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!

Comparative effects of crop residue incorporation and inorganic potassium fertilization on soil C and N characteristics and microbial activities in cotton field

[Background] Crop residue incorporation into the soil is an effective method to augment soil potassium (K) content, and effects of crop residue and K fertilizer on soil K balance have been compared. However, their influences on other soil characteristics such as carbon (C) and nitrogen (N) characteristics and microbial activities have not been quantified. To address this, field experiments were conducted in 2011 at Dafeng (sandy loam) and Nanjing (clay loam) in China with treatments including blank control without crop residue incorporation and K fertilizer application, 0.9 t·ha− 1 wheat straw incorporation (W1C0), 0.7 t·ha− 1 cotton residue incorporation (W0C1), 0.9 t·ha− 1 wheat straw + 0.7 t·ha− 1 cotton residue incorporation (W1C1) and two K fertilizer rates (150 and 300 kg·ha− 1 (K2O)) during the cotton season.

[Results] Compared with control, K fertilizer treatments did not alter soil water-soluble organic carbon/soil organic carbon (WSOC/SOC) ratio, microbial biomass carbon (MBC)/SOC ratio, MBC/microbial biomass nitrogen (MBN) ratio, water inorganic nitrogen/total nitrogen ratio (WIN/TN), the number of cellulose-decomposing bacteria, or related enzymes activities, however, W0C1, W1C0 and W1C1 treatments significantly increased WSOC/SOC ratio, MBC/SOC ratio and MBC/ MBN ratio, and decreased WIN/TN ratio at both sites. W0C1, W1C0 and W1C1 treatments also increased the number of soil cellulose-decomposing bacteria and activities of cellulase, β-glucosidase and arylamidase. Regarding different crop residue treatments, W1C0 and W1C1 treatments had more significant influences on above mentioned parameters than W0C1 treatment. Moreover, MBC/MBN ratio was the most important factor to result in the differences in the number of cellulose-decomposing bacteria and soil enzymes activities among different treatments.

[Conclusions] This study provided a detailed phenotypic diversity description of a population representing a wide range of upland cotton germplasm. Our findings provide useful information about possible elite fibre quality parents for cotton breeding programs.

[Title] Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

[Authors] HU Wei, SUI Ning , YU Chaoran, YANG Changqin, LIU Ruixian and ZHOU Zhiguo

Journal of Cotton Research2019; 2:24

Bt insecticidal efficacy variation and agronomic regulation in Bt cotton

Abstract: The bollworm can be controlled effectively with Bacillus thuringiensistransgenic cotton (Bt cotton) which is being applied worldwide. However, the insecticidal efficacy is not stable. Here we give a summary of research progress for the mechanism of the altered insecticidal efficacy, factors affecting the expression of insect resistance, agronomic practices on regulation of insecticidal efficacy in Bt cotton. To realize the transgenic potential of Bt cotton cultivars, future research may be conducted by increasing synthesis and reducing degradation of Bt protein to maintain high insecticidal ability in the transgenic cotton by agronomic management.

[Title] Bt insecticidal efficacy variation and agronomic regulation in Bt cotton

[Authors] LIU Zhenyu, ELTAYIB H M. A. Abidallha, WU Huimin, ZHOU Mingyuan, ZHANG Xiang, CHEN Yuan and CHEN Dehua

Journal of Cotton Research2019; 2:23

Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

[Background] Evaluating phenotypic traits is very important for the selection of elite lines in Gossypium hirsutum L. Cotton breeders are interested in using diverse genotypes in hybridization that can segregate for traits of interested with the possibility of selection and genetic gain. Information on phenotypic and molecular diversity helps the breeders for parental selection.

[Methods] In this study, 719 global collections of G. hirsutum L. were evaluated for five fibre-related traits during two consecutive years in eight different environments. A series of phenotypic data for fibre quality traits were obtained and the elite accessions were further screened using principal component analysis and phylogenetic tree construction based on single nucleotide polymorphism markers.

[Results] We found that fibre quality traits showed a wide range of variation among the G. hirsutum accessions over 2 years. In general, accessions from outside China tended to have higher fibre length (FL) and fibre strength (FS) than did Chinese accessions. Among different regional accessions in China, North/Northwest accessions tended to have the highest FL, FS and best fibre macronaire. By assessing five fibre quality traits over 2 years with genotypic data, 31 elite germplasms reaching double-thirty quality values (FL ≥ 30 mm and FS ≥ 30 cN·tex− 1) were selected.

