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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience Research » Research » Research Project #424867

Research Project: Molecular Approaches for More Efficient Breeding to Improve Cotton Fiber Quality Traits

Location: Cotton Fiber Bioscience Research

Publications (Clicking on the reprint icon Reprint Icon will take you to the publication reprint.)

Genomic insights into genetic divergences between two cultivated tetraploid cottons. - (Peer Reviewed Journal)

Cotton hairy root culture as an alternative tool for cotton functional genomics Reprint Icon - (Book / Chapter)
Kim, H.J. 2018. Cotton hairy root culture as an alternative tool for cotton functional genomics. Springer Verlag. pp. 213-221. https://doi.org/10.1007/978-1-4939-8952-2_18.

Cotton fiber biosynthesis Reprint Icon - (Book / Chapter)
Kim, H.J. 2018. Cotton fiber biosynthesis. Cotton Fiber: Physics, Chemistry and Biology. pp. 133-150. https://doi.org/10.1007/978-3-030-00871-0_7.

General description of cotton Reprint Icon - (Book / Chapter)
Fang, D.D. 2018. General description of cotton. Cotton Fiber: Physics, Chemistry and Biology. pg. 1-11. https://doi.org/10.1007/978-3-030-00871-0_1.

Advances in understanding of cotton fiber cell differentiation and elongation Reprint Icon - (Book / Chapter)
Naoumkina, M.A. 2018. Advances in understanding of cotton fiber cell differentiation and elongation. Book Chapter. pp. 179-191. https://doi.org/10.1007/978-3-030-00871-0_8.

Cotton fiber structure Reprint Icon - (Book / Chapter)
French, A.D., Kim, H.J. 2018. Cotton fiber structure. Cotton Fiber: Physics, Chemistry and Biology. pp. 13-40. https://doi.org/10.1007/978-3-030-00871-0_2.

Cotton fiber genes and stable quantitative trait loci Reprint Icon - (Book / Chapter)
Fang, D.D. 2018. Cotton fiber genes and stable quantitative trait loci. Cotton Fiber: Physics, Chemistry and Biology. pp. 151-178. https://doi.org/10.1007/978-3-030-00871-0_8.

Effect of fiber maturity on bundle and single fiber strength of Upland cotton Reprint Icon - (Peer Reviewed Journal)
Kim, H.J., Delhom, C.D., Rodgers III, J.E., Jones, D.C. 2018. Effect of fiber maturity on bundle and single fiber strength of Upland cotton. Crop Science. 59(1):115-124. https://doi.org/10.2135/cropsci2018.05.0324.

The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.) Reprint Icon - (Peer Reviewed Journal)
Thyssen, G.N., Naoumkina, M.A., McCarty, J.C., Jenkins, J.N., Florane, C.B., Li, P., Fang, D.D. 2018. The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.). Biomed Central (BMC) Plant Biology. 18:186. https://doi.org/10.1186/s12870-018-1414-2.

Unraveling cotton fiber development using fiber mutants in the post-genomic era Reprint Icon - (Peer Reviewed Journal)
Fang, D.D., Naoumkina, M.A., Kim, H.J. 2018. Unraveling cotton fiber development using fiber mutants in the post-genomic era. Crop Science. 58(6):2214-2228. https://doi.org/10.2135/cropsci2018.03.0184.

Genetic and transcriptomic dissection of the fiber length trait using a cotton (Gossypium hirsutum L.) MAGIC population. - (Abstract Only)

History of cotton fiber bioscience research at USDA-ARS Southern Regional Research Center - (Peer Reviewed Journal)
Fang, D.D., Kim, H.J. 2018. History of cotton fiber bioscience research at USDA-ARS Southern Regional Research Center. Journal of Cotton Science. 22:12-23.

Quantitative trait locus mapping of drought and salt tolerance in as introgressed recombinant inbred line population of upland cotton under the greenhouse and field conditions Reprint Icon - (Peer Reviewed Journal)
Abdelraheem, A., Fang, D.D., Zhang, J. 2017. Quantitative trait locus mapping of drought and salt tolerance in as introgressed recombinant inbred line population of upland cotton under the greenhouse and field conditions. Journal of Euphytica. (2018)214:8. https://doi.org/10.1007/s10681-017-2095-x.

