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!

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

https://doi.org/10.1007/s40995-019-00781-7.

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.

GENE FLOW FROM MAJOR GENETICALLY MODIFIE D CROPS AND STRATEGIES FOR C ONTAINMENT AND MITIG ATION OF TRANSGENE ESCAPE: A

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; 2:19
https://doi.org/10.1186/s42397-019-0037-y
https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0037-y

Down regulation of cotton GbTRP1 leads to accumulation of anthranilates and confers resistance to Verticillium dahliae

Journal of Cotton Research

[Background] Verticillium wilt, caused by Verticillium dahliae, is called a “cancer” disease of cotton. The discovery and identification of defense-related genes is essential for the breeding of Verticillium wilt-resistant varieties. In previous research we identified some possible broad-spectrum resistance genes. Here, we report a tryptophan synthesis-related gene GbTRP1 and its functional analysis in relation to the resistance of cotton to V. dahliae.

[Results] Expression analysis shows that GbTRP1 is suppressed at 1 h and 6 h post V. dahliae infection, but activated at 12 h and 24 h, and the expression of GbTRP1 is highly induced by treatment with salicylic acid and jasmonic acid. Sub-cellular localization studies show that GbTRP1 is localized in the chloroplast. Suppression of GbTRP1 expression leads to lesion-mimic phenotypes and activates the immune response in cotton by showing enhanced resistance to V. dahliae and B. cinerea. Metabolomic analysis shows that anthranilic compounds significantly accumulated in GbTRP1-silenced plants, and these metabolites can inhibit the growth of V. dahliae and B. cinerea in vitro.

[Conclusions] Our results show that suppression of GbTRP1 expression dramatically activates the immune response and increases resistance of cotton to V. dahliae and B. cinerea, possibly due to the accumulation of anthranilate compounds. This study not only provides genetic resources for disease resistance breeding, but also may provide a basis for new chemical control methods for combatting of fungal disease in cotton.

[Title] Down regulation of cotton GbTRP1 leads to accumulation of anthranilates and confers resistance to Verticillium dahliae

[Authors] MIAO Yuhuan, ZHU Longfu and ZHANG Xianlong

Journal of Cotton Research. 2019; 2:19

https://doi.org/10.1186/s42397-019-0034-1

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0034-1

Abstracts of “3rd Sino-Pak ICICBB” Changji, China 4-9 September 2019

3rd Sino-Pak 2019.part01 3rd Sino-Pak 2019.part02 3rd Sino-Pak 2019.part03 3rd Sino-Pak 2019.part04 3rd Sino-Pak 2019.part05 3rd Sino-Pak 2019.part06 3rd Sino-Pak 2019.part07 3rd Sino-Pak 2019.part08 3rd Sino-Pak 2019.part09 3rd Sino-Pak 2019.part10 3rd Sino-Pak 2019.part11 3rd Sino-Pak 2019.part12 3rd Sino-Pak 2019.part13 3rd Sino-Pak 2019.part14 3rd Sino-Pak 2019.part15 3rd Sino-Pak 2019.part16

High-throughput phenotyping in cotton: a review

Abstract

Recent technological advances in cotton (Gossypium hirsutum L.) phenotyping have offered tools to improve the efficiency of data collection and analysis. High-throughput phenotyping (HTP) is a non-destructive and rapid approach of monitoring and measuring multiple phenotypic traits related to the growth, yield, and adaptation to biotic or abiotic stress. Researchers have conducted extensive experiments on HTP and developed techniques including spectral, fluorescence, thermal, and three-dimensional imaging to measure the morphological, physiological, and pathological resistance traits of cotton. In addition, ground-based and aerial-based platforms were also developed to aid in the implementation of these HTP systems. This review paper highlights the techniques and recent developments for HTP in cotton, reviews the potential applications according to morphological and physiological traits of cotton, and compares the advantages and limitations of these HTP systems when used in cotton cropping systems. Overall, the use of HTP has generated many opportunities to accurately and efficiently measure and analyze diverse traits of cotton. However, because of its relative novelty, HTP has some limitations that constrains the ability to take full advantage of what it can offer. These challenges need to be addressed to increase the accuracy and utility of HTP, which can be done by integrating analytical techniques for big data and continuous advances in imaging.

Authors:

PABUAYON Irish Lorraine B., SUN Yazhou, GUO Wenxuan & RITCHIE  Glen L.

 

Journal of Cotton Research2019; 2:18

https://doi.org/10.1186/s42397-019-0035-0

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0035-0

Identification and Functional Analysis of Betv1 in Three D Genome-containing Wild Cotton Varieties

Abstract:

[Objective] By analyzing the major birch pollen allergen Betv1 gene family in D genomes of cotton and comparing the expression patterns of three diploid D-genome cotton varieties with different Verticillium wilt resistance levels, we aimed to provide a theoretical basis for further studies on the role of Betv1 genes in cotton resistant to Verticillium wilt. [Method] The Betv1 genes were identified, and a bioinformatics analysis of the physicochemical properties of their encoded sequences in Gossypium raimondii (D5) was performed. The transcriptome sequencing and quantitative real time-PCR of G. raimondii (D5), Gossypium trilobum (D8) and Gossypium thurberi (D1) were used to verify the expression patterns of Bet v 1 genes under Verticillium dahlia infection stress. Betv1 genes were silenced by virus-induced gene silencing in G. hirsutum to identify their functions. [Result] The D genome of cotton contains 59 members, 58 of which have introns and are distributed on eight chromosomes, and most encode hydrophilic proteins that localize to the cytoplasm. The expression levels of Betv1 genes in three wild cotton species having D genomes after being inoculated with V. dahliae were consistent with their disease resistance levels. The genes were separated into three groups based on their expression levels. Genes of Group 3 responded to V. dahliae infection and were highly expressed in disease-resistant cotton species G. thurberi. This indicated that Group 3 genes may be involved in the immune response of Verticillium wilt. A gene with a high expression level was screened out of Group 3. A corresponding homologous gene was silenced in G. hirsutum by virus-induced gene silencing, and gene-silenced plants were more susceptible to V. dahliae, indicating that the gene plays a positive regulatory role in the progress of Verticillium wilt resistance in cotton. [Conclusion] The Betv1 genes act in response to V. dahliae infection and are critical in cotton resistance to Verticillium wilt. The information obtained provides a basis for further studies of the cotton Bet v 1 family genes and their functions.

Key words: wild cotton; Verticillium wilt; Betv1 gene; transcriptome; quantitative real time-PCR (qRT-PCR); virus-induced gene silencing (VIGS)

Cotton Science. 2019, 31(5):361-380.

https://doi.org/10.11963/1002-7807.dqmzy.20190723