cotton Research 2020, 334

Insect resistance management in Bacillus thuringiensis cotton by MGPS (multiple genes pyramiding and silencing)

[Abstract] The introduction of Bacillus thuringiensis (Bt) cotton has reduced the burden of pests without harming the environment and human health. However, the efficacy of Bt cotton has decreased due to field-evolved resistance in insect pests over time. In this review, we have discussed various factors that facilitate the evolution of resistance in cotton pests. Currently, different strategies like pyramided cotton expressing two or more distinct Bt toxin genes, refuge strategy, releasing of sterile insects, and gene silencing by RNAi are being used to control insect pests. Pyramided cotton has shown resistance against different cotton pests. The multiple genes pyramiding and silencing (MGPS) approach has been proposed for the management of cotton pests. The genome information of cotton pests is necessary for the development of MGPS-based cotton. The expression cassettes against various essential genes involved in defense, detoxification, digestion, and development of cotton pests will successfully obtain favorable agronomic characters for crop protection and production. The MGPS involves the construction of transformable artificial chromosomes, that can express multiple distinct Bt toxins and RNAi to knockdown various essential target genes to control pests. The evolution of resistance in cotton pests will be delayed or blocked by the synergistic action of high dose of Bt toxins and RNAi as well as compliance of refuge requirement.

[Title]Insect resistance management in Bacillus thuringiensis cotton by MGPS (multiple genes pyramiding and silencing)

[Authors] ZAFAR Muhammad Mubashar, RAZZAQ Abdul, FAROOQ Muhammad Awais, REHMAN Abdul, FIRDOUS Hina, SHAKEEL Amir, MO Huijuan and REN Maozhi

Journal of Cotton Research 2020, 333

COTTON WEBINARS 6 January 2021

WCRC-7 Monthly Plenary Lecture Series
Time & Date: 8.00 to 10.00 AM (Eastern time, Washington DC) 6 Jan 2021
Prof. Hezhong Dong

Director and Senior Principal Scientist, Shandong Academy of Agricultural Sciences, China

8.00 to 9.00 AM (Eastern Time)
Prof. Keerti Rathore, 

Professor, Department of Soil & Crop Sciences, Texas A & M University

9.00 to 10.00 AM (Eastern Time)

Dr. Michel Fok Resignation

Dear Researchers;

I am extremely shocked on the resignation of Dr. Michel Fok. He was with me from the very beginning for the formation of ICRA. Michel is a big supporter of cooperation among researchers. I found him always coming forward with new ideas and willingness to work with anybody who extended him a hand. His contributions to the work of the ICAC through his active role on the SEEP (Social, Environmental and Economic Performance of Cotton) are immense. His work at CIRAD is much appreciated and he owns a great respect among researchers in the West African countries. I can say with confidence that he played a significant role in bringing CIRAD and ICAC closer to work together for common interests of the research community. He has a high number of publications to his credit. He lead ICRA very well and dedicated his full abilities and time for ICRA uplift for the last over 8 years.

Michel was going to retire in April which he already indicated to ICRA community. Now what lead him to resign is terrible. There are some elements that forced him to resign. I am not really in the loop for all the correspondence among EC members but the forces behind his resignation are not that secret either. It is disappointing that some people failed to play their role to resolve issues and the research community had to lose the leadership role of Michel.

I will humbly submit that it is time for the research community to stay united. ICRA is a great organization and has to achieve a lot yet.

M. Rafiq Chaudhry


Time has come

After having joined the Executive Committee since the inception of ICRA, hence for about ten years, I thought it was time for me to step out as I am at a few months to be retired.  So, I have just sent my letter of resignation (mfok_resignation) to the Executive Committee.

My decision to leave my position earlier than scheduled is linked to the discomfort I have perceived among a number of ICRA members and that I created by my decision to suspend the elections for the renewal of the Executive Committee. While I still believe that the decision was necessary, I do not want to be an obstacle in any way to the operation of ICRA and to its evolution.

I believe in exchanges between persons in mutual respect and in the inter-generational transfer of knowledge in implementing research. This website has been conceived for this purpose, so I will stay among you and keep contributing in any area where I could share my experience, at least as long as the membership to ICRA is not strictly restrained to active researchers.

All the best to you all.