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ARS Home » Southeast Area » New Orleans, Louisiana » Southern Regional Research Center » Cotton Fiber Bioscience and Utilization Research » People » David Fang
David Fang

Supervisory Research Geneticist (Plants)

Fellow of Crop Science Society of America

2023 Cotton Genetics Research Award Recipient

International Cotton Researcher of the Year 2024 Award Recipient

(504) 286-4527(O)  (504) 655-0068 (C)

Cotton Fiber Bioscience & Utilization Research Unit

USDA-ARS, Southern Regional Research Center

1100 Allen Toussaint Blvd

New Orleans, LA 70124-4305

 

 

My research focuses on following areas:

1) development of molecular markers for cotton genetics and breeding

2) mapping QTL for fiber quality and yield

3) elucidating molecular mechanisms of fiber development especially elongation and secondary cell wall thickening

4) implementation of marker assisted selection and genomic selection in breeding

5) studying the effects of global climate changes on cotton fiber quality

6) using nanotechnologies to improve cotton fiber properties

 

Current research projects are:

1) Association mapping fiber and yield QTL using a MAGIC population

2) Fiber QTL identification and utilization based on bi-parental population mapping 

3) Effects of global climate changes on fiber quality

4) Elucidating fiber development through dissection of fiber mutants

5) Developing novel technologies to add value to cotton non-woven products

 

link to Google Scholar

link to LinkedIn

link to ORCID

link to Scopus

 

     Peer-Reviewed Journal Publications (127)

