, 215:74 | Cite as

Genomic analysis of marker-associated fiber development genes in upland cotton (Gossypium hirsutum L)

  • John Z. YuEmail author
  • Kyle A. Gervers


Understanding genetic control of fiber development is essential for cotton improvement. This study analyzed several thousand fiber Unigenes in Upland cotton (Gossypium hirsutum). They included 2423 Unigenes for fiber initiation (IN), 1841 for fiber elongation (EL) and 86 for secondary cell wall deposition (SCWD). These Unigenes were located on recombination hotspots between At and Dt subgenomes with nearly equal frequency (51% vs. 49%). Sequence analysis with Upland cotton TM-1 genome assembly showed that 477 IN, 464 EL, 20 SCWD and 367 non-fiber Unigenes intersect with predicted coding sequences. There were 140 IN, 118 EL and one SCWD Unigenes that do not overlap between individual stages of fiber development. Annotation of top scoring Unigenes with Kyoto encyclopedia of genes and genomes indicated mitochondrial biogenesis for IN Unigene #18205, conversion of PRPP to histidine for IN #25329, and spliceosome pathways for IN #24380. EL Unigene #11669 appeared to be responsible for septum site-determining protein, EL #11916 for vacuolar protein, and EL #17251 for protein trichome birefringence-like 33. One SCWD Unigene #190099 was responsible for legumin A-like protein. In addition, Unigene #03070 overlapped three fiber development stages and involved in fatty acid biosynthesis. Unigenes that shared same genomic positions for all fiber stages are of particular interest as they may have possible pleiotropic function. On the other hand, Unigenes from one fiber development stage that did not share with any other stage may have stage-specific function. This information would be useful for plant breeders to exploit fiber genes in cotton breeding programs.


Upland cotton (Gossypium hirsutumFiber development EST unigenes Pleiotropic function Tetraploid genome 



This work was supported by the United States Department of Agriculture, Agricultural Research Service (USDA-ARS Project 3091-21000-044-00D).