Comparison and validation of Fourier transform infrared spectroscopic methods for monitoring secondary cell wall cellulose from cotton fibers - (Peer Reviewed Journal)
Kim, H.J., Liu, Y., French, A.D., Lee, C.M., Kim, S.H. 2018. Comparison and validation of Fourier transform infrared spectroscopic methods for monitoring secondary cell wall cellulose from cotton fibers. Cellulose. 25:49-64.

Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (liy) in cotton (Gossypium hirsutum L.) - (Peer Reviewed Journal)
Naoumkina, M.A., Bechere, E., Fang, D.D., Thyssen, G.N., Florane, C.B. 2017. Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (liy) in cotton (Gossypium hirsutum L.). Genomics. 109:320-329.

Role of xyloglucan in cotton (Gossypium hirsutum L.) fiber elongation of the short fiber mutant Ligon-lintless-2 (Li2) - (Peer Reviewed Journal)
Naoumkina, M.A., Hinchliffe, D.J., Fang, D.D., Florane, C.B., Thyssen, G.N. 2017. Role of xyloglucan in cotton (Gossypium hirsutum L.) fiber elongation of the short fiber mutant Ligon-lintless-2 (Li2). Gene. 626:227-233.

Comparative physical and chemical analyses of cotton fibers from two near isogenic upland lines differing in fiber wall thickness - (Peer Reviewed Journal)
Kim, H.J., Lee, C.M., Dazen, K., Delhom, C.D., Liu, Y., Rodgers III, J.E., French, A.D., Kim, S.H. 2017. Comparative physical and chemical analyses of cotton fibers from two near isogenic upland lines differing in fiber wall thickness. Cellulose. 24:2385-2401.

Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons - (Peer Reviewed Journal)
Fang, L., Gong, H., Lui, C., Zhou, B., Huang, T., Wang, Y., Chen, S., Fang, D.D., Du, X., Chen, H., Chen, J., Wang, S., Wang, Q., Wan, Q. 2017. Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biology. 18:33. doi:10.1186/s13059-017-1167-5.

A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and F-actin organization resulting in dwarf, lintless cotton plants Reprint Icon - (Peer Reviewed Journal)
Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Mattison, C.P., Naoumkina, M.A. 2017. A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and F-actin organization resulting in dwarf, lintless cotton plants. Plant Journal. 90(1):111-121. https://doi.org/10.1111/tpj.13477.

A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton Reprint Icon - (Peer Reviewed Journal)
Islam, M.S., Thyssen, G.N., Jenkins, J.N., Zeng, L., Delhom, C.D., McCarty, J.C., Deng, D.D., Hinchliffe, D.J., Jones, D.C., Fang, D.D. 2016. A MAGIC population-based genome-wide association study reveals functional association of GhRBB1_A07 gene with superior fiber quality in cotton. BMC Genomics. 17:903. https://doi.org/10.1186/s12864-016-3249-2.

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 Reprint Icon - (Peer Reviewed Journal)
Naoumkina, M.A., Thyssen, G.N., Fang, D.D., Hinchliffe, D.J., Florane, C.B., Jenkins, J.N. 2016. 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. https://doi.org/10.1186/s12864-016-2715-1.

The immature fiber mutant phenotype of cotton (Gossypium hirsutum) is linked to a 22-bp frame-shift deletion in a mitochondria targeted pentatricopeptide repeat gene - (Peer Reviewed Journal)
Thyssen, G.N., Fang, D.D., Zeng, L., Song, X., Delhom, C.D., Condon, T.L., Li, P., Kim, H.J. 2016. The immature fiber mutant phenotype of cotton (Gossypium hirsutum) is linked to a 22-bp frame-shift deletion in a mitochondria targeted pentatricopeptide repeat gene. G3, Genes/Genomes/Genetics. 6:1627-1633.

Comparative phenotypic analysis of Gossypium raimondii with Upland cotton - (Peer Reviewed Journal)
Kim, H.J., Liu, Y., Dowd, M.K., Frelichowski, J.E., Delhom, C.D., Rodgers III, J.E., Thibodeaux, D.P. 2016. Comparative phenotypic analysis of Gossypium raimondii with Upland cotton. Journal of Cotton Science. 20:132-144.

