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R1. Cotton Germplasm Innovation and Breeding

Coordinator: Xianlong Zhang; Yichun Nie; Xiaoping Guo; Longfu Zhu; Zhongxu Lin 


Current Research Activities

Germplasm Innovation and Evaluation: Germplasm is the basis of plant breeding. In order to broaden the narrow genetic basis of upland cotton, chromosome segment substitution lines (CSSLs) were developed via crossing and backcrossing upland cotton with other tetraploid cotton species and marker assisted selection. Presently, we have developed 336G. barbadense CSSLs, 1300G. darwinii CSSLs, 550G. mustelinum CSSLs, and 54G. tomentosum CSSLs. These CSSLs are being applied in cotton genetics and breeding. More genes with important roles in cotton yield, fiber qulity or biotic/abiotic stress resistance have been introduced in breeding germplasms and evaluated in field for cotton

Cotton Breeding: Cottoncultivar, selected by traditional and modern biotechnology, are the application form of genetics and breeding. To meet production demands in future, whole coordination in yield, fiber quality and stress tolerance is focused in cotton breeding with the abundant gremplasm. Totally, there are 6cultivarauthorized by China government, including ‘Huazamian 1’, ‘Huazamian 2’, ‘Huahui 103’, ‘Huazamian 4’, ‘Huazamian H318’ and ‘Huamian 3109’. The ‘Huazamian 2’ is suitable in Yellow River Basin cotton-growing areas; and the other five varieties are widely applied in Yangtze River Basin cotton-growing areas.Among them, ‘Huazamian H318’, a new cotton cultivar developed by Prof. Xianlong Zhang and Prof. Yichun Nie, is ranking first in national cotton regional trial with high yield, good fiber quality, feature easy growth, early maturity, and more resistance to biotic and abiotic stresses.‘Huazamian H318’ has been widely applied in Yangtze River Basin cotton-growing areasand achieved remarkable economic and social benefits.


The Second Class National Award of Scientific and Technological Progress in China (2013)

The First Class Provincial Award of Scientific and Technological Progress in Hubei province (2012)

The Second Class Provincial Award of Technological Innovation in Hubei province (2008)

Varieties authorized by Chinese government

‘Huamian 3109’ (2014);

‘Hua Zamian H318’ (2009);

‘Hua Zamian 4’ (2009);

‘Hua Hui 103’ (2006);

‘Hua Zamian 1’ (2005);

‘Hua Zamian 2’ (2005);


R2. Germplasm and Molecular Quantitative Genetics

Coordinator: Zhongxu Lin

Current Research Activities

Molecular markers and germplasms development; high-density linkage maps construction, QTL mapping and cloning

Research Highlight

Molecular Marker development: We firstly applied SRAP markers and applied them in cotton; we have developed nearly 4000 EST-SSRs fromGossypium barbadense,G. hirsutum,G. arboretum,G. ramondii, andG. herbaceum, which account for about 1/4 of total SSRs in the world. In recent years, we focus on developing functional markers (FMs) in cotton. We have developed FMs for cellulose synthase genes, which have been proved to have similar discriminability as SSRs. We developed FMs from genes specifically or preferentially expressed during fiber development, some of which are associated with fiber quality by QTL mapping. IP and IDP markers were developed based on cotton coding sequences, which are effective in genetic map construction. FMs were developed for miRNAs and their targets to view their genomic distribution and their expression pattern were characterized during fiber development.

Genetic linkage map construction and QTL mapping: With the help of the markers developed in our lab and other researchers worldwide, a high-density interspecific genetic map was constructed (1st generation: nearly 1000 loci; 2nd generation: more than 2000 loci; and 3rd generation: more than 5000 loci). This map has been effectively applied in genomic structure explanation, general QTL mapping, QTL fine mapping, and introgression lines development by MAS. An intraspecific linkage map of upland cotton with 1013 loci was also constructed to map QTLs for yield and fiber related traits.

