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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.
PABUAYON Irish Lorraine B., SUN Yazhou, GUO Wenxuan & RITCHIE Glen L.
Journal of Cotton Research. 2019; 2:18
[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.
Aphis gossypii is a worldwide sap-sucking pest with a variety of hosts and a vector of more than 50 plant viruses. The strategy of wing polyphenism, mostly resulting from population density increasing, contributes to the evolutionary success of this pest. However, the related molecular basis remains unclear. Here, we identified the effects of postnatal crowding on wing morph determination in cotton aphid, and examined the transcriptomic differences between wingless and wing morphs.
Effect of postnatal crowding on wing determination in A. gossypii was evaluated firstly. Under the density of 5 nymphs·cm− 2, no wing aphids appeared. Proportion of wing morphs rised with the increase of density in a certain extent, and peaked to 56.1% at the density of 20 nymphs·cm− 2, and reduced afterwards. Then, transcriptomes of wingless and wing morphs were assembled and annotated separately to identify potentially exclusively or differentially expressed transcripts between these two morphs, in which 3 126 and 3 392 unigenes annotated in Nr (Non-redundant protein sequence) database were found in wingless or wing morphs exclusively. Moreover, 3 187 up- and 1 880 down-regulated genes were identified in wing versus wingless aphid. Pathways analysis suggested the involvement of differentially expressed genes in multiple cellular signaling pathways involved in wing morphs determination, including lipid catabolic and metabolism, insulin, ecdysone and juvenile hormone biosynthesis. The expression levels of related genes were validated by the reverse transcription quantitative real time polymerase chain reaction (RT-qPCR) soon afterwards.
The present study identified the effects of postnatal crowding on wing morphs induction and demonstrated that the critical population density for wing morphs formation in A. gossypii was 20 nymphs·cm− 2. Comparative transcriptome analysis provides transcripts potentially expressed exclusively in wingless or wing morph, respectively. Differentially expressed genes between wingless and wing morphs were identified and several signaling pathways potentially involved in cotton aphid wing differentiation were obtained.
JI Jichao, ZHANG Shuai, LUO Junyu, WANG Li, ZHU Xiangzhen, ZHANG Kaixin, ZHANG Lijuan & CUI Jinjie
Journal of Cotton Research. 2019,2:17
[Background] DNA methylation is an important epigenetic factor that maintains and regulates gene expression. The mode and level of DNA methylation depend on the roles of DNA methyltransferase and demethylase, while DNA demethylase plays a key role in the process of DNA demethylation. The results showed that the plant’s DNA demethylase all contained conserved DNA glycosidase domain. This study identified the cotton DNA demethylase gene family and analyzed it using bioinformatics methods to lay the foundation for further study of cotton demethylase gene function.
[Results] This study used genomic information from diploid Gossypium raimondii JGI (D), Gossypium arboreum L. CRI (A), Gossypium hirsutum L. JGI (AD1) and Gossypium barbadebse L. NAU (AD2) to Arabidopsis thaliana. Using DNA demethylase genes sequence of Arabidopsis as reference, 25 DNA demethylase genes were identified in cotton by BLAST analysis. There are 4 genes in the genome D, 5 genes in the genome A, 10 genes in the genome AD1, and 6 genes in the genome AD2. The gene structure and evolution were analyzed by bioinformatics, and the expression patterns of DNA demethylase gene family in Gossypium hirsutum L. were analyzed. From the phylogenetic tree analysis, the DNA demethylase gene family of cotton can be divided into four subfamilies: REPRESSOR of SILENCING 1 (ROS1), DEMETER (DME), DEMETER-LIKE 2 (DML2), and DEMETER-LIKE3 (DML3). The sequence similarity of DNA demethylase genes in the same species was higher, and the genetic relationship was also relatively close. Analysis of the gene structure revealed that the DNA demethylase gene family members of the four subfamilies varied greatly. Among them, the number of introns of ROS1 and DME subfamily was larger, and the gene structure was more complex. For the analysis of the conserved domain, it was known that the DNA demethylase family gene member has an endonuclease III (ENDO3c) domain.
[Conclusions] The genes of the DNA demethylase family are distributed differently in different cotton species, and the gene structure is very different. High expression of ROS1 genes in cotton were under abiotic stress. The expression levels of ROS1 genes were higher during the formation of cotton ovule. The transcription levels of ROS1 family genes were higher during cotton fiber development.
[Title]Genome-wide identification and expression analysis of DNA demethylase family in cotton
[Authors] YANG Xiaomin, LU Xuke, CHEN Xiugui, WANG Delong, WANG Junjuan, WANG Shuai, GUO Lixue, CHEN Chao, WANG Xiaoge, WANG Xinlei & YE Wuwei *
Journal of Cotton Research. 2019, 2: 16
[Background] Soil salinity seriously affects cotton growth, leading to the reduction of yield and fiber quality. Recently, genetic engineering has become an efficient tool to increase abiotic stress tolerance in crops.
[Results] In this study, isopentyl transferase (IPT), a key enzyme involved in cytokinin (CTK) biosynthesis from Agrobacterium tumefaciens, was selected to generate transgenic cotton via Agrobacterium-mediated transformation. A senescence-inducible SAG12promoter from Arabidopsis was fused with the IPT gene. Ectopic-expression of SAG12::IPT significantly promoted seed germination or seedling tolerance to salt stress. Two IPTtransgenic lines, OE3 as a tolerant line during seed germination, and OE8 as a tolerant line at seedling stage, were selected for further physiological analysis. The data showed that ectopic-expression of SAG12::IPT induced the accumulation of CTKs not only in leaves and roots, but also in germinating seeds. Moreover, ectopic-expressing IPT increased the activity of antioxidant enzymes, which was associated with the less reactive oxygen species (ROS) accumulation compared with control plants. Also, ectopic-expression of IPT produced higher K+/Na+ ratio in cotton shoot and root.
[Conclusions] The senescence-induced CTK accumulation in cotton seeds and seedlings positively regulates salt stress partially by elevating ROS scavenging capability.
[Title] An isopentyl transferase gene driven by the senescence-inducible SAG12 promoter improves salinity stress tolerance in cotton
[Authors] SHAN Yi, ZHAO Peng, LIU Zhao, LI Fangjun* & TIAN Xiaoli
Journal of Cotton Research. 2019, 2: 15
07 October 2019 has been announced as World Cotton Day by WTO. Cotton community will celebrate this day across the globe. The WTO Secretariat is organizing the event at WTO Headquarters Geneva in collaboration with the Secretariats of the United Nations Food and Agriculture Organization (FAO), the United Nations Conference on Trade and Development (UNCTAD), the International Trade Centre (ITC) and the International Cotton Advisory Committee (ICAC). This event stems from the Cotton-4’s official application for the recognition of a World Cotton Day by the United Nations General Assembly, reflecting the importance of cotton as a global commodity.