[Conclusions] This study provided a detailed phenotypic diversity description of a population representing a wide range of upland cotton germplasm. Our findings provide useful information about possible elite fibre quality parents for cotton breeding programs.
[Title] Evaluation of the genetic diversity of fibre quality traits in upland cotton (Gossypium hirsutum L.) inferred from phenotypic variations

[Authors] SUN Zhengwen, WANG Xingfen, LIU Zhengwen, GU Qishen, ZHANG Yan, LI Zhikun, KE Huifeng, YANG Jun, WU Jinhua, WU Liqiang, ZHANG Guiyin and MA Zhiying
Journal of Cotton Research2019; 2:22

Towards improving drought resistance and lodging resistance in cotton

Abstract: Cotton is one of the most important fiber and oil crop in the world and the fiber yield as well as quality traits are negatively affected by drought and lodging. Improving root gravitropism is a very effective way to enhance the crop resistance to drought and lodging stresses. Recent advance in origin and formation of root gravitropism may provide new insights to increase drought and lodging resistance in cotton.

[Title] Towards improving drought resistance and lodging resistance in cotton

[Authors] LI Fuguang

Journal of Cotton Research2019; 2:21

Antioxidant and Physiological Responses of Upland Cotton Accessions Grown Under High-Temperature Regimes

Increased temperature caused by climate change is exerting negative impacts on productivity of cotton crop. Therefore, breeding cultivars tolerant of high temperature are need of the time. Realizing the situation, 154 accessions of upland cotton were sown under alpha lattice design in three replications in two sowing dates. The first sowing date was planned to coincide the flowering stage with maximum annual temperature (± 48 °C) of the region. The data were recorded at appearance of first flower for physiological traits like viability of pollen grains and cell membrane thermostability. Enzymatic and non-enzymatic antioxidants, i.e., peroxidase activity and proline contents were also quantified along with hydrogen peroxide. K-means cluster and biplot analysis revealed the differential response of genotypes. FH-Lalzar, IUB-13, GH-Mubarak and Shahkar exhibited higher values for antioxidants and physiological traits. The yield and fibre quality of these genotypes were also superior as compared to others. It was suggested that diversity in germplasm for aforementioned traits can be utilized in further breeding programs.

  • Sajid Majeed, Tanwir Ahmad Malik, Iqrar Ahmad Rana, Muhammad Tehseen   AzharEmail author

Iranian Journal of Science and Technology, Transactions A: Science

Transgenic crops for the agricultural improvement in Pakistan

Transgenic technologies have emerged as a powerful tool for crop improvement in terms of yield, quality, and quantity in many countries of the world. However, concerns also exist about the possible risks involved in transgenic crop cultivation. In this review, literature is analyzed to gauge the real intensity of the issues caused by environmental stresses in Pakistan. In addition, the research work on genetically modified organisms (GMOs) development and their performance is analyzed to serve as a guide for the scientists to help them select useful genes for crop transformation in Pakistan. The funding of GMOs research in Pakistan shows that it does not follow the global trend. We also present socio-economic impact of GM crops and political dimensions in the seed sector and the policies of the government. We envisage that this review provides guidelines for public and private sectors as well as the policy makers in Pakistan and in other countries that face similar environmental threats posed by the changing climate.


Recent advancements in biotechnology resulted in rapid adoption of genetically modified (GM) crops in the agriculture systems. At the same time, transgene escape has also been reported and examples reveal global dimension of the problem. Pollen mediated gene flow (PMGF) is the major pathway for transgene escape. Almost all transgenes have been escaped into their Non-GM counterpart and wild relatives. Although gene flow varies between species, crops, and ecological zones/environments but intraspecific gene flow (> 10%) is not uncommon in adjacent populations. Whereas in outcrossing species, 1% gene flow at thousand meters’ isolation is not unusual, and magnitude is even higher than the mutation rate. It is well documented that transgene flow is deteriorating different production systems in agriculture and famers choice to cultivate GM, conventional and organic crops. If comprehensive policy is not implemented, then in future it will be difficult to detect and remove transgenes from the environment; if unexpected problems arise.

Genetic effects conferring heat tolerance in upland cotton (Gossypium hirsutum L.)