Representative Publications

Ren G F, Li X M, Lin Z X*. (2014).Mining, genetic mapping and expression analysis of EST-derived resistance gene homologs (RGHs) in cotton. BMC Plant Biology. 14: 203

ChenX M, GaoW H, ZhangJ F, ZhangX L,LinZ X*. (2013).Linkage mapping and expression analysis of miRNAs and their target genes during fiber development in cotton.BMC Genomics.14: 706.

Li XM, Yuan DJ, Zhang JF, Lin ZX*, Zhang XL. (2013).Genetic Mapping and Characteristics of Genes Specifically or Preferentially Expressed during Fiber Development in Cotton.PLoSOne.8(1): e54444.

Wang B, Nie Y C, Lin Z X*, Zhang X L, Liu J J,Bai J. (2012).Molecular diversity, genomic constitution, and QTL mapping
of fiber quality by mapped SSRs in introgression lines derived fromGossypium hirsutum × G. darwinii Watt.Theor Appl Genet.125:1263-1274.

Yu Y, Yuan DJ, Liang SG, Li XM, Wang XQ,Lin ZX*, Zhang XL. (2011).Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1population betweenGossypium hirsutumandG. barbadense.BMC Genomics. 12: 15.  

R3. Cotton Fiber Development

Coordinator: Lili Tu

Current Research Activities

Elucidating the mechanism of cotton fiber development and cloning genes related to high quality fiber.

Research Highlight

Ca2+/CaM signal and fiber elongation: Overexpressing GhCaM7 promoted early fiber elongation. GhCaM7 overexpression increased ROSlevels, while GhCaM7 RNAi reduced ROS levels. H2O2 enhances Ca2+ influx into the fiber and feedback regulates the expression of GhCaM7. GhCaM7 could be a molecular link between Ca2+and ROS signal pathways.

Flavonoids metabolic pathways and fiber development: Flavonoid, NAR, could obviously retard fiber development during ovule culture. Silencing the F3H gene significantly increased the NAR content and suppressed fiber development. More serious retardation of fiber growth was observed after the introduction of the F3H-RNAi segment into the high-flavonoid brown fiber cotton T586 line.

Hormones, transcription factors and miRNA regulatory networks: Peptide hormone, PSK, could enhance fiber elongation in ovule culture. Overexpression of GhPSK resulted in longer and finer fibers. RNAi silencing of the transcript factorGbTCPproduced shorter fiber and a reduced lint percentage. GbTCPcould positively regulate the level of JA and activate downstream genes necessary for elongation of fibers. Suppressing miRNA156/157 resulted in shorter fiber.

Cell wall proteins and Secondary cell wall synthesis: A novel truncated α-expansin, GbEXPATR, was found to be specifically expressed at the fiber elongation stage inG. barbadense, and had a strong effect on cell elongation through delaying secondary cell wall synthesis and, as a
result, enhanced fiber length, fineness and strength.

Representative Publications

Liu N, Tu L L, Tang W X, Gao W H, Lindsey K, Zhang X L*. (2014). Small RNA and degradome profiling reveals a role for miRNAs and their targets in the developing fibers ofGossypium barbadense.Plant J. doi: 10.1111/tpj.12636.

Han J, Tan J F, Tu L L*, Zhang X L. (2014). A peptide hormone gene, GhPSK promotes fiber elongation and contributes to longer and finer cotton fiber,Plant Biotechnol J. 12: 861-871.

Tang W X, Tu L L*, Yang X Y, Tan J F, Deng F L, Hao J, Guo K, Lindsey K, Zhang X L*. (2014). The calcium sensor GhCaM7 promotes cotton fiber elongation by modulating ROS production, New Phytol. 202: 509-520.

Tan J F, Tu L L, Deng F L, Hu H Y, Nie Y C, Zhang X L*. (2013). A Genetic and Metabolic Analysis Revealed that Cotton Fiber Cell Development Was Retarded by Flavonoid Naringenin,Plant Physiol. 162: 86-95.

Hao J, Tu L L, Hu H Y, Tan J F, Deng F L, Tang W X, Nie Y C and Zhang X L*. (2012).GbTCP, a cotton TCP transcription factor, confers fibre elongation and root hair development by a complex regulating system.J Exp Bot. 63: 6267-6281. 


