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 Cotton Fiber Bioscience and Utilization Research: New Orleans, LA
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ARS Home Southeast Area New Orleans, Louisiana Southern Regional Research Center Cotton Fiber Bioscience and Utilization Research People







Marina  Naoumkina    Research Molecular Biologist  504)286-4262 Cotton Fiber Bioscience Research Unit USDA-ARS, Southern Regional Research Center 1100 Allen Toussaint  Blvd New Orleans, LA 70124-4305  link to Google Scholar  **Peer-Reviewed Journal Papers (40)**  Zabrodina, M., Khodoun, M., **Naumkina, M****.A.,** Khavkin, E. (2000) NBS and LRR homologies of genes of vertical resistance to fungi diseases of annual and perennial rye (*Secale* L). Doclady RASHN (in Russian), 3:16-18, 2000.
Ivashuta, S., **Naumkina, M.A.**, Gau, M., Uchiyama, K., Isobe, S., Mizukami, Y., Shimamoto, Y. Genotype-dependent transcriptional activation of novel repetitive elements during cold acclimation of alfalfa (*Medicago sativa*). The Plant Journal. 31(5):615-627, 2002.
Suzuki, H., Reddy, S., **Naoumkina, M.A.**, Aziz, N., May, G., Huhman, D., Sumner, L., Blount, J., Mendes, P., Dixon, R.A. Methyl jasmonate and yeast elicitor induce differential genetic and metabolic re-programming in cell suspension cultures of the model legume *Medicago truncatula*. Planta, 220:698-707, 2005.
Dixon, R.A., Achnine, L., Deavours, B., Farag, M., **Naoumkina, M.**, Sumner, L.W. Integrated transcript and metabolite profiling for gene discovery in plant natural product pathways. Journal of Biotechnology,118:S143-S143, 2005.
Deavours, B.E., Liu, C.J., **Naoumkina, M.A.**, Tang, Y., Farag, M.A., Sumner, L.W., Noel, J.P. and Dixon, R.A. Functional analysis of members of the isoflavone and isoflavanone O-methyltransferase enzyme families from the model legume *Medicago truncatula*. Plant Molecular Biology,62(4-5):715-33, 2006.
Modolo, L., Blount, J.W., Achnine, L., **Naoumkina, M.A.**, Wang, X. and Dixon, R.A. A functional genomics approach to (iso)flavonoid glycosylation in the model legume *Medicago truncatula*. Plant Molecular Biology, 64, 499-518, 2007.
**Naoumkina M.,** Farag M.A., Sumner L.W., Tang Y., Liu C.J., Dixon R.A. Different mechanisms for phytoalexin induction by pathogen and wound signals in *Medicago truncatula*. Proceedings of the National Academy of Sciences USA, 104(46):17909-15, 2007.
**Naoumkina, M.,** Torres-Jerez, I., Allen, S., He, J., Zhao, P., Dixon, R.A. and May, G.D. Analysis of cDNA libraries from developing seeds of guar (*Cyamopsis tetragonoloba* (L.) Taub) BMC Plant Biology, 7(1):62, 2007.
**Naoumkina, M.A**., He, XZ., and Dixon, R.A. Elicitor-induced transcription factors for metabolic reprogramming of secondary metabolism in *Medicago truncatula*. BMC Plant Biology, 8(1):132, 2008.
**Naoumkina, M.,** Vaghchhipawala, S., Tang, Y., Ben, Y., Powell, R. and Dixon, R.A. Metabolic and genetic perturbations accompany the modification of galactomannan in seeds of Medicago truncatula expressing mannan synthase from guar (*Cyamopsis tetragonoloba*). Plant Biotechnology Journal, 6(6):619-31, 2008.
**Naoumkina, M.A**. and Dixon, R.A. Subcellular Localization of Flavonoid Natural Products - A Signaling Function? Plant Signaling & Behavior, 3(8):573-575, 2008.
Farag, M.A., Deavours, B.E., De-Fatima, M.A., **Naoumkina, M.A**., Dixon, R.A., and Sumner, L.W. Integrated metabolite and transcript profiling identify a biosynthetic mechanism for hispidol in *Medicago truncatula* cell cultures. Plant Physiology, 151(3): 1096-1113, 2009.
**Naoumkina, M.A.,** Modolo L.V., Huhman, D., Urbanczyk-Wochniaka, E., Tang, Y., Sumner, L.W., and Dixon, R.A. Genomic and co-expression analyses predict genes involved in triterpene saponin biosynthesis in *Medicago truncatula*. Plant Cell, 22(3): 850-866, 2010.
