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.


Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 populations derived from wild cotton species of the D genome

[Background] Segregation distortion (SD) is a common phenomenon among stable or segregating populations, and the principle behind it still puzzles many researchers. The F2:3 progenies developed from the wild cotton species of the D genomes were used to investigate the possible plant transcription factors within the segregation distortion regions (SDRs). A consensus map was developed between two maps from the four D genomes, map A derived from F2:3 progenies of Gossypium klotzschianum and G. davidsonii while Map B from G. thurberi and G. trilobumF2:3 generations. In each map, 188 individual plants were used.

[Results] The consensus linkage map had 1 492 markers across the 13 linkage groups with a map size of 1 467.445 cM and an average marker distance of 1.037 0 cM. Chromosome D502 had the highest percentage of SD with 58.6%, followed by Chromosome D507 with 47.9%. Six thousand and thirty-eight genes were mined within the SDRs on chromosome D502 and D507 of the consensus map. Within chromosome D502 and D507, 2 308 and 3 730 genes were mined, respectively, and were found to belong to 1 117 gourp out of which 622 groups were common across the two chromosomes. Moreover, genes within the top 9 groups related to plant resistance genes (R genes), whereas 188 genes encoding protein kinase domain (PF00069) comprised the largest group. Further analysis of the dominant gene group revealed that 287 miRNAs were found to target various genes, such as the gra-miR398, gra-miR5207, miR164a, miR164b, miR164c among others, which have been found to target top-ranked stress-responsive transcription factors such as NAC genes. Moreover, some of the stress- responsive cis-regulatory elements were also detected. Furthermore, RNA profiling of the genes from the dominant family showed that higher numbers of genes were highly upregulated under salt and osmotic stress conditions, and also they were highly expressed at different stages of fiber development.

[Conclusion] The results indicated the critical role of the SDRs in the evolution of the key regulatory genes in plants.

[Title]Genetic map construction and functional characterization of genes within the segregation distortion regions (SDRs) in the F2:3 populations derived from wild cotton species of the D genome

[Authors] KIRUNGU Joy Nyangasi, MAGWANGA Richard Odongo, SHIRAKU Margaret Linyerera, LU Pu, MEHARI Teame Gereziher, XU Yuanchao, HOU Yuqing, AGONG Stephen Gaya, ZHOU Yun, CAI Xiaoyan,  ZHOU Zhongli, WANG Kunbo & LIU Fang 

Journal of Cotton Research 2020, 332

A project worth consideration

An Australian initiative of global relevance

The project is called “Intimidation and voice of research scientists” and is self-clear by its title. It is based on a survey that is elaborated and endorsed in the following documents:

endorsement letter2-compressed 2020 Participant INFORMATION SHEET-2019459_V2

Participant INFORMATION SHEET-2019459_V2


Efficient research asks for protection from pressure

This is my personal belief and hopefully shared by many. Pressure and intimidation exist. Less than ten years ago, I got to withdraw a paper from a renown journal because of the pressure my co-author faced in his institution less than 48 hours the paper was submitted to the journal.

The extent of the phenomenon is nevertheless hard to assess and hence seldom assessed. This is the reason why I took part to the survey that is open to scientists feeling interest for the topic.

Click here to do the survey:

It took me about 20 minutes and I found the survey properly built.

I hope that that I am not upsetting ICRA members with this  non-specifically cotton post.