  1. Zhou, Z. D., Zhang, P. T., Fang Deqiu, Zheng, Y. F. and Huang, J. C. Investigation in Vitis in Meiling area, Nanchang suburbs of Jiangxi province. Journal of Jiangxi Agricultural University. 8(2):37-42. 1986.
  2. Fang Deqiu and Zhang, H. Z. Peroxidase isozymes in Eriobotrya. Journal of Huazhong Agricultural University. 8(2):144-150. 1989.
  3. Zhang, H. Z., Peng, S. A., Cai, L. H. and Fang Deqiu§. The germplasm resources of the genus Eriobotrya with special reference on the origin of E. japonica Lindl. Acta Horticulturae Sinica. 17(1):5-12. 1990. (§Corresponding author)
  4. Fang Deqiu, Xiao, S. Y. and Zhang, W. C. Studies on developmental and organic specificities of citrus isozymes. Zhejiang Citrus. (4):4-6. 1991.
  5. Fang Deqiu and Zhang, W. C. Studies on the taxonomy and evolution of mandarins in China by isozymes. Journal of Wuhan Botanical Research. 10(4):305-312. 1992.
  6. Fang Deqiu and Zhang, W. C. Comparisons among the application of four cluster analysis methods in the chemotaxonomy of citrus species. Journal of Huazhong Agricultural University. 11(3):256-262. 1992.
  7. Fang Deqiu, Zhang, W. C. and Xiao, S. Y. Studies on taxonomy and evolution of Citrus and its related genera by isozyme analysis. Acta Phytotaxonomica Sinica. 31(4):329-352. 1993.
  8. Fang Deqiu. New methods in citrus taxonomy. Journal of Fruit Science. 10:29-33. 1993.
  9. Fang Deqiu. Intra and intergeneric relationships of Poncirus polyandra: investigation by leaf isozymes. Journal of Wuhan Botanical Research. 11(1):34-40. 1993.
  10. Fang Deqiu. Citrus taxonomy---past, present and future. Journal of Wuhan Botanical Research. 11(4):375-382. 1993.
  11. Rodov, R., Ben-Yehoshua, S., Albagli, R. and Fang Deqiu. Hot water dip as a means to improve keeping qualities of citrus fruits as compared to long-term heat treatment (curing). Hassadeh. 74:1084-1087. 1994.
  12. Fang Deqiu, Zhang, W. C. and Xiao, S. Y. Isozymes and classification of Citrus species in China. Journal of Integrative Plant Biology. 36:124-138. 1994. 
  13. Fang Deqiu, Hou, S. S., Li, X. M., Ye, H. C. and Li, G. F. Effects of pH value and hormones on cell growth and shikonin derivative formation in suspension cultures of Arnebia euchroma cells. Journal of Wuhan Botanical Research. 12(2):159-164. 1994.
  14. Fang Deqiu, Hou, S. S., Li, X. M., Ye, H. C. and Li, G. F. Effects of nutritional factors on cell growth and shikonin derivative formation in suspension cultures of Arnebia euchroma cells. Journal of Wuhan Botanical Research. 12(4):348-354. 1994.
  15. Fang Deqiu and Xiao, S. Y. Antimicrobiological activity of citral and related essential oils. Natural Product Research and Development. 6(2):75-78. 1994.
  16. Rodov, V., D’hallewin, G., Ben-Yehoshua, S., Fang Deqiu and Castia, T.  Accumulation of phytoalexins scoparone and scopoletin in citrus fruits subjected to various postharvest treatments.  Acta Horticulturae. 381:517-523. 1994.
  17. Rodov, V., Ben-Yehoahua, S., Fierman, T. and Fang Deqiu. Modified humidity packaging reduces decay of harvested red bell pepper fruit. HortScience. 30(2):299-302.  https://doi.org/10.21273/HORTSCI.30.2.299. 1995.
  18. Rodov, V., Ben-Yehoshua, S., Albagli, R. and Fang Deqiu. Reducing chilling injury and decay of stored citrus fruit by hot water dips. Postharvest Biology and Technology. 5:119-127. https://doi.org/1016/0925-5214(94)00011-G.  1995.
  19. Rodov, V., Ben-Yehoshua, S., Fang Deqiu, Kim, J. J. and Ashkenazi, R. Preformed antifungal compounds of lemon fruit: citral and its relation to disease resistance. Journal of Agricultural and Food Chemistry. 43(4):1057-1061. https://doi.org/10.1021/jf00052a039. 1995.
  20. Ben-Yehoshua, S., Rodov, V., Fang Deqiu and Kim, J. J. Preformed antifungal compounds of citrus fruit: effect of postharvest treatments with heat and growth regulators. Journal of Agricultural and Food Chemistry. 43(4):1062-1066. https://doi.org/10.1021/jf00052a040. 1995.
  21. Ben-Yehoshua, S., Fang Deqiu, Rodov, V. and Fishman, S. New developments in modified atmosphere packaging (Part I). Plasticulture. 106:29-37. 1995.
  22. Ben-Yehoshua, S., Fang Deqiu, Rodov, V. and Fishman, S. New developments in modified atmosphere packaging (Part II). Plasticulture. 107:33-40. 1995.
  23. Fang Deqiu, Zhang, W. C. and Xiao, S. Y. Studies on the origin of satsuma mandarin by isozyme analysis. Journal of Fruit Science. 12(supplement):16-20. 1995.
  24. Fang Deqiu, Roose, M. L., Krueger, R. R. and Federici, C. T. Fingerprinting trifoliate orange germ plasm accessions with isozymes, RFLPs and inter-simple sequence repeat markers.  Theoretical and Applied Genetics. 95:211-219. https://doi.org/1007/s001220050550.  1997.
  25. Fang Deqiu, Federici, C. T. and Roose, M. L. Development of molecular markers linked to a gene controlling fruit acidity in citrus. Genome.  40:841-849. https://doi.org/10.1139/g97-809.  1997.
  26. Fang Deqiu and Roose, M. L. Identification of closely related citrus cultivars with inter-simple sequence repeat markers. Theoretical and Applied Genetics. 95:408-417. https://doi.org/1007/s001220050577. 1997.
  27. Federici, C. T., Fang Deqiu, Scora, R. W. and Roose, M. L. Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theoretical and Applied Genetics. 96:812-822. https://doi.org/1007/s001220050807. 1998.
  28. Fang Deqiu, Krueger, R. R. and Roose, M. L. Phylogenetic relationships among selected Citrus germplasm accessions revealed by inter-simple sequence repeat (ISSR) markers. Journal of American Society for Horticultural Science. 123(4):612-617. https://doi.org/10.21273/JASHS.123.4.612. 1998.
  29. Fang Deqiu, Federici, C. T. and Roose, M. L. A high resolution linkage map of the citrus tristeza virus resistance gene region in Poncirus trifoliata (L.) Raf.. Genetics. 150(2):883-890. https://www.genetics.org/content/150/2/883. 1998.
  30. Fang Deqiu and Roose, M. L. A novel gene conferring citrus tristeza virus resistance in Citrus maxima (Burm.) Merrill. HortScience. 34(2):334-335. https://doi.org/10.21273/HORTSCI.34.2.334. 1999.