**Naoumkina, M.A.**, Zhao, Q., Gallego-Giraldo, L., Dai, X., Zhao, P.X., Dixon, R.A. Genome-wide analysis of phenylpropanoid defence pathways. Molecular plant pathology, 11(6):829-46, 2010.
**Naoumkina, M.**, Dixon, R.A. Characterization of the mannan synthase promoter from guar (*Cyamopsis tetragonoloba*). Plant Cell Reports, 30(6):997-1006, 2011.
Hinchliffe, D.J., Turley, R.B., **Naoumkina, M**., Kim, H.J., Tang, Y., Yeater, K.M., Li, P., Fang, D.D. A combined functional and structural genomics approach identified an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (*Gossypium hirsutum*). BMC Genomics, 12: 445, 2011.
Young, N.D., Debellé, F., Oldroyd, G.E., Geurts, R., Cannon, S.B., Udvardi, M.K., Benedito, V.A., Mayer, K.F., Gouzy, J., Schoof, H., Van de Peer, Y., Proost, S., Cook, D.R., Meyers, B.C., Spannagl, M., Cheung, F., De Mita, S., Krishnakumar, V., Gundlach, H., Zhou, S., Mudge, J., Bharti, A.K., Murray, J.D., **Naoumkina, M.A.**, Rosen, B., Silverstein, K.A., Tang, H., et al. The Medicago genome provides insight into the evolution of rhizobial symbioses. Nature, 480(7378):520-5254, 2011.
**Naoumkina, M.**, Hinchliffe, D.J., Turley, R.B., Bland, J.M., Fang, D.D. Integrated metabolomics and genomics analysis provides new insights into the fiber elongation process in Ligon lintless-2 mutant cotton (*Gossypium hirsutum* L.). BMC Genomics, 14(1):155, 2013. §Corresponding author.
Gilbert, M.K., Turley, R.B., Kim, H.J., Li, P., Thyssen, G., Tang, Y., Delhom, C.D., **Naoumkina, M**., Fang, D.D. Transcript profiling by microarray and marker analysis of the short cotton (*Gossypium hirsutum*) fiber mutant Ligon lintless-1 (*Li1*). BMC Genomics,14(1): 403, 2013.
Gilbert, M.K., Bland, J.M., Shockey, J.M., Cao, H., Hinchliffe, D.J., Fang, D.D., **Naoumkina, M.** Transcript profiling approach reveals an abscisic acid specific glycosyltransferase (UGT73C14) induced in developing fiber of Ligon lintless-2 mutant of cotton (*Gossypium hirsutum* L.). PLOS ONE | Volume 8 | Issue 9 | e75268, 2013. §Corresponding author.
**Naoumkina, M**., Thyssen, G., Fang, D.D., Hinchliffe, D.J., Florane, C., Yeater, K.M., Page, J.T., and Udall, J.A. The *Li2* Mutation Results in Reduced Subgenome Expression Bias in Elongating Fibers of Allotetraploid Cotton (*Gossypium hirsutum* L.). PLOS ONE | Volume 9 | Issue 3 | e90830, 2014. §Corresponding author.
Gilbert, M.K., Kim, H.J., Tang, Y., **Naoumkina, M.**, Fang, D.D. Comparative Transcriptome Analysis of Short Fiber Mutants Ligon-Lintless 1 And 2 Reveals Common Mechanisms Pertinent to Fiber Elongation in Cotton (*Gossypium hirsutum*). PLOS ONE; 18; 9(4):e95554, 2014.
Thyssen, G.N., Song, X., **Naoumkina, M**., Kim, H.J., Fang, D.D. Independent replication of mitochondrial genes supports the transcriptional program in developing cotton (*Gossypium hirsutum*) fiber cells. Gene, 544 (1), 41-48, 2014.
Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C., Li, P., **Naoumkina, M**. Next generation genetic mapping of the Ligon-lintless-2 (*Li2*) locus in upland cotton (*Gossypium hirsutum* L.).Theor Appl Genet. 127:2183–2192, 2014. §Corresponding author.
**Naoumkina,** M., Thyssen, G.N., Fang, D.D. RNA-seq analysis of short fiber mutants Ligon-lintless-1 (*Li1*) and – 2 (*Li2*) revealed important role of aquaporins in cotton (*Gossypium hirsutum* L.) fiber elongation. BMC Plant Biology, 15:65, 2015.§Corresponding author.
Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C., Li, P., **Naoumkina, M**. Mapping-by-sequencing of Ligon-lintless-1 (*Li1*) reveals a cluster of neighboring genes with correlated expression in developing fibers of Upland cotton (*Gossypium hirsutum* L.). Theor Appl Genet. 128: 1703-1712, 2015. §Corresponding author.