Cotton belongs to family Malvaceae containing more than
200 genera and about 2 300 species. There are more than
50 species of Gossypium reported till now, which are native
to Africa, Australia, Central and South America and Asia,
respectively (Fryxell 1992; Wendel and Grover 2015). Out
of 50 species, only four are domesticated and widespread.
Two diploid (2n = 26) species, namely G. arboreum and G.
herbaceum belong to Old World cotton produce only 1%
of the total cotton production in the world, whereas two
tetraploid (2n = 52) species, namely G. barbadense and G.
hirsutum belong to New World cotton produce 94% of the
total world cotton production. G. barbadense produces 4%,
while G. hirsutum also known as upland cotton produces
about 90% of the total cotton production in the world (Lu
et al. 1997; McCarty et al. 2004).
Upland cotton is a key source of spinnable fiber and cultivated
in more than 61 countries in the world on an area of
29.3 million hectares (ICAC 2018). Cotton and cottonbased
industry has a pivoting role in the economy of
Pakistan. Pakistan ranks the fourth in terms of area and
production in the world after India, China and USA, 3rd in
consumption and 2nd in yarn production in the world.
Cotton contributes 1% share in GDP, while 55% in total foreign
exchange earnings of Pakistan. Cotton was planted on
an area of 2.7 million hectares in 2017, showing an increase
of 10% over the previous year. About 8% more cotton production,
i.e., 11.54 million bales was recorded during 2017/
2018 as compared with 2016/2017 where 10.72 million
bales was recorded (PCCC 2017). However, in terms of per
acre yield (679 kg·hm− 2), Pakistan is lagging far behind
from the major cotton producing countries like Australia
(1 816 kg·hm− 2), China (1 719 kg·hm− 2), Turkey (1 826
kg·hm− 2) and USA (985kg·hm− 2) (ICAC 2018).
A loss of about one-third of cotton produce was recorded
in Pakistan during 2015/2016 due to adverse climatic conditions
particularly heavy rains during reproductive phase
of crop. But high temperature with dry weather conditions
favored the spread of whitefly in 2016 and 2017 which affected
the productivity of cotton crop on a wide range of
area in Punjab province. In recent times besides drought,
salinity, insect pests, diseases and seed quality: high
temperature has emerged as a major threat to cotton productivity.
It is estimated that the global temperature is increasing
by 0.4~0.8 °C/year (PMD 2016). The consequences
of high temperature in cotton could be low germination,
higher fruit shedding (≥ 30 °C/22 °C), pollen sterility and
abortion (Guilioni et al. 1997; Ismail and Hall 1999), unavailability
of macro and micro nutrients due to increase in
soil pH, higher levels of CO2 in the air will increase photosynthetic
activity resulting in enhanced nutrient requirement
of cotton plants.

Role of SNPs in determining QTLs for major traits in cotton

A single nucleotide polymorphism is the simplest form of genetic variation among individuals and can induce
minor changes in phenotypic, physiological and biochemical characteristics. This polymorphism induces various
mutations that alter the sequence of a gene which can lead to observed changes in amino acids. Several assays
have been developed for identification and validation of these markers. Each method has its own advantages and
disadvantages but genotyping by sequencing is the most common and most widely used assay. These markers are
also associated with several desirable traits like yield, fibre quality, boll size and genes respond to biotic and abiotic
stresses in cotton. Changes in yield related traits are of interest to plant breeders. Numerous quantitative trait loci
with novel functions have been identified in cotton by using these markers. This information can be used for crop
improvement through molecular breeding approaches. In this review, we discuss the identification of these markers
and their effects on gene function of economically important traits in cotton

Large-scale inversions majorly drive upland cotton population differentiation

Journal of Cotton Research

Abstract: Recently, Li and his team hosted a project on roles of inversion in upland cotton population differentiation. Strikingly, genomic comparison identified, and subsequent RIL population and germplasm panel haplotype analyses confirmed, that large-scale inversions on chromosome At08 are widely distributed and have over time mediated the reduction of meiotic recombination that has ultimately driven genetically isolated haplotypes of G. hirsutum. This work is likely to become the new benchmark for cotton functional genomics research, and the scientific insights from the comparative analyses contributed substantially to our basic understanding of how genomic inversions influence meiotic recombination and thus lower genetic diversity in plant populations.

[Title] Large-scale inversions majorly drive upland cotton population differentiation

[Authors] TIAN Shilin &MA  Zhiying

Journal of Cotton Research2019; 2:20