  31. Fang Deqiu and Roose, M. L. Inheritance of intersimple sequence repeat markers in citrus. Journal of Heredity. 90:247-249. https://doi.org/1093/jhered/90.1.247. 1999.
  32. Roose, M. L., Fang Deqiu, Cheng, F. S., Tayyar, R. I., Federici, C. T. and Kupper, R. S. Mapping the Citrus genome. Acta Horticulturae. 535:25-32. 2000.
  33. Blenda A, Scheffler, J., Scheffler, B., Palmer, M., Lacape, J. M., Yu, J. Z., Jesudurai, C., Jung, S., Muthukumar, S., Yellambalase, P., Ficklin, S., Staton, M., Eshelman, R., Ulloa, M., Saha, S., Burr, B., Liu, S., Zhang, T. Z., Fang Deqiu, Pepper, A., Kumpatla, S., Jacobs, J., Tomkins, J., Cantrell, R. G. and Main, D. CMD: a cotton microsatellite database resource for Gossypium genomics. BMC Genomics. 7:131. https://doi.org/10.1186/1471-2164-7-132. 2006.
  34. Xiao, J., Wu, K., Fang, D.D., Stelly, D. M., Yu, J, and Cantrell, R.G. New SSR markers for use in cotton (Gossypium spp.) Journal of Cotton Science. 13:75-157.  http://www.cotton.org/journal/2009-13/2/upload/JCS13-75.pdf. 2009.
  35. Romano, G. B., Sacks, E. J., Stetina, S. R., Robinson, A. F., Fang, D.D., Gutierrez, O. A., and Scheffler, J. A. Identification and genomic location of a reniform nematode (Rotylenchulus reniformis) resistance locus (Renari) introgressed from Gossypium aridum into upland cotton (G. hirsutum). Theoretical and Applied Genetics. 120:139-150. https://doi.org/10.1007/s00122-009-1165-4.  2009. 
  36. Fang, D.D., Xiao, J., Canci, P. C., and Cantrell, R. G. A new SNP haplotype associated with blue disease resistance gene in cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 120:943-953. https://doi.org/10.1007/s00122-009-1223-y.  2010. 
  37. Xiao, J., Fang, D.D.§, Bhatti, M., Hendrix B., and Cantrell, R. G. A SNP haplotype associated with a gene resistant to Xanthomonas axonopodis pv. Malvacearum in upland cotton (Gossypium hirsutum L.). Molecular Breeding. 25:593-602. https://doi.org/10.1007/s11032-009-9355-y. 2010. (§co-first author)
  38. Kim, H. J., Murai, N., Fang, D.D., and Triplett, B. A. Functional analysis of Gossypium hirsutum cellulose synthase catalytic subunit 4 promoter in transgenic Arabidopsis and cotton tissues. Plant Science. 180:323-332. ttps://doi.org/1016/j.plantsci.2010.10.003.  2011.
  39. Hinchliffe, D. J., Meredith, W. R., Delhom, C. D., Thibodeaux, D. P. and Fang, D.D.§ Elevated growing degree days influence transition stage timing during cotton (Gossypium hirsutum L.) fiber development and result in increased fiber strength. Crop Science. 51(4):1683-1692 https://doi.org/10.2135/cropsci2010.10.0569. 2011. (§Corresponding author)
  40. Fang, D.D. and Stetina, S. R. Improving cotton (Gossypium hirsutum ) plant resistance to reniform nematodes by pyramiding Ren1 and Ren2. Plant Breeding. 130:673-678. https://doi.org/10.1111/j.1439-0523.2011.01889.x. 2011.
  41. Hinchliffe, D.J., Turley, R. B., Naoumkina, M., Kim, H. J., Tang, Y. H., Yeater, K. M., Li, P., Fang, D.D.§ A combined functional and structural genomics approach identifies an EST-SSR marker with complete linkage to the Ligon lintless-2 genetic locus in cotton (Gossypium hirsutum L.). BMC Genomics. 12:445. https://doi.org/10.1186/1471-2164-12-445. 2011. (§Corresponding author)
  42. Gore, M., Percy, R. G., Zhang, J., Fang, D.D., and Cantrell, R. G. Registration of the TM-1/NM24016 cotton recombinant inbred mapping population. Journal of Plant Registrations. 6(1):124-127. https://doi.org/3198/jpr2011.06.0334crmp.  2012. 
  43. Yu, J. Z., Kohel, R. J., Fang, D.D., Cho, J., Van Deynze, A., Ulloa, M., Hoffman, S. M., Pepper, A. E., Stelly, D. M., Jenkins, J. N., Saha, S., Kumpatla, S. P., Shah, M. R., Hugie, W. V., and Percy, R. G. A high-density simple sequence repeat and single nucleotide polymorphism genetic map of the tetraploid cotton genome. G3, Genes|Genomes|Genetics.  2(1):43-58. https://doi.org/10.1534/g3.111.001552.   2012. 
  44. Kim, H.J., Triplett, B. A., Zhang, H. B., Lee, M. K., Hinchliffe, D. J., Li, P., Fang, D.D. Cloning and characterization of homeologous cellulose synthase catalytic subunit 2 genes from allotetraploid cotton (Gossypium hirsutum). Gene. 494:181-189. https://doi.org/10.1016/j.gene.2011.12.018.  2012 
  45. Yu, J. Z., Fang, D.D., Kohel, R. J., Ulloa, M., Hinze, L. L., Percy, R. G., Zhang, J., Chee, P., Scheffler, B. E., and Jones, D. C. Development of a core set of SSR markers for the characterization of Gossypium germplasm. Euphytica. 187:203-213. https://doi.org/10.1007/s10681-012-0643-y.  2012.
  46. Han, X. Y., Xu, X. Y., Fang, D.D., Zhang, T. Z., and Guo, W. Z. Cloning and expression analysis of novel Aux/IAA family genes in Gossypium hirsutum. Gene. 503:83-91. https://doi.org/10.1016/j.gene.2012.03.069. 2012.
  47. Fang, D.D., and Yu, J. Z. Addition of 455 microsatellite marker loci to the high-density Gossypium hirsutum TM-1 x barbadense 3-79 genetic map. Journal of Cotton Science. 16:229-248. http://www.cotton.org/journal/2012-16/4/loader.cfm?csModule=security/getfile&pageid=140585. 2012.
  48. Blenda, A., Fang, D.D., Rami, J.F., Garsmeur, O., Luo, F., and Lacape, J.M. A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. PLoS ONE. 7(9):e45739. https://doi.org/1371/journal.pone.0045739. 2012.
  49. Kim, H.J., Moon, H.S., Delhom, C.D., Zeng, L., and Fang, D.D.§ Molecular markers associated with the immature fiber (im) gene affecting the degree of fiber cell wall thickening in cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 126:23-31. https://doi.org/10.1007/s00122-012-1956-x. 2013. (§Corresponding author)
  50. Fang, D.D., Hinze, L.L., Percy, R.G., Li, P., Deng, D., and Thyssen, G.N. A microsatellite-based genome-wide analysis of genetic diversity and linkage disequilibrium in Upland cotton (Gossypium hirsutum) cultivars from major cotton-growing countries. Euphytica. 191:391-401. https://doi.org/10.1007/s10681-013-0886-2. 2013.