R4. Disease Resistance of Cotton

Coordinator: Longfu Zhu

Current Research Activities

Verticillium wilt caused byVerticillium dahliaeis the most devastating disease for cotton (Gossypium hirsutum) production in China. Our group is interested in elucidating plant immune signaling pathways and virulence factors from fungus involved in cotton-V. dahliaeinteraction through cellular, functional genomic, genetic, biochemical and bioinformatic approaches with the resistant germplasm ‘7124’ (G. barbadense) and the high aggressive strain ‘V991’. In addition, plant immunity is inextricably linked with plant development and environmental stresses. We are also interested inunderstanding the signaling crosstalk that orchestrates plant development and immune response. Ultimately, knowledge gained from fundamental research will be applied to improve cotton resistance toVerticilliumwilt and other biotic/abioticstresses.

Representative Publications

Sun L Q, Zhu L F, Xu L, Yuan D J, Min L, Zhang X L*. (2014).Cotton Cytochrome P450CYP82D regulates systemic cell death by modulating the octadecanoid pathway.Nature Communication.Accepted article.

Li C, He X, Luo X Y, Xu L, Liu L L, Min L, Jin L, Zhu L F*, Zhang X L. (2014).GbWRKY1mediates plant defense-to-development transition during infection of Verticillium dahliae by activating JAZ1 expression. Plant Physiology, Provisional Acceptance/Under Revision.

Xu L, Zhang W, He X, Liu M, Zhang K, Shaban M, Sun L Q, Zhu J C, Luo Y J, Yuan D J, Zhang X L, and Zhu L F*. (2014).
Functional characterization of cotton genes responsive to Verticillium dahliaethrough bioinformatics and reverse genetics
strategies. J Exp Bot. Accepted article.

Liu L L, Zhang W W, Zhou Y, Miao Y H, Xu L, Liu M, Zhang K, Zhang X L, Zhu L F*. (2014). The resistance of cotton and tomato to Verticillium dahliaefrom cotton is independent on Ve1. Scientia Sinica Vitae. 44: 803-814.

Gao W, Long L, Zhu L F*, Xu L, Gao W H, Sun L Q, Liu L L, and Zhang X L*. (2013). Proteomic and virus-induced gene silencing (VIGS) analyses reveal that gossypol, brassinosteroids, and jasmonic acid contribute to the resistance of cottontoVerticillium dahliae. Mol Cell Proteomics. 12: 3690-3703.

Xu L, Jin L, Long L, Liu L L, He X, Gao W, Zhu L F*, Zhang X L. (2012). Overexpression of GbWRKY1 positively regulates the Pi starvation response by alteration of auxin sensitivity in Arabidopsis. Plant Cell Rep. 31(12): 2177-2188.

Xu L, Zhu L F, Tu L L, Liu L L, Yuan D J, Jin L, Long L, and Zhang X L*. (2011). Lignin metabolism has a central role in the resistance of cotton to the wilt fungus Verticillium dahliaeas revealed by RNA-Seq-dependent transcriptional analysis and histochemistry. J Exp Bot. 62: 5607-5621.

Xu L, Zhu L F, Tu L L, Guo X P, Long L, Sun L Q, Gao W, Zhang X L. (2011).Differential Gene Expression in Cotton Defence Response to Verticillium dahliaeby SSH. Journal of Phytopathology.159: 606-615.


R5. Stress Resistance of Cotton

Coordinator: Longfu Zhu; Xiyan Yang 

Current research activities

Molecular mechanism ofresistance todrought stress in cotton

Molecular mechanism oftolerancetohigh/low-temperature stress in cotton

Balance regulation of plant development and stress resistance 

Research Highlight

Using transcriptome analysis of Gossypium hirsutum ‘84021’ (HT-tolerance) and ‘H05’ (HT-sensitive) anthers responsive to HT stress, sugar and auxin signaling pathways were considered to respond to HT stress during anther development. Furthermore, HT induced expression of GhCKI in ‘H05’, coupled with the suppression of starch synthase activity, decreases in the glucose level during anther development, and increases in the indole-3-acetic acid (IAA) level in late-stage anthers. Moreover, PIFs, which are involved in linking sugar and auxin and are regulated by sugar, might positively regulate IAA biosynthesis in the cotton anther response to HT. Additionally, exogenous IAA application revealed that high background IAA may be a disadvantage for late-stage cotton anthers during HT stress. Overall, the linking of HT, sugar, PIFs, and IAA, together withGhCKI, may provide dynamic coordination of plant anther responses
to HT stress. 

