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!

Extrafloral nectary–the sleeping beauty of plant science

Journal of Cotton Research

Abstract: Cotton is one of the most important cash crops, its growth season coincides with a high incidence of diverse groups of pests, leading to heavy use of pesticides. Recent identification of a signaling protein as a candidate regulator of cotton extrafloral nectary provides a new insight into the formation of sophisticated defense mechanisms in plants.

[Title] Extrafloral nectary–the sleeping beauty of plant science

[Author] CHEN Xiaoya

https://doi.org/10.1186/s42397-020-00051-7

QTL mapping for plant height and fruit branch number based on RIL population of upland cotton

Journal of Cotton Research

[Background] Plant height (PH) and fruit branch number (FBN) are important traits for improving yield and mechanical harvesting of cotton. In order to identify genes of PH and FBN in cotton germplasms to develop superior cultivars, quantitative trait loci (QTLs) for these traits were detected based on the phenotypic evaluation data in nine environments across four locations and 4 years and a previously reported genetic linkage map of an recombinant inbred line (RIL) population of upland cotton.

[Results] In total, 53 QTLs of PH and FBN, were identified on 21 chromosomes of the cotton genome except chromosomes c02, c09-c11, and c22. For PH, 27 QTLs explaining 3.81%–8.54% proportions of phenotypic variance were identified on 18 chromosomes except c02, c08-c12, c15, and c22. For FBN, 26 QTLs explaining 3.23%–11.00% proportions of phenotypic variance were identified on 16 chromosomes except c02-c03, c06, c09-c11, c17, c22-c23, and c25. Eight QTLs were simultaneously identified in at least two environments. Three QTL clusters containing seven QTLs were identified on three chromosomes (c01, c18 and c21). Eleven QTLs were the same as previously reported ones, while the rest were newly identified.

[Conclusions] The QTLs and QTL clusters identified in the current study will be helpful to further understand the genetic mechanism of PH and FBN development of cotton and will enhance the development of excellent cultivars for mechanical managements in cotton production.

[Title] QTL mapping for plant height and fruit branch number based on RIL population of upland cotton

[Authors] LIU Ruixian, XIAO Xianghui, GONG Juwu, LI Junwen, ZHANG Zhen, LIU Aiying, LU Quanwei, SHANG Haihong, SHI Yuzhen, GE Qun, IQBAL Muhammad Sajid, CHEN Quanjia, YUAN Youlu & GONG Wankui

https://doi.org/10.1186/s42397-020-0046-x

https://rdcu.be/b2bT3

The GhREV transcription factor regulate the development of shoot apical meristem in cotton (Gossypium hirsutum)

Journal of Cotton Research

[Background] Manual topping is a routine agronomic practice for balancing the vegetative and reproductive growth of cotton (Gossypium hirsutum) in China, but its cost-effectiveness has decreased over time. Therefore, there is an urgent need to replace manual topping with new approaches, such as biological topping. In this study, we examined the function of GhREV transcription factors (a class III homeodomain-leucine zipper family, HD-ZIP III) in regulating the development of shoot apical meristem (SAM) in cotton with the purpose of providing candidate genes for biological topping of cotton in the future.

[Results] We cloned four orthologous genes of AtREV in cotton, namely GhREV1GhREV2GhREV3, and GhREV4. All the GhREVs expressed in roots, stem, leaves, and SAM. Compared with GhREV1 and GhREV3, the expression level of GhREV2 and GhREV4 was higher in the SAM. However, only GhREV2 had transcriptional activity. GhREV2 is localized in the nucleus; and silencing it via virus-induced gene silencing (VIGS) produced an abnormal SAM. Two key genes, GhWUSA10 and GhSTM, which involved in regulating the development of plant SAM, showed about 50% reduction in their transcripts in VIGS-GhREV2 plants.

[Conclusion] GhREV2 positively regulates the development of cotton SAM by regulating GhWUSA10 and GhSTM potentially.

[Title] The GhREV transcription factor regulate the development of shoot apical meristem in cotton (Gossypium hirsutum)

[Authors] YANG Doudou, AN Jing, LI Fangjun, ENEJI A. Agrinya, TIAN Xiaoli & LI Zhaohu

https://doi.org/10.1186/s42397-020-0045-y

https://rdcu.be/b18jh

Identification of QTLs and candidate genes for physiological traits associated with drought tolerance in cotton

Journal of Cotton Research

[Background] Cotton is mainly grown for its natural fiber and edible oil. The fiber obtained from cotton is the indispensable raw material for the textile industries. The ever changing climatic condition, threatens cotton production due to a lack of sufficient water for its cultivation. Effects of drought stress are estimated to affect more than 50% of the cotton growing regions. To elucidate the drought tolerance phenomenon in cotton, a backcross population was developed from G. tomentosum, a drought tolerant donor parent and G. hirsutum which is highly susceptible to drought stress.

[Results] A genetic map of 10 888 SNP markers was developed from 200 BC2F2 populations. The map spanned 4 191.3 centi-Morgan (cM), with an average distance of 0.104 7 cM, covering 51% and 49% of At and Dt sub genomes, respectively. Thirty stable Quantitative trait loci (QTLs) were detected, in which more than a half were detected in the At subgenome. Eighty-nine candidate genes were mined within the QTL regions for three traits: cell membrane stability (CMS), saturated leaf weight (SLW) and chlorophyll content. The genes had varied physiochemical properties. A majority of the genes were interrupted by introns, and only 15 genes were intronless, accounting for 17% of the mined genes. The genes were found to be involved molecular function (MF), cellular component (CC) and biological process (BP), which are the main gene ontological (GO) functions. A number of miRNAs were detected, such as miR164, which is associated with NAC and MYB genes, with a profound role in enhancing drought tolerance in plants. Through RT-qPCR analysis, 5 genes were found to be the key genes involved in enhancing drought tolerance in cotton. Wild cotton harbors a number of favorable alleles, which can be exploited to aid in improving the narrow genetic base of the elite cotton cultivars. The detection of 30 stable QTLs and 89 candidate genes found to be contributed by the donor parent, G. tomentosum, showed the significant genes harbored by the wild progenitors which can be exploited in developing more robust cotton genotypes with diverse tolerance levels to various environmental stresses.