  51. Naoumkina, M., Hinchliffe, D.J., Turley, R.B., Bland, J., and Fang, D.D. Integrated metabolomics and genomics analysis provides new insights into the fiber elongation process in Ligon lintless-2 (Li2) mutant cotton (Gossypium hirsutum). BMC Genomics. 14:155. https://doi.org/10.1186/1471-2164-14-155.  2013.
  52. Gilbert, M.K., Turley, R.B., Kim, H.J., Li, P., Thyssen, G.N., Tang, Y., Delhom, C.D., Naoumkina, M., and Fang, D.D.§ Transcript profiling by microarray and marker analysis of the short cotton (Gossypium hirsutum L.) fiber mutant Ligon lintlesss-1 (Li1). BMC Genomics. 14:403. https://doi.org/10.1186/1471-2164-14-403.  2013. (§Corresponding author)
  53. Gilbert, M.K., Bland, J.M., Shockey, J., Cao, H., Hinchliffe, D.J., Fang, D.D., and Naoumkina, M. A transcript profiling approach reveals an abscisic acid specific glycosyltransferase (UGT73C14) induced in developing fiber of Ligon lintless-2 mutant of cotton (Gossypium hirsutum). PLoS ONE. 8(9):e75268. https://doi.org/10.1371/journal.pone.0075268.   2013.
  54. Kim, H.J., Tang, Y., Moon, H.S., Delhom, C.D., and Fang, D.D. Functional analyses of cotton (Gossypium hirsutum ) immature fiber (im) mutant infer that fiber cell wall development is associated with sensitivity to stress responses. BMC Genomics. 14:889. https://doi.org/10.1186/1471-2164-14-889.  2013.
  55. Thyssen, G.N., McCarty, J.C., Li, P., Jenkins, J.N. and Fang, D.D.§ Genetic mapping of non-target site resistance to a sulfonylurea herbicide (Envoke®) in Upland cotton (Gossypium hirsutum L.). Molecular Breeding. 33:341-348. https://doi.org/10.1007/s11032-013-9953-6. 2014. (§Corresponding author)
  56. Gore, M.A., Fang, D.D.§, Poland, J.A., Zhang, J., Percy, R.G., Cantrell, R.G. and Thyssen, G.N. Linkage map construction and quantitative trait locus analysis of agronomic and fiber quality traits in cotton. The Plant Genome. 7(1):1-10. https://doi.org/10.3835/plantgenome2013.07.0023.  2014. (§co-first author) 
  57. Fang, H., Zhou, H., Sanogo, S., Lipka, A.E., Fang, D.D., Percy, R.G., Hughs, S.E., Jones, D.C., Gore, M., and Zhang, J. Quantitative trait locus analysis of Verticillium wilt resistance in an introgressed recombinant inbred population of Upland cotton. Molecular Breeding. 33:709-720. https://doi.org/1007/s11032-013-9987-9. 2014.
  58. Islam, M.S., Zeng, L., Delhom, C.D., Song, X., Kim, H.J., Li, P., and Fang, D.D.§ 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. https://doi.org/10.1007/s11032-014-0040-4.  2014. (§Corresponding author) 
  59. Naoumkina, M., Thyssen, G.N., 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). PLoS ONE. 9(3):e90830. https://doi.org/10.1371/journal.pone.0090830.   2014.
  60. Gilbert, M.K., Kim, H.J., Tang, Y., Naoumkina, M., and 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 L.). PLoS ONE. 9(4):e95554. https://doi.org/10.1371/journal.pone.0095554.  2014. (§Corresponding author) 
  61. Thyssen, G.N., Song, X., Naoumkina, M., Kim, H.J. and Fang, D.D.§ Independent replication of mitochondrial genes supports the transcriptional program in developing cotton (Gossypium hirsutum L.) fiber cells. Gene. 544:41-48. https://doi.org/10.1016/j.gene.2014.04.038.  2014. (§Corresponding author) 
  62. Fang, D.D., Jenkins, J.D., Deng, D., McCarty, J.C., Li, P., and Wu, J. Quantitative trait loci analysis of fiber quality traits using a random-mated recombinant inbred population in Upland cotton (Gossypium hirsutum). BMC Genomics. 15:397. https://doi.org/10.1186/1471-2164-15-397.  2014
  63. Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C., Li, P., and Naoumkina, M. Next generation genetic mapping of the Ligon-lintless-2 (Li2) locus in upland cotton (Gossypium hirsutum). Theoretical and Applied Genetics. 127:2183-2192. https://doi.org/10.1007/s00122-014-2372-1.  2014
  64. Yu, J.Z., Ulloa, M., Hoffman, S.M., Kohel, R.J., Pepper, A.E., Fang, D.D., Percy, R.G., and Burke, J. Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum x G. barbadense L.) RIL population. Molecular Genetics and Genomics.  289:1347-1367. https://doi.org/10.1007/s00438-014-0930-5.   2014.
  65. Li, X., Gao, W., Guo, H., Zhang, X.L., Fang, D.D., and Lin, Z. Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping. BMC Genomics. 15:1046. https://doi.org/1186/1471-2164-15-1046.  2014.
  66. Islam, M.S., Thyssen, G.N., Jenkins, J.N., and Fang, D.D.§ Detection, validation and application of genotyping-by-sequencing based single nucleotide polymorphisms in Upland cotton. The Plant Genome. 8(1):1-10. https://doi.org/10.3835/plantgenome2014.07.0034.  2015. (§Corresponding author) 
  67. Hinze, L.L., Fang, D.D., Gore, M.A., Scheffler, B., Yu, J.Z., Frelichowski, J. and Percy, R.G. Molecular characterization of the Gossypium diversity reference set of the U.S. National Cotton Germplasm Collection. Theoretical and Applied Genetics. 128:313-327. https://doi.org/1007/s00122-014-2431-7.  2015.
  68. Said, J.I., Song, M., Wang, H., Lin, Z., Zhang, X., Fang, D.D. and Zhang, J. A comparative meta-analysis of QTL between intraspecific Gossypium hirsutum and interspecific hirsutum × G. barbadense populations. Molecular Genetics and Genomics. 290:1003-1025. https://doi.org/10.1007/s00438-014-0963-9.   2015.
  69. Naoumkina, M., Thyssen, G.N., and Fang, D.D. RNA-seq analysis of short fiber mutants Lingon-lintless-1 (Li1) and -2 (Li2) revealed important role of aquaporins in cotton (Gossypium hirsutum) fiber elongation. BMC Plant Biology. 15:65. https://doi.org/10.1186/s12870-015-0454-0. 2015.
  70. Kim, H.J., Hinchliffe, D.J., Triplett, B.A., Chen, J.Z., Stelly, D.M., Yeater, K.M., Moon, H., Gilbert, M.K., Thyssen, G., Turley, R.B., and Fang, D.D. Phytohormonal networks promote differentiation of fiber initials on pre-anthesis cotton ovules grown in vitro and in planta. PLoS ONE. 10(4):e0125046. https://doi.org/1371/journal.pone.0125046.  2015.
  71. Hulse-Kemp, A.M., Ashrafi, H., Stoffel, K., Zheng, X., Saski, C., Scheffler, B.E., Fang, D.D., Chen, Z.J., Van Deynze, A., and Stelly, D.M. BAC-end sequence-based SNP mining in allotetraploid cotton (Gossypium) utilizing resequencing data, phylogenetic inferences and perspectives for genetic mapping. G3, Genes|Genomes|Genetics. 5:1095-1105. https://doi.org/1534/g3.115.017749. 2015.
