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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » People » Marina Naoumkina

Marina Naoumkina

Research Molecular Biologist



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)


  1. 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.
  2. 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.
  3. 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.
  4. 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.
  5. 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.
  6. 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.
  7. 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.
  8. 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.
  9. 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.
  10. 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.
  11. Naoumkina, M.A. and Dixon, R.A. Subcellular Localization of Flavonoid Natural Products - A Signaling Function? Plant Signaling & Behavior, 3(8):573-575, 2008.
  12. 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.
  13. 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.
  14. 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.
  15. Naoumkina, M., Dixon, R.A. Characterization of the mannan synthase promoter from guar (Cyamopsis tetragonoloba). Plant Cell Reports, 30(6):997-1006, 2011.
  16. 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.
  17. 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.
  18. 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.
  19. 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.
  20. 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.
  21. 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.
  22. 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.
  23. 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.
  24. 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.
  25. 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.
  26. 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.
  27. 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.
  28. 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.
  29. 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.
  30. 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.
  31. 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.
  32. Fang DD, Naoumkina M, Kim HJ (2018) Unraveling Cotton Fiber Development Using Fiber Mutants in the Post‐Genomic Era. Crop Science: 2214-2228.
  33. 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.
  34. 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.
  35. Bechere E, Fang DD, Naoumkina M (2020) A new Ligon-lintless mutant (liy) in upland cotton. J. Cotton Sci 24: 168-174.
  36. 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
  37. 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.
  38. 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.
  39. 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.
  40. 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)


  1. 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).
  2. 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.