Comparative fiber property and transcriptome analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum L.) line MD52ne - (Peer Reviewed Journal)
Islam, M.S., Fang, D.D., Thyssen, G.N., Delhom, C.D., Liu, Y., Kim, H.J. 2016. Comparative fiber property and transcriptome analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum L.) line MD52ne. Biomed Central (BMC) Plant Biology. 16:36.

Mapping by sequencing in cotton (Gossypium hirsutum) line MD52ne identified candidate genes for fiber strength and its related quality attributes - (Peer Reviewed Journal)
Islam, M.S., Zeng, L., Thyssen, G.N., Delhom, C.D., Kim, H.J., Li, P., Fang, D.D. 2016. Mapping by sequencing in cotton (Gossypium hirsutum) line MD52ne identified candidate genes for fiber strength and its related quality attributes. Theoretical and Applied Genetics. 129:1071-1086.

Understanding the cotton fiber elongation process using short fiber mutants, the Ligon lintless-1 (Li1) and -2 (Li2) as an experiment model system - (Abstract Only)

Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.) - (Peer Reviewed Journal)
Hulse-Kemp, A.M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D.D., Frelichowski, J.E., Giband, M., Hague, S., Hinze, L.L., Kochan, K., Riggs, R., Scheffler, J.A., Udall, J.A., Ulloa, M., Wang, S., Zhu, Q., Bag, S.K., Bhardwaj, A., Burke, J.J., Byers, R.L., Claverie, M., Gore, M.A., Harker, D.B., Islam, M.S., Jenkins, J.N., Jones, D.C., Lacape, J., Llewellyn, D.J., Percy, R.G., Pepper, A.E., Poland, J.A., Rai, K., Sawant, S.V., Singh, S., Spriggs, A., Taylor, J.M., Wang, F., Yourstone, S.M., Zheng, X., Lawley, C.T., Ganal, M.W., Van Deynze, A., Wilson, L.W., Stelly, D.M. 2015. Development of a 63K SNP array for Gossypium and high-density mapping of intra- and inter-specific populations of cotton (G. hirsutum L.). Genes, Genomes, Genetics. 5:1187-1209. doi:10.1534/g3.115.018416.

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.) - (Peer Reviewed Journal)
Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Naoumkina, M.A. 2015. 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.). Journal of Theoretical and Applied Genetics. 128:1703-1712.

Phytohormonal networks promote differentiation of fiber initials on pre-anthesis cotton ovules grown in vitro and in planta - (Peer Reviewed Journal)
Kim, H.J., Hinchliffe, D.J., Triplett, B.A., Chen, Z.J., Stelly, D.M., Yeater, K.M., Moon, H.S., Gilbert, M.K., Thyssen, G.N., Turley, R.B., Fang, D.D. 2015. Phytohormonal networks promote differentiation of fiber initials on pre-anthesis cotton ovules grown in vitro and in planta. PLoS ONE. 10(4):e0125046.

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 - (Peer Reviewed Journal)
Naoumkina, M.A., Thyssen, G.N., Fang, D.D. 2015. 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. Biomed Central (BMC) Plant Biology. 15:65.

Cotton as a World Crop: Origin, History, and Current Status - (Book / Chapter)
Lee, J.A., Fang, D.D. 2015. Cotton as a World Crop: Origin, History, and Current Status. Cotton. 1-23, DOI:10.2134/agronmonogr57.2013.0019.

Development of EST-based SNP and indel markers and their utilization in tetraploid cotton genetic mapping - (Peer Reviewed Journal)
Li, X., Gao, W., Guo, H., Zhang, X., Fang, D.D., Lin, Z. 2014. Development of EST-based SNP and indel markers and their utilization in tetraploid cotton genetic mapping. Biomed Central (BMC) Genomics. 15:1046.

Fiber biology - (Book / Chapter)
Kim, H.J. 2015. Fiber biology. Cotton. 97-127, doi:10.2134/agronmonogr57.2013.0022.