  72. Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C., Li, P., and 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). Theoretical and Applied Genetics. 128:1703-1712. https://doi.org//10.1007/s00122-015-2539-4. 2015.
  73. Hulse-Kemp,A.M., Lemm, J., Plieske, J., Ashrafi, H., Buyyarapu, R., Fang, D.D., Frelichowski, J., Giband, M., Hague, S., Hinze, L.L., Kochan, K., Riggs, P., Scheffler, J.A., Udall, J.A., Ulloa, M., Wang, S.S., Zhu, Q.H., 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.M., Llewellyn, D.J., Percy, R.G., Pepper, A.E., Poland, J.A., Rai, K.M.,  Riggs, P., Sawant, S.V., Singh, S.K.,  Spriggs, A. Taylor, J.M., Wang, F., Yourstone, S.M., Zheng, X.,  Lawley, C.T., Ganal, M.W., Van Deynze, A., Wilson, I.W., AND Stelly, D.M. Development of a 63K SNP array for cotton  and high-density mapping of intra- and inter-specific populations of Gossypium G3, Genes|Genomes|Genetics. 5:1187-1209. https://doi.org/10.1534/g3.115.018416.   2015.
  74. Hinze, L.L., Gazave, E., Gore, M.A., Fang, D.D., Scheffler, B.E., Yu, J.Z., Jones, D.C., Frelichowski, J., and Percy, R.G. Genetic diversity of tetraploid cotton in the Gossypium Diversity Reference Set. Journal of Heredity. 107(3):274-286. https://doi.org/1093/jhered/esw004.  2016.
  75. Islam, S.M., Fang, D.D., Thyssen, G.N., Delhom, C., Liu, Y., and Kim, H.J. Comparative fiber property and transcriptomic analyses reveal key genes potentially related to high fiber strength in cotton (Gossypium hirsutum) line MD52ne.  BMC Plant Biology. 16:36. https://doi.org/10.1186/s12870-016-0727-2.   2016.
  76. Islam, M.S., Zeng, L., Thyssen, G.N., Delhom, C.D., Kim, H.J., Li, P., and Fang, D.D.§ Mapping by sequencing in upland cotton (Gossypium hirsutum) line MD52ne identified candidate genes for fiber strength and its related quality attributes. Theoretical and Applied Genetics. 129:1071-1086. https://doi.org/10.1007/s00122-016-2684-4. 2016. (§Corresponding author) 
  77. Naoumkina, M., Thyssen, G.N., Fang, D.D., Hinchliffe, D.J., Florane, C.B., and Jenkins, J.N. Small RNA sequencing and degradome analysis of developing fibers of short fiber mutants Ligon-lintels-1 (Li1) and -2 (Li2) revealed a role of miRNAs and their targets in cotton fiber elongation. BMC Genomics. 17:360. https://doi.org/1186/s12864-016-2715-1. 2016.
  78. Thyssen, G.N., Fang, D.D., Zeng, L., Song, X.L., Delhom, C.D., Tracy, C.L., Li, P., and Kim, H.J. The immature fiber phenotype of cotton (Gossypium hirsutum) is linked to a 22-bp frame-shift deletion in a mitochondrial targeted pentatricopeptide repeat gene. G3, Genes|Genomes|Genetics. 6(6):1627-1633. https://doi.org/1534/g3.116.027649. 2016.
  79. Hinchliffe, D.J., Condon, B.D., Thyssen, G.N., Naoumkina, M., Madison, C.A., Reynolds, M., Delhom, C.D., Fang, D.D., Li, P., McCarty, J.A. The GhTT2_A07 gene is linked to the brown colour and natural flame retardancy phenotypes of Lc1 cotton Gossypium hirsutum ) fibres. Journal of Experimental Botany. 67:5461-5471. https://doi.org/10.1093/jxb/erw312.  2016.
  80. Hugie, K.L., Fang, D.D., Smith, C.W., Li, P., Hinze, L., Hague, S.S., and Jones, D.C. Utility assessment of published microsatellite markers for fiber length and bundle strength QTL in a cotton breeding program. Crop Science. 56:2983-2995. https://doi.org/2135/cropsci2016.02.0093.  2016.
  81. 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., and Fang, D.D.§ 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.  2016. (§Corresponding author) 
  82. Thyssen, G.N., Fang, D.D., Turley, R.B., Florane, C., Li, P., Mattison, C.P., and Naoumkina, M. ­­ A Gly65Val substitution in an actin, GhACT_LI1, disrupts cell polarity and F-actin organization resulting in dwarf, lintless cotton plants. The Plant Journal. 90:111-121. https://doi.org/1111/tpj.13477. 2017.
  83. Hinze, L.L., Hulse-Kemp, A.M., Wilson, I.W., Zhu, Q.H., Llewellyn, D.J., Taylor, J.M., Spriggs, A., Fang, D.D., Ulloa, M., Burke, J.J., Giband, M., Lacape, J.M., Van Deynze, A., Udall, J.A., Scheffler, J.A., Hague, S., Wendel, J., Pepper, A.E., Frelichowski, J., Lawley, C.T., Jones, D.C., Percy, R.G., and Stelly, D.M. Diversity analysis of cotton (Gossypium hirsutum) germplasm using the CottonSNP63K Array. BMC Plant Biology. 17:37. https://doi.org/10.1186/s12870-017-0981-y.  2017.
  84. Fang, L., Gong, H., Hu, Y., Liu, C., Zhou, B., Huang, T., Wang, Y., Chen, S., Fang, D.D., Du, X.M., Chen, H., Chen, J., Wang, S., Wang, Q., Wan, Q., Liu, B., Pan, M., Chang, L., Wu, H.T., Mei, G., Xiang, D., Li, X., Cai, C., Zhu, X., Chen, J.Z., Han, B., Chen, X., Guo, W., Zhang, T.Z., and Huang, X. Genomic insights into divergence and dual domestication of cultivated allotetraploid cottons. Genome Biology. 18:33. https://doi.org/1186/s13059-017-1167-5. 2017.
  85. Naoumkina, M., Hinchliffe, D.J., Fang, D.D., Florane, C.B., and Thyssen, G.N. Role of xyloglucan in cotton (Gossypium hirsutum) fiber elongation of the short fiber mutant Ligon-lintless-2 (Li2). Gene. 626:227-233. https://doi.org/10.1016/j.gene.2017.05.042. 2017.
  86. Naoumkina, M., Bechere, E., Fang, D.D., Thyssen, G.N., and Florane, C.B. Genome-wide analysis of gene expression of EMS-induced short fiber mutant Ligon lintless-y (liy) in cotton (Gossypium hirsutum). Genomics. 109:320-329. https://doi.org/10.1016/j.ygeno.2017.05.007. 2017.
  87. Bechere, E., Fang, D.D., Kebede, H., Hardin, B., Islam, M.S., Li, P., and Scheffler, J. Quantitative trait loci analysis for net ginning energy requirements in upland cotton (Gossypium hirsutum). Euphytica. 213:160. https://doi.org/10.1007/s10681-017-1951-z. 2017.
  88. Abdelraheem, A., Fang, D.D., and Zhang, J. Quantitative trait locus mapping of drought and salt tolerance in an introgressed recombinant inbred line population of Upland cotton under the greenhouse and field conditions. Euphytica. 214:8. https://doi.org/1007/s10681-017-2095-x.  2018.