Representative Publications

Min L, Li Y Y, Hu Q, Zhu L F, Gao W, Wu Y L, Ding Y H, Liu S M, Yang X Y, and Zhang X L*.(2014). Sugar and Auxin
Signaling Pathways Respond to High-Temperature Stress during Anther Development as Revealed by Transcript Profiling Analysis in Cotton. Plant Physiology. 164: 1293-1308. (Poster)

Long L, Gao W, Xu L, Liu M, Luo X, He X, Yang X Y, Zhang X L, and Zhu L F*. (2014). GbMPK3, a mitogen-activated protein kinase from cotton, enhances drought and oxidative stress tolerance in tobacco. Plant Cell Tiss Organ Cult. 116: 153-162.

Zhou T, Yang X Y*, Wang L C, Xu J, and Zhang X L. (2014). GhTZF1 regulates drought stress responses and delays leaf senescence by inhibiting reactive oxygen species accumulation in transgenic Arabidopsis. Plant Mol Biol.85: 163-77.
Liu G Z, Li X L, Jin S X, Liu X Y, Zhu L F, Nie Y C, Zhang X L*. (2014). Overexpression of Rice NAC Gene SNAC1 Improves Drought and Salt Tolerance by Enhancing Root Development and Reducing Transpiration Rate in Transgenic Cotton. PLoS One. 9(1):e86895.

Min L, Zhu L F*, Tu L L, Deng F L, Yuan D J, and Zhang X L*. (2013). Cotton GhCKI disrupts normal male reproduction by delaying tapetum programmed cell death via inactivating starch synthase. Plant J. 75: 823-835.

Xu L, Zahid K R, He L R, Zhang W W, He X, Zhang X L,Yang X Y, Zhu L F*. (2013). GhCAX3, a novel Ca2+/H+exchanger from cotton, confers regulation of cold response and ABA induced signal transduction. PLoS One. 8: e66303.

He L R, Yang X Y*, Wang L C, Zhu L F, Zhou T, Deng J W, Zhang X L. (2013).Molecular cloning and functional characterization of a novel cotton CBL-interacting protein kinase gene (GhCIPK6) reveals its involvement in multiple abiotic stress tolerance in transgenic plants. Biochem Bioph Res Co. 435(2): 209-215. 


R6. Cotton Genetic Engineering and Biotechnology

Coordinator: Xianlong Zhang; Xiyan Yang; Shuangxia Jin

Current research activities
Selection of high efficient regeneration varieties in cotton
Genetic transformation system in cotton

Construction of T-DNA insertion mutationlibrary
Molecular mechanism of somatic embryogenesis in cotton

Research Highlight

Usingembryogenic cell lines to understandthebalance regulation of plant development and resistance:In our study,duringasuitable stress treatment, the tendency of proliferation and differentiationindicatesthat embryogenic cellsarefaced with a fate choice: continue proliferating ordevelopinto embryos. The stress factors acted as selectors to regulate the balance between proliferation and differentiating to embryos.Despite attempts to create suitable cultures for somatic embryogenesis, the artificial culture is an abnormal process for in vitro plant cell. Those artificial and extreme conditions might result in stress response in cells that would provide diverse resources for stress tolerance research.

Representative Publications

Jin F Y, Hu L S, Yuan D J, Xu J, Gao WH, He L R, Yang X Y*, Zhang X L*.(2014).Comparative transcriptome analysis between somatic embryos (SEs) and zygotic embryos in cotton: evidence for stress response functions in SE development.Plant Biotechnol J.12:161-173.