[Conclusion] This was the first study involving genome wide association mapping for drought tolerance traits in semi wild cotton genotypes. It offers an opportunity for future exploration of these genes in developing highly tolerant cotton cultivars to boost cotton production.

[Title] Identification of QTLs and candidate genes for physiological traits associated with drought tolerance in cotton

[Authors] MAGWANGA Richard Odongo, LU Pu, KIRUNGU Joy Nyangasi, CAI Xiaoyan, ZHOU Zhongli, AGONG Stephen Gaya, WANG Kunbo & LIU Fang

https://doi.org/10.1186/s42397-020-0043-0

https://rdcu.be/b1502

Transient expression of SbDhr2 and MeHNL in Gossypium hirsutum for herbivore deterrence assay with Spodoptera litura

Journal of Cotton Research

[Background] Spodoptera litura (Lepidoptera: Noctuidae), commonly known as tobacco cutworm or cotton leafworm, is a polyphagous pest which causes considerable damage to cotton (Gossypium hirsutum) and other crops. Herbivore-induced defence response is activated in plants against chewing pests, in which plant secondary metabolites play an important role. Dhurrinase2 (SbDhr2), a cyanogenic β-glucosidase from Sorghum bicolor, is the key enzyme responsible for the hydrolysis of dhurrin (cyanogenic β-glucosidic substrate) to p-hydroxymandelonitrile. Hydroxynitrile lyase (MeHNL) from Mannihot esculanta catalyses the dissociation of cyanohydrins to hydrogen cyanide and corresponding carbonyl compound, both enzymes play a pivotal role in plant defence mechanism.

[Results] SbDhr2 and MeHNL genes were expressed individually and co-expressed transiently in cotton leaves. We examined the feeding response of S. litura to leaves in the choice assay. The Slitura population used in this study showed better feeding deterrence to leaves co-expressing both genes compared with the expression of an individual gene.

[Conclusion] Our results suggest that co-expression of SbDhr2 and MeHNL genes in cotton leaves demonstrate feeding deterrence to S. litura. Engineering cyanogenic pathway in aerial parts of cotton would be an additional defence strategy against generalist pests and can be enhanced against specialist pests.

[Title] Transient expression of SbDhr2 and MeHNL in Gossypium hirsutum for herbivore deterrence assay with Spodoptera litura

[Authors] MAHAJAN Chavi, NASER Rafiuddin & GUPTA Shantikumar

https://doi.org/10.1186/s42397-020-0044-z

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-020-0044-z

Soil replacement combined with subsoiling improves cotton yields

[Background] Long-term rotary tillage has led to the deterioration of cotton production in northern China. This deterioration is due to the disturbance of topsoil, a dense plough pan at the 20–50 cm depth, and the decreased water storage capacity. A 2-yr field experiment was performed from 2014 to 2015 to explore a feasible soil tillage approach to halting the deterioration. The experiment consisted of four treatments: replacing the topsoil from the 0–15 cm layer with the subsoil from the 15–30 cm layer (T1); replacing the topsoil from the 0–20 cm layer with the subsoil from the 20–40 cm layer and subsoiling at the 40–55 cm layer (T2); replacing the topsoil from the 0–20 cm layer with the subsoil from the 20–40 cm layer and subsoiling at the 40–70 cm layer (T3); and conventional surface rotary tillage within 15 cm as the control (CK).

[Results] The results indicated that the soil bulk densities at the 20–40 cm layer in T2 were 0.13 g·cm− 3and 0.15 g·cm− 3 lower than those obtained from CK in 2014 and 2015, respectively. The total nitrogen (N) and the available phosphorus (P) and potassium (K) contents from the 20–40 cm layer in T2 and T3 were significantly higher than those in CK and T1. The amount of soil water stored in the 0–40 cm layer of T2 at the squaring stage of cotton was 15.3 mm and 13.4 mm greater than that in CK in 2014 and 2015, respectively, when the weather was dry. Compared with CK, T2 increased cotton lint yield by 6.1 and 10.2 percentage points in 2014 and 2015, respectively, which was due to the improved roots within the 20–60 cm layer, the greater number of bolls per plant and the higher boll weight in the T2 treatment.

[Conclusions] The results suggested that soil replacement plus subsoiling would be a good alternative to current practices in order to break through the bottleneck constraining cotton production in northern China. Replacing the topsoil in the 0–20 cm layer with the soil from the 20–40 cm layer plus subsoiling at the 40–55 cm layer would be the most effective method.

[Title] Soil replacement combined with subsoiling improves cotton yields

[Authors] LI Pengcheng, WANG Shulin, QI Hong, WANG Yan, ZHANG Qian, FENG Guoyi, ZHENG Cangsong, YU Xueke, LIN Yongzeng & DONG Helin

Journal of Cotton Research2019; 2:25

https://doi.org/10.1186/s42397-019-0038-x

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0038-x

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

https://doi.org/10.1186/s42397-019-0040-3

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0040-3

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

https://doi.org/10.1186/s42397-019-0042-1

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0042-1

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

https://doi.org/10.1186/s42397-019-0041-2

https://jcottonres.biomedcentral.com/articles/10.1186/s42397-019-0041-2

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