  89. Fang, D.D. and Kim, H.J. History of cotton fiber bioscience research at USDA-ARS Southern Regional Research Center. Journal of Cotton Science. 22:12-23. http://www.cotton.org/journal/2018-22/1/upload/JCS22-012.pdf. 2018.
  90. Thyssen, G.N., Naoumkina, M., McCarty, J.C., Jenkins, J.N., Florane, C., Li, P., and Fang, D.D.§ The P450 gene CYP749A16 is required for tolerance to the sulfonylurea herbicide trifloxysulfuron sodium in cotton (Gossypium hirsutum L.). BMC Plant Biology. 18:186. https://doi.org/10.1186/s12870-018-1414-2.  2018. (§Corresponding author)
  91. Fang, D.D., Naoumkina, M., and Kim, H.J. 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. 2018.
  92. Thyssen, G.N., Jenkins, J.N., McCarty, J.C., Zeng, L., Campbell, B.T., Delhome, C.D., Islam, M.S., Li, P., Jones, D.C., Condon, B.D. and Fang, D.D.§ Whole genome sequencing of a MAGIC population identified genomic loci and candidate genes for major fiber quality traits in cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 132:989-999. https://doi.org/10.1007/s00122-018-3254-8. 2019. (§Corresponding author) 
  93. Naoumkina, M., Thyssen, G.N., Fang, D.D., Jenkins, J.N., McCarty, J.C., and Florane, C.B. Genetic and transcriptome dissection of the fiber length trait from cotton (Gossypium hirsutum) MAGIC population. BMC Genomics. 20:112. https://doi.org/10.1186/s12864-019-5427-5  2019.
  94. Wubben, M.J., Thyssen, G.N., Callahan, F.E., Fang, D.D., Deng, D.D., McCarty, J.C., Li, P., Islam, M.S., and Jenkins, J.N. A novel variant of Gh_D02G0276 is required for root-knot nematode resistance on chromosome 14 in Upland cotton. Theoretical and Applied Genetics. 132:1425-1434. https://doi.org/10.1007/s00122-019-03289-1. 2019.
  95. Hu, Y., Chen, J.D., Fang, L., Zhang, Z.Y.,  Ma, W.,  Niu, Y.,  Ju, R.Z.,  Zhao, T.,  Lian, J., Baruch, K.,  Fang, D.D.,  Liu, X.,  Ruan, , Rahman, M.,  Wang, Q.,  Deng, J.Q., Wu, H.T., Mei, G.P.,  Han, Z.G., Zhou, L.,  Huang, F.,   Brodt, A.,  Ben-Hamo, H.,  Zan, Y.H., Zhu, X.F., Zhou, B.L.,  Guan, X.Y., Zhu, S.J., Chen, X.Y.,  and Zhang, T.Z. Gossypium barbadense and Gossypium hirsutum genomes provide insights into the origin and evolution of allotetraploid cotton. Nature Genetics. 51:739-748. https://doi.org/10.1038/s41588-019-0371-5.  2019.
  96. Kim, H.J., Liu, Y., Fang, D.D., and Delhom, C.D. Feasibility assessment of phenotyping cotton fiber maturity using infrared spectroscopy and algorithms for genotyping analyses. Journal of Cotton Research. 2:8. https://doi.org/10.1186/s42397-019-0027-0. 2019.
  97. Islam, M.S., Fang, D.D., Jenkins, J.N., Guo, J., McCarty, J.C. and Jones, D.C. Evaluation of genomic selection methods for predicting fiber quality traits in upland cotton. Molecular Genetics and Genomics. 295:67-79. https://doi.org/10.1007/s00438-019-01599-z. 2020.
  98. Fang, D.D., Naoumkina, M., Thyssen, G.N, Bechere, E., Li, P., and Florane, C.B. 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. https://doi.org/10.1007/s00122-019-03456-4. 2020.
  99. Zhang, J., Abdelraheem, A., Thyssen, G.N., Fang, D.D., Jenkins, J.N., McCarty, J.C., and Wedegaertner, T. Evaluation and genome-wide association study of Verticillium wilt resistance in a MAGIC population derived from intermating of 11 Upland cotton (Gossypium hirsutum) parents. Euphytica. 216:9. https://doi.org/10.1007/s10681-019-2547-6. 2020.
  100. Naoumkina, M., Zeng, L., Fang, D.D., Wang, M., Thyssen, G.N, Florane, C.B., Li, P., and Delhom, C.D. Mapping and validation of a fiber length QTLon chromosome D11 using two independent F2 populations of upland cotton. Molecular Breeding. 40:31. https://doi.org/10.1007/s11032-020-01111-1. 2020.
  101. Li, Z.H., Wang, P.C., You, C.Y., Yu, J., Zhang, X., Yan, F., Ye, Z., Shen, C., Li, B., Guo, K., Liu, N., Thyssen, G.N., Fang, D.D., Lindsey, K., Zhang, X., Wang, M., and Tu, L. Combined GWAS and eQTL analysis uncovers a genetic regulatory network orchestrating the initiation of secondary cell wall development in cotton. New Phytologist. 226:1738-1752. https://doi.org/10.1111/nph.16468. 2020.
  102. Abdelraheem, A., Fang, D.D., Dever, J., and Zhang, J. QTL analysis of agronomic, fiber quality, and abiotic stress tolerance traits in a recombinant inbred population of pima cotton. Crop Science. 60:1823-1843. https://doi.org/10.1002/csc2.20153. 2020
  103. He, Z., Zhang, H., Fang, D.D., Zeng, L., Jenkins, J.N., and McCarty, J.C. Effects of inter-species chromosome substitution on cottonseed mineral and protein nutrition profiles. Agronomy Journal. 112:3963-3974. https://doi.org/10.1002/agj2.20264.  2020.
  104. Kim, H.J., Delhom, C.D., Fang, D.D., Zeng, L., Jenkins, J.N., McCarty, J.C., and Jones, D.C. Application of the Cottonscope for determining fiber maturity and fineness of an Upland cotton MAGIC population. Crop Science. 60:2266-2279. https://doi.org/10.1002/csc2.20197. 2020.
  105. Bechere, E., Fang, D.D., and Naoumkina, M. A new Ligon-lintless mutant (liy) in Upland cotton. Journal of Cotton Science. 24:168-174. http://www.cotton.org/journal/2020-24/4/upload/JCS24-168.pdf. 2020.
  106. Abdelraheem, A., Thyssen, G.N., Fang, D.D., Jenkins, J.N., McCarty, J.C., Wedegaertner, T., and Zhang, J. GWAS reveals consistent QTL for drought and salt tolerance in a MAGIC population of 550 lines derived from intermating of 11 Upland cotton (Gossypium hirsutum) parents. Molecular Genetics and Genomics. 296:119-129. https://doi.org/10.1007/s00438-020-01733-2. 2021.
  107. Naoumkina, M., Thyssen, G.N., Fang, D.D., Li, P., and Florane, B. Elucidation of sequence polymorphism in fuzzless-seed cotton lines. Molecular Genetics and Genomics. 296:193-206. https://doi.org/10.1007/s00438-020-01736-z. 2021.
  108. Fang, D.D., Zeng, L., Thyssen, G.N., Delhom,D., Bechere, E., Jones, D.C., and Li, P. Stability and transferability assessment of a cotton fiber strength QTL qFS-c7-1 on chromosome A07. The Crop Journal. 9:380-386. https://doi.org/10.1016/j.cj.2020.06.016. 2021.