**Naoumkina M**, Thyssen GN, Fang DD, Hinchliffe DJ, Florane CB, Jenkins JN. Small RNA sequencing and degradome analysis of developing fibers of short fiber mutants Ligon-lintles-1 (*Li1*) and -2 (*Li2*) revealed a role for miRNAs and their targets in cotton fiber elongation. BMC Genomics, 17:360. doi: 10.1186/s12864-016-2715-1, 2016. §Corresponding author.
Hinchliffe DJ, Condon BD, Thyssen GN, **Naoumkina M**, Madison CA, Reynolds M, Delhom CD, Fang DD, Li P, McCarty J. The GhTT2_A07 gene is linked to the brown colour and natural flame retardancy phenotypes of Lc1 cotton (*Gossypium hirsutum*) fibres. J Exp Bot. 67(18):5461-5471, 2016.
Thyssen GN, Fang DD, Turley RB, Florane CB, Li P, Mattison CP, **Naoumkina M**. A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and F-actin organization resulting in dwarf, lintless cotton plants. Plant J. 2017 Apr;90(1):111-121. doi: 10.1111/tpj.13477. §Corresponding author.
**Naoumkina M**, Hinchliffe DJ, Fang DD, Florane CB, Thyssen GN. Role of xyloglucan in cotton (*Gossypium hirsutum* L.) fiber elongation of the short fiber mutant Ligon lintless-2 (Li2). Gene. 2017 Aug 30;626:227-233. doi: 10.1016/j.gene.2017.05.042. §Corresponding author.
**Naoumkina M**, Bechere E, Fang DD, Thyssen GN, Florane CB. Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (liy) in cotton (*Gossypium hirsutum* L.). Genomics. 2017 Jul; 109(3-4):320-329. doi: 10.1016/j.ygeno.2017.05.007. §Corresponding author.
Fang DD, **Naoumkina M**, Kim HJ (2018) Unraveling Cotton Fiber Development Using Fiber Mutants in the Post‐Genomic Era. Crop Science: 2214-2228.
Thyssen GN, **Naoumkina M**, McCarty JC, Jenkins JN, Florane C, Li P, Fang DD (2018) The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (*Gossypium hirsutum*). BMC plant biology 18: 1-8.
**Naoumkina M**, Thyssen GN, Fang DD, Jenkins JN, McCarty JC, Florane CB (2019) Genetic and transcriptomic dissection of the fiber length trait from a cotton (*Gossypium hirsutum* L.) MAGIC population. BMC genomics 20: 1-14. §Corresponding author.
Bechere E, Fang DD, **Naoumkina M** (2020) A new Ligon-lintless mutant (*liy*) in upland cotton. J. Cotton Sci 24: 168-174.
Fang DD, **Naoumkina M**, Thyssen GN, Bechere E, Li P, Florane CB (2020) An EMS-induced mutation in a tetratricopeptide repeat-like superfamily protein gene (Ghir_A12G008870) on chromosome A12 is responsible for the *liy* short fiber phenotype in cotton. Theoretical and Applied Genetics 133: 271-282
**Naoumkina M**, Zeng L, Fang DD, Wang M, Thyssen GN, Florane CB, Li P, Delhom CD (2020) Mapping and validation of a fiber length QTL on chromosome D11 using two independent F2 populations of upland cotton. Molecular Breeding 40: 1-12. §Corresponding author.
**Naoumkina M**, Thyssen GN, Fang DD, Bechere E, Li P, Florane CB (2021) Mapping-by-sequencing the locus of EMS-induced mutation responsible for tufted-fuzzless seed phenotype in cotton. Molecular Genetics and Genomics 296: 1041-1049. §Corresponding author.
**Naoumkina M**, Thyssen GN, Fang DD, Li P, Florane CB (2021) Elucidation of sequence polymorphism in fuzzless-seed cotton lines. Molecular Genetics and Genomics 296: 193-206. §Corresponding author.
Wang M, Qi Z, Thyssen GN, **Naoumkina M**, Jenkins JN, McCarty JC, Xiao Y, Li2 J, Zhang X, Fang DD (2022) Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton. communications biology 60.  ******Book chapter (2)** **** Dixon, R.A., Achnine, L., Deavours, B.E. and **Naoumkina, M.A.** Metabolomics and gene identification in plant natural product pathways. In: Biotechnology in Agriculture and Forestry, “Plant Metabolomics”, edited by K. Saito, R. A. Dixon and L. Willmitzer, Springer, pp 243-259, 2006 (Peer-Reviewed Book chapter).
**Naoumkina M** (2018) Advances in Understanding of Cotton Fiber Cell Differentiation and Elongation. In Cotton Fiber: Physics, Chemistry and Biology. Springer, Cham, pp 179-191.


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