Detection, validation, and application of genotyping-by-sequencing based single nucleotide polymorphisms in upland cotton - (Peer Reviewed Journal)
Islam, M.S., Thyssen, G.N., Jenkins, J.N., Fang, D.D. 2014. Detection, validation, and application of genotyping-by-sequencing based single nucleotide polymorphisms in upland cotton. The Plant Genome. 8(1):1-10.

Next generation genetic mapping of the Ligon-lintless-2 (Li2) locus in upland cotton (Gossypium hirsutum L.) - (Peer Reviewed Journal)
Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C.B., Li, P., Naoumkina, M.A. 2014. Next generation genetic mapping of the Ligon-lintless-2 (Li2) locus in upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 127:2183-2192.

Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.) Reprint Icon - (Peer Reviewed Journal)
Fang, D.D., Jenkins, J.N., Deng, D.D., McCarty Jr, J.C., Li, P., Wu, J. 2014. Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum L.). Biomed Central (BMC) Genomics. 15:397.

Independent replication of mitochondrial genes supports the transcriptional program in developing fiber cells of cotton (Gossypium hirsutum L.). - (Peer Reviewed Journal)
Thyssen, G.N., Song, X., Naoumkina, M.A., Kim, H.J., Fang, D.D. 2014. Independent replication of mitochondrial genes supports the transcriptional program in developing fiber cells of cotton (Gossypium hirsutum L.). Gene. 544:41-48.

The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.) - (Peer Reviewed Journal)
Naoumkina, M.A., Thyssen, G.N., Fang, D.D., Hinchliffe, D.J., Florane, C.B., Yeater, K.M., Page, J.J., Udall, J.A. 2014. The Li2 mutation results in reduced subgenome expression bias in elongating fibers of allotetraploid cotton (Gossypium hirsutum L.). PLoS One. 9(3):e90830.

Comparisons of methods measuring fiber maturity and fineness of Upland cotton fibers containing different degree of fiber cell wall development. - (Peer Reviewed Journal)
Kim, H.J., Rodgers III, J.E., Delhom, C.D., Cui, X. 2014. Comparisons of methods measuring fiber maturity and fineness of Upland cotton fibers containing different degree of fiber cell wall development. Textile Research Journal. 84:1622-1633.

Identification of cotton fiber quality quantitative trait loci using intraspecific crosses derived from two near-isogenic lines differing in fiber bundle strength. Reprint Icon - (Peer Reviewed Journal)
Islam, M.S., Zeng, L., Delhom, C.D., Song, X., Kim, H.J., Li, P., Fang, D.D. 2014. Identification of cotton fiber quality quantitative trait loci using intraspecific crosses derived from two near-isogenic lines differing in fiber bundle strength. Molecular Breeding. 34:373-384.

Quantitative trait locus analysis of Verticillium wilt resistance in an introgressed recombinant inbred population of Upland cotton - (Peer Reviewed Journal)
Fang, H., Zhou, H., Sanogo, S., Lipka, A.E., Fang, D.D., Percy, R.G., Hughs, S.E., Jones, D.C., Gore, M.A., Zhang, J. 2014. Quantitative trait locus analysis of Verticillium wilt resistance in an introgressed recombinant inbred population of Upland cotton. Molecular Breeding. 33:709-720.

Linkage map construction and QTL analysis of agronomic and fiber quality traits in cotton Reprint Icon - (Peer Reviewed Journal)
Gore, M.A., Fang, D.D., Poland, J.A., Zhang, J., Percy, R.G., Cantrell, R.G., Thyssen, G.N. 2014. Linkage map construction and QTL analysis of agronomic and fiber quality traits in cotton. The Plant Genome. 7(1):1-10.

Comparative transcriptome analysis of short fiber mutants ligon-lintless 1 and 2 reveals common mechanisms pertinent to fiber elongation in cotton (Gossypium hirsutum L.) Reprint Icon - (Peer Reviewed Journal)
Gilbert, M.K., Kim, H.J., Tang, Y., Naoumkina, M.A., Fang, D.D. 2014. Comparative transcriptome analysis of short fiber mutants ligon-lintless 1 and 2 reveals common mechanisms pertinent to fiber elongation in cotton (Gossypium hirsutum L.). PLoS One. 9:e95554.