  1. Beasley JO (1940) The origin of American tetraploid Gossypium species. Am Nat 74:285–286CrossRefGoogle Scholar
  2. Blenda A, Fang DD, Rami JF, Garsmeur O, Luo F, Lacape JM (2012) A high density consensus genetic map of tetraploid cotton that integrates multiple component maps through molecular marker redundancy check. PLoS ONE 7(9):e45739. CrossRefPubMedPubMedCentralGoogle Scholar
  3. Camacho C, Coulouris G, Avagyan V, Ma N, Papadopoulos J, Bealer K, Madden TL (2009) BLAST+: architecture and applications. BMC Bioinform. CrossRefGoogle Scholar
  4. Campbell BT, Saha S, Percy R, Frelichowski J, Jenkins JN, Park W, Mayee CD, Gotmare V, Dessauw D, Giband M, Du X, Jia Y, Constable G, Dillon S, Abdurakhmonov IY, Abdukarimov A, Rizaeva SM, Adullaev A, Barroso PAV, Pádua JG, Hoffmann LV, Podolnaya L (2010) Status of the global cotton germplasm resources. Crop Sci 50(4):1161–1179CrossRefGoogle Scholar
  5. Esbroeck GV, Bowman DT (1998) Cotton germplasm diversity and its importance to cultivar development. J Cotton Sci 2:121–129Google Scholar
  6. Hinze LL, Fang D, Gore M, Scheffler B, Yu J, Frelichowski J, Percy R (2015) Molecular characterization of the Gossypium diversity reference set of the US National cotton germplasm collection. Theor Appl Genet 128:313–327CrossRefGoogle Scholar
  7. Hinze LL, Gazave E, Gore MA, Fang DD, Scheffler BE, Yu JZ, Jones DC, Frelichowski J, Percy RG (2016) Genetic diversity of the two commercial tetraploid cotton species in the Gossypium diversity reference set. J Hered 107:274–286CrossRefGoogle Scholar
  8. Kanehisa M, Sato Y, Kawashima M, Furumichi M, Tanabe M (2016) KEGG as a reference resource for gene and protein annotation. Nucleic Acids Res 44(D1):D457–D462CrossRefGoogle Scholar
  9. Kanehisa M, Furumichi M, Tanabe M, Sato Y, Morishima K (2017) KEGG: new perspectives on genomes, pathways, diseases and drugs. Nucleic Acids Res 45(D1):D353–D361CrossRefGoogle Scholar
  10. Kent WJ (2002) BLAT—the BLAST-like alignment tool. Genome Res 12:656–664CrossRefGoogle Scholar
  11. Kim HJ, Triplett BA (2001) Cotton fiber growth in planta and in vitro: models for plant cell elongation and cell wall biogenesis. Plant Physiol 127:1361–1366CrossRefGoogle Scholar
  12. Kohel RJ, Yu JZ (2002) Molecular characterization of Gossypium germplasm for cotton improvement. In: Engles JMM, Rao VR, Brown AHD, Jackson MT (eds) Managing plant genetic diversity. CAB International, Wallingford, UK, pp 67–76Google Scholar
  13. Kohel RJ, Richmond TR, Lewis CF (1970) Texas marker-1, description of a genetic standard for Gossypium hirsutum. Crop Sci 10:670–671CrossRefGoogle Scholar
  14. Leitch IJ, Bennett MD (1997) Polyploidy in angiosperms. Trends Plant Sci 2:470–476CrossRefGoogle Scholar
  15. Li F, Fan G, Lu C, Xiao G, Zou C, Kohel RJ, Ma Z, Shang H, Ma X, Wu J, Liang X, Huang G, Percy RG, Liu K, Yang W, Chen W, Du X, Shi C, Yuan Y, Ye W, Liu X, Zhang X, Liu W, Wei H, Wei S, Huang G, Zhang X, Zhu S, Zhang H, Sun F, Wang X, Liang J, Wang J, He Q, Huang L, Wang J, Cui J, Song G, Wang K, Xu X, Yu JZ, Zhu Y, Yu S (2015) Genome sequence of cultivated Upland cotton (Gossypium hirsutum TM-1) provides insights into genome evolution. Nat Biotechnol 33:524–530CrossRefGoogle Scholar
  16. Mochida K, Yoshida T, Sakurai T, Ogihara Y, Shinozaki K (2009) TriFLDB: a database of clustered full-length coding sequences from triticeae with applications to comparative grass genomics. Plant Physiol 150(3):1135–1146. Google Scholar
  17. Ogata H, Goto S, Sato K, Fujibuchi W, Bono H, Kanehisa M (1999) KEGG: kyoto encyclopedia of genes and genomes. Nucleic Acids Res 27(1):29–34CrossRefGoogle Scholar
  18. Percy RG, Frelichowski JE, Arnold M, Campbell BT, Dever J, Fang DD, Hinze LL, Main D, Scheffler JA, Sheehan M, Ulloa M, Yu J, Yu JZ (2014) The U.S. National cotton germplasm collection—its contents, preservation, characterization, and evaluation. In: Abdurakhmonov (ed) World cotton germplasm Resources. Rijeka, InTech, pp 167–201Google Scholar
  19. Quinlan AR, Hall IM (2010) BEDTools: a flexible suite of utilities for comparing genomic features. Bioinformatics 26(6):841–842CrossRefGoogle Scholar
