Unraveling the puzzle of the origin and evolution of cotton A-genome

[Abstract] Gossypium hirsutum, the most widely planted cotton species, its evolution has long been an unsolved puzzle because of its hybrid origin from D-genome and A-genome species. To better understand the genetic component of cotton, Huang et al. recently sequenced and assembled the first A1-genome G. herbaceum, and updated the A2-genome G. arboreum and (AD)1-genome G. hirsutum. On the basis of the three reference genomes, they resolved existing controversial concepts and provided novel evolutionary insights surrounding the A-genome.

[Title] Unraveling the puzzle of the origin and evolution of cotton A-genome

[Authors] MA Zhiying

Journal of Cotton Research 3, Article number: 17 (2020)

https://doi.org/10.1186/s42397-020-00056-2

Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway

Journal of Cotton Research

[Background] Verticillium wilt, caused by the soil-borne fungus of Verticillium dahliae Kleb., is one of the most devastating diseases of cotton. The complex mechanism underlying cotton resistance to Verticillium wilt remains uncharacterized. Identifying an endogenous resistance gene may be helpful to control this disease. Previous studies revealed that succinate dehydrogenase (SDH) is involved in reactive oxygen species (ROS)-induced stress signaling pathway that is likely to be triggered by salicylic acid (SA). Here, through the metabolomics and differential expression analyses in wilt-inoculated cotton (Gossypium hirsutum), we noticed that GhSDH1–1gene in cotton may play an important role in the resistance to V. dahlia. Then we reported GhSDH1–1 gene and its functional analysis in relation to the resistance of cotton to V. dahliae.

[Results] The GhSDH1–1 gene in cotton root was significantly up-regulated after V. dahlia inoculation, and its expression level peaked at 12 and 24 h post-infection. SA can also induce the up-regulation of GhSDH1–1. Additionally, the functional analysis showed that GhSDH1–1-silenced cotton was more susceptible to V. dahliae than the control because of the significant decrease in abundance of immune-related molecules and severe damage to the SA-signaling pathway. In Arabidopsis thaliana, high expression of GhSDH1–1 conferred high resistance to V. dahliaeArabidopsis that overexpressed GhSDH1–1 had higher resistance to V. dahliae infection compared with the wild-type.

[Conclusions] Our findings provide new insights into the role of GhSDH1–1; it positively regulates cotton resistance to Verticillium wilt. The regulatory mechanism of GhSDH1–1 is closely related to SA-related signaling pathway.

[Title] Succinate dehydrogenase SDH1–1 positively regulates cotton resistance to Verticillium dahliae through a salicylic acid pathway
[Authors] ZHANG Xiangyue, FENG Zili, ZHAO Lihong, LIU Shichao, WEI Feng, SHI Yongqiang, FENG Hongjie & ZHU Heqin

https://doi.org/10.1186/s42397-020-00052-6

GbAt11 gene cloned from Gossypium barbadense mediates resistance to Verticillium wilt in Gossypium hirsutum

Journal of Cotton Research

[Background] Gossypium hirsutum is highly susceptible to Verticillium wilt, and once infected Verticillium wilt, its yield is greatly reduced. But G. barbadense is highly resistant to Verticillium wilt. It is possible that transferring some disease-resistant genes from G. barbadense to G. hirsutummay contribute to G. hirsutum resistance to Verticillium wilt.

[Results] Here, we described a new gene in G. barbadense encoding AXMN Toxin Induced Protein-11, GbAt11, which is specifically induced by Verticillium dahliae in G. barbadense and enhances Verticillium wilt resistance in G. hirsutum. Overexpression in G. hirsutum not only significantly improves resistance to Verticillium wilt, but also increases the boll number per plant. Transcriptome analysis and real-time polymerase chain reaction showed that GbAt11overexpression can simultaneously activate FLS2BAK1 and other genes, which are involved in ETI and PTI pathways in G. hirsutum.

[Conclusions] These data suggest that GbAt11 plays a very important role in resistance to Verticillium wilt in cotton. And it is significant for improving resistance to Verticillium wilt and breeding high-yield cotton cultivars.

[Title] GbAt11 gene cloned from Gossypium barbadense mediates resistance to Verticillium wilt in Gossypium hirsutum

[Authors] QIU Tingting, WANG Yanjun, JIANG Juan, ZHAO Jia, WANG Yanqing & QI Junsheng

https://doi.org/10.1186/s42397-020-00047-3

Towards complete deconstruction of cotton transcriptional landscape

Journal of Cotton Research

Abstract: Recently, Wang et al. systematically explored the transcription landscape in diploid cotton Gossypium arboreum. In the study, they integrated four high-throughput sequencing techniques, including Pacbio sequencing, strand-specific RNA sequencing (ssRNA-seq), Cap analysis gene expression sequencing (CAGE-seq), and PolyA sequencing (PolyA-seq) to profile the RNA transcriptome of G. arboreum. They developed a pipeline, IGIA to construct accurate gene structure annotation based on the updated genome of G. arboreum and the multi-strategic RNA-seq data. Their study revealed some intriguing phenomena and potential novel mechanisms in the regulation of RNA transcription in plants, and also provided valuable resources for further functional genomic research in cotton.

[Title] Towards complete deconstruction of cotton transcriptional landscape

[Author] LI Fuguang

https://doi.org/10.1186/s42397-020-00050-8

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

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.