  109. He, Z., Nam, S., Fang, D.D., Cheng, H.N., and He, J. Surface and thermal characterization of cotton fibers of phenotypes differing in fiber length. Polymers. 13:194. https://doi.org/10.3390/polym13070994. 2021.
  110. Naoumkina, M., Thyssen, G.N., Fang, D.D., Bechere, E., Li, P., and Florane, C.B. Mapping-by-sequencing the locus of EMS-induced mutation responsible for tufted-fuzzless seed phenotype in cotton. Molecular Genetics and Genomics. 296:1041-1049.   https://doi.org/10.1007/s00438-021-01802-0. 2021.
  111. Jenkins, J.N., McCarty, J.C., Hayes, R.W., Wubben, M.J., Fang, D.D., Thyssen, G.N., Zeng, L., Campbell, T.B. and Jones, D.C. Registration of seven recombinant inbred lines of upland cotton with improved fiber length and/or strength.  Journal of Plant Registrations. 16:94-99. https://doi.org/10.1002/plr2.20193.   2022. 
  112. Wang, M., Qi, Z.Y., Thyssen, G.N., Naoumkina, M., Jenkins, J.N., McCarty, J.C., Xiao, Y., Li, J., Zhang, X., and Fang, D.D.§ Genetic dissection of a MAGIC population highlights genetic and epistatic factors controlling fiber quality traits in cotton. Communications Biology. 5:60. https://doi.org/10.1038/s42003-022-03022-7.    2022. (§Corresponding author)  
  113. Pei, L.L., Huang, X.H., Liu, Z.P., Wang, P.C., Tian, X.H., You, J.Q., Li, J.Y., Fang, D.D., Lindsey, K., Zhu, L.F., Zhang, X.L., and  Wang, M.J.  Dynamic 3D genome architecture of cotton fiber reveals subgenome-coordinated chromatin topology for 4-staged single-cell differentiation. Genome Biology. 23:45. https://doi.org/10.1186/s13059-022-02616-y.  2022.
  114. Zhu, Y., Thyssen, G.N., Abdelraheem, A., Teng, Z., Fang, D.D., Jenkins, J.N., McCarty, J.C., Wedegaertner, T., Hake, K., and Zhang, J. A GWAS identified a major QTL for resistance to Fusarium wilt (Fusarium oxysporum sp. vasinfectum) race 4 in a MAGIC population of Upland cotton and a meta-analysis of QTLs for Fusarium wilt resistance. Theoretical and Applied Genetics. 135:2297-2312.  https://doi.org/10.1007/s00122-022-04113-z. 2022.   
  115. Naoumkina, M., Thyssen, G.N., Fang, D.D., Florane, C.B., and Li, P. A deletion/duplication in the Ligon-lintless-1locus induces siRNAs that inhibit cotton fiber cell elongation. Plant Physiology. 190:1792-1805.  https://doi.org/10.1093/plphys/kiac384.  2022.
  116. Wang, M., Li, J., Qi, Z., Long, Y., Pei, L., Huang, X., Grover, C.E., Liu, F., Du, X.M.,  Xia, C., Wang, P., Liu, Z., You, J., Tian, X.,  Ma, Y., Wang, R., Chen, X., He, X., Fang, D.D., Sun, Y., Tu, L., Jin, S., Zhu, L., Wang, K., Wendel, J.F., and Zhang, X. Genomic innovation and regulatory rewiring during evolution of the cotton genus (Gossypium). Nature Genetics. 54:1959-1971.  https://doi.org/10.1038/s41588-022-01237-2. 2022. 
  117. Fang, D.D., Thyssen, G.N., Wang, M., Jenkins, J.N., McCarty, J.C., and Jones, D.C. Genomic confirmation of Gossypium barbadense introgression into hirsutum and a subsequent MAGIC population. Molecular Genetics and Genomics. 298:143-152. https://doi.org/10.1007/s00438-022-01974-3. 2023.
  118. Thyssen, G.N., Condon, B.D., Hinchliffe, D.J., Zeng, L., Naoumkina, N., Jenkins, J.N., McCarty, J.C., Sui, R., Madison, C., Li, L., Fang, D.D. Flame resistant cotton lines generated by synergistic epistasis in a MAGIC population. PLoS ONE. 18(1): e0278696. https://doi.org/10.1371/journal.pone.0278696.  2023.
  119. Zeng, L., Fang, D.D., Li, P., and Delhom, C.D. A comparative study between trait selection and marker-assisted selection to improve fiber strength in Upland cotton. Crop Science. 63(2):1092-1101. https://doi.org/10.1002/csc2.20881.   2023.
  120. He, Z.Q., Nan S. and Fang, D.D. Raman spectroscopic assessment of fibers and seeds of six cotton genotypes. Agricultural and Environmental Letters. 8:e20102.  https://doi.org/10.1002/ael2.20102   2023.
  121. Zeng, L.H., Hinze, L., Fang, D.D., Delhom, C.D., and Zhang, J. Analysis of a cotton introgression population derived through multiple generations of random mating in multiple-parents crosses. Euphytica. 219:101. https://doi.org/10.1007/s10681-023-03213-1. 2023.
  122. You, J., Liu, Z., Qi, Z., Ma, Y.,  Sun, M., Chen, X., Su, L., Niu, H., Peng, Y., Luo, X.,   Zhu, M., Huang, Y., Chang, X.,  Hu, X., Pi, R., Liu, Y., Meng, Q., Li, J., Zhu, L., Lin, Z.,  Min, L., Yuan, D., Grover, C.E., Fang, D.D., Lindsey, K., Wendel, J.F., Tu, L., Zhang, X., and Wang, M. Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton. Nature Genetics.55:1987-1997. https://doi.org/10.1038/s41588-023-01530-8. 2023. 
  123. Nam, S., Liu, Y.L., He, Z., Hinchliffe, D.J., and Fang, D.D. Assessment of Segal method for identifying crystallinity evolution in developing cotton fibers. Agricultural and Environmental Letters. 9:e20138. https://doi.org/10.1002/ael2.20138. 2024.
  124. Garcia, A.A., Frisch, M., Weng, Y., Varshnev, R., Sorrells, M., and Fang, D.D. Heterosis and hybrid breeding. Theoretical and Applied Genetics. 2024.
  125. Nam, S., Easson, M.W., Jordan, J.H., He, Z., Lima, I.M., Hillyer, M.B., Ernst, N.E., Fang, D.D., and Islam, M.H. Repurposing cotton gin trash for cellulose nanofibril−silver hybrid and ultralight silver-infused aerogel.  ACS Omega. https://doi.org/10.1021/acsomega.4c05728.  2024.
  126. Naoumkina, M., Thyssen, G.N., Zeng, L.H., Shockey, J., Neumann, N., Florane, C.B., Jenkins, J.N., McCarty, J.C., and Fang, D.D. Interaction of the cyclin-dependent kinase inhibitor GhKRP6 with RING-Type E3 ligase influences the fiber length in Upland cotton. Industrial Crops and Products. 222:119789. https://doi.org/10.1016/j.indcrop.2024.119789.   2024.
  127. Kim, HJ., Thyssen, G.N., Delhom, C.D., Fang, D.D., Naoumkina, M., Florane, C.B., Li, P., Jenkins, J.N., McCarty, J.C., Zeng, L., Campbell, T.B., and Jones, D.C. Genome-wide association studies of bundle and single fiber length traits reveal the genetic basis of within-sample variation in upland cotton fiber length. Frontier in Plant Sciences. 15:1472675. https://doi.org/10.3389/fpls.2024.1472675.  2024.