Yang X Y†, Wang L C†, Yuan D J, Lindsey K, Zhang X L*. (2013).Small RNA and degradome sequencing reveal complex miRNA regulation during cotton somatic embryogenesis,JExpBot.64(6): 1521-1536.

YangX Y, ZhangX L*, YuanD J, JinF Y, ZhangY C,XuJ. (2012).Transcript profiling reveals complex auxin signalling pathway and transcription regulation involved in dedifferentiation and redifferentiation during somatic embryogenesis in cotton. BMC Plant Biol.110.

Liu G Z, Jin S X, Liu X Y, Tan J F, Yang X Y, Zhang X L*. (2012).Overexpression of Arabidopsis cyclin D2;1 in cotton results in leaf curling and other plant architectural modifications. Plant Cell Tiss Organ Cult.110(2): 261-273.

Jin S X, Liu G Z, Zhu H G, Yang X Y and Zhang X L. (2012). Transformation of Upland Cotton (Gossypium hirsutum L.) with gfp Gene as a Visual Marker .Journal of Integrative Agriculture. 11(6): 910-919.

Hu L S, Yang X Y, Yuan D J, Zeng F C, Zhang X L*. (2011).GhHmgB3 deficiency deregulates proliferation and differentiation of cells during somatic embryogenesis in cotton.Plant Biotechnol J.9: 1038-1048.

Yang X Y, Tu L L, Zhu L F, Fu L L, Ming L, Zhang X L*. (2008).Expression profile analysis of genes involved in cell wall regeneration during protoplast culture in cotton by suppression subtractive hybridization and macroarray.JExpBot.59:


R7. Pest Resistance of cotton/ Chloroplast /Mitochondria genomics

Coordinator: Shuangxia Jin

Research Interests:

1.Cotton & Tobacco: plastid genetic engineering;

2. Chloroplast /Mitochondria genomics and evaluation;

4. Insects (whitefly/aphid) and cotton host molecular interaction.

Research Highlight

The gene expression ofGossypium hirsutumcultivars ‘Z42’(whitefly-resitance) and ‘HY’ (whitefly-sensitive) were compared by transcriptome analysis when they infested by whitefly, several candidate insect resistant genes were indefiled and acomprehensive insect resistance mechanism was revealed.

Chloroplast genetic engineering in plant for insect resistance, salt /heavy metal tolerance and industrial enzyme production.

Representative Publications

Jin S X,Daniell H. (2014). Expression of γ-tocopherol methyltransferase in chloroplasts results in massive proliferation of the inner envelope membrane and decreases susceptibility to salt and metal-induced oxidative stress by reducingreactive oxygen species. Plant Biotech. J. doi:10.1111/pbi.12224.

Li L B, Zhu Y,Jin S X, Zhang X L. (2014) Pyramiding Btgenes for increasing resistance of cotton to two major lepidopteranPests:S. lituraandH.armigera. Acta Physiologiae Plantarum.Online.

Jin S X, Zhang X L, Daniell H. (2012)Pinellia ternataagglutinin expression in chloroplasts confers broad spectrum resistance against aphid, whitefly, lepidopteran insects, bacterial and viral pathogens. Plant Biotech J. 10(3): 313-327. (Cover Story).

Jin S X, Lange T, Daniell H. (2011). Release of Hormones from Conjugates: Chloroplast Expression of ß-glucosidaseResults in Elevated Phytohormone Levels Associated with Significant Increase in Biomass and Protection from Aphids or Whiteflies Conferred by Sucrose Esters. Plant Physiology. 155: 222-235.

Lee S B, Li B C,Jin S X, Daniell H. (2011). Expression and characterization of antimicrobial peptides Retrocyclin-101 and Protegrin-1 inchloroplasts to prevent sexual transmission of diseases. Plant Biotechnol J. 9: 100-115.

Verma D, Kanagaraj A,Jin S X, Singh N, Daniell H. (2010). Chloroplast-derived enzyme cocktails hydrolyse lignocellulosic biomass and release fermentable sugars. Plant Biotechnol. J.8: 332-350.