    Book Chapters (6)

  1. Percy, R.G., Frelichowski, J.E., Arnold, M., Campbell, B.T., Dever, J., Fang, D.D., Hinze, L.L., Main, D., Scheffler, J.A., Sheehan, M., Ulloa, M., Yu, J., Yu, J. The U.S. National Cotton Germplasm Collection – its contents, preservation, characterization, and evaluation. In: Abdurakhmonov, I. Editor. World Cotton Germplasm Resources. Rijeka, Croatia: InTech. pp167-201. 2014.
  2. Fang, D.D. Molecular breeding. In: Fang, D.D. and Percy, R.G. (eds) Cotton 2nd ASA-CSSA-SSSA, Madison, WI, USA. pp 255-288. DOI: 10.2134/agronmonogr57.2013.0019. 2015.
  3. Lee, J.A., and Fang, D.D. Cotton as a world crop: origin, history and current status. In: Fang, D.D. and Percy, R.G. (eds) Cotton 2nd ASA-CSSA-SSSA, Madison, WI, USA. pp 1-24. DOI:0.2134/agronmonogr57.2013.0027. 2015.
  4. Fang, D.D. Chapter 1: General description of cotton. In: Fang, D.D (ed) Cotton fiber: physics, chemistry and biology. Springer-Nature Publishing Group. Gewerbestrasse 11, 6330 Cham, Switzerland. pp 1-11. DOI: 1007/978-3-030-00871-0_1. 2018.
  5. Fang, D.D. Chapter 8: Cotton fiber genes and stable quantitative trait loci. In: Fang, D.D (ed) Cotton fiber: physics, chemistry and biology. Springer-Nature Publishing Group. Gewerbestrasse 11, 6330 Cham, Switzerland. pp 151-178. DOI: 1007/978-3-030-00871-0_8. 2018.
  6. Fang, D.D. Chapter 7: Genomics-based breeding. In: Zhang, J. (ed) Cotton Genome. Springer-Nature Publishing Group. Gewerbestrasse 11, 6330 Cham, Switzerland. 2025. (Book chapter)