  20. Rong JK, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS, Park C, Pierce GJ, Rainey KM, Rastogi VK, Schulze SR, Trolinder NL, Wendel JF, Wilkins TA, Williams-Coplin TD, Wing RA, Wright RJ, Zhao X, Zhu L, Paterson AH (2004) A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics 166:389–417. CrossRefPubMedPubMedCentralGoogle Scholar
  21. Shi Y, Li W, Li A, Ge R, Zhang B, Li J, Liu G, Li J, Liu A, Shang H, Gong J, Gong W, Yang Z, Tang F, Liu Z, Zhu W, Jiang J, Yu X, Wang T, Wang W, Chen T, Wang K, Zhang Z, Yuan Y (2014) Constructing a high- density linkage map for Gossypium hirsutum x Gossypium barbadense and identifying QTLs for lint percentage. Integr Plant Biology 57:450–467CrossRefGoogle Scholar
  22. Tanksley SD, McCouch SR (1997) Seed banks and molecular maps: unlocking genetic potential from the wild. Science 277:1063–1066CrossRefGoogle Scholar
  23. Udall JA, Swanson JM, Haller K, Rapp RA, Sparks ME, Hatfield J, Yu Y, Wu Y, Dowd C, Arpat AB, Sickler BA, Wilkins TA, Guo JY, Chen XY, Scheffler J, Taliercio E, Turley R, McFadden H, Payton P, Klueva N, Allen R (2006) A global assembly of cotton ESTs. Genome Res 16(3):441–450CrossRefGoogle Scholar
  24. Wallace TP, Bowman D, Campbell BT, Chee P, Gutierrez OA, Kohel RJ, McCarty J, Myers G, Percy R, Robinson F, Smith W, Stelly DM, Stewart JM, Thaxton P, Ulloa M, Weaver DB (2009) Status of the USA cotton germplasm collection and crop vulnerability. Genet Resour Crop Evol 56(4):507–532CrossRefGoogle Scholar
  25. Wendel JF, Grover CE (2015) Taxonomy and evolution of the cotton genus, Gossypium. In: Cotton Agronomy Monograph 57 ASA, CSSA, and SSSA, 2nd edn. Madison, WI, pp 25–44.
  26. Wendel JF, Flagel LE, Adams KL (2012) Jeans, genes, and genomes: cotton as a model for studying polyploidy. In: Soltis PS, Soltis DE (eds) Polyploidy and genome evolution. Springer, New York, pp 181–207CrossRefGoogle Scholar
  27. Xiao J, Li J, Grandillo S, Ahn S, McCouch S, Tanksley S, Yuan L (1995) A wild species contains genes that may significantly increase the yield of rice. Nature 384:233–235Google Scholar
  28. Xu Z, Kohel RJ, Song G, Cho J, Yu J, Yu S, Tomkins J, Yu JZ (2008a) An integrated genetic and physical map of homoeologous chromosomes 12 and 26 in Upland cotton (G. hirsutum L.). BMC Genomics. 9:108. CrossRefPubMedPubMedCentralGoogle Scholar
  29. Xu Z, Kohel RJ, Song G, Cho J, Alabady M, Yu J, Koo P, Chu J, Yu S, Wilkins TA, Zhu Y, Yu JZ (2008b) Gene-rich islands for fiber development in the cotton genome. Genomics 92(3):173–183CrossRefGoogle Scholar
  30. Xu Z, Yu J, Kohel RJ, Percy RG, Beavis WD, Main D, Yu JZ (2015) Distribution and evolution of cotton fiber development genes in the fibreless Gossypium raimondii genome. Genomics 106(1):61–69CrossRefGoogle Scholar
  31. Yu J, Kohel RJ, Smith CW (2010) The construction of a tetraploid cotton genome-wide comprehensive reference map. Genomics 95(4):230–240CrossRefGoogle Scholar
  32. Yu Y, Yuan D, Liang S, Li X, Wang X, Lin Z, Zhang X (2011) Genome structure of cotton revealed by a genome-wide SSR genetic map constructed from a BC1 population between Gossypium hirsutum and G. barbadense. BMC Genomics 12:15. CrossRefPubMedPubMedCentralGoogle Scholar
  33. Yu JZ, Kohel RJ, Fang DD, Cho J, Van Deynze A, Ulloa M, Hoffman SM, Pepper AE, Stelly DM, Jenkins JN, Saha S, Kumpatla SP, Shah MR, Hugie WV, Percy RG (2012) A high-density SSR and SNP genetic map of the tetraploid cotton genome. G3: genes. Genomes Genet 2:43–58Google Scholar
  34. Yu J, Jung S, Cheng CH, Ficklin SP, Lee T, Zheng P, Jones D, Percy RG, Main D (2014a) CottonGen: a genomics, genetics and breeding database for cotton research. Nucleic Acids Res 42:D1229–D1236CrossRefGoogle Scholar
  35. Yu JZ, Ulloa M, Hoffman SM, Kohel RJ, Pepper AE, Fang DD, Percy RG, Burke JJ (2014b) Mapping genomic loci for cotton plant architecture, yield components, and fiber properties in an interspecific (Gossypium hirsutum L. x G. barbadense L.) RIL population. Mol Genet Genom 289:1347–1367CrossRefGoogle Scholar
  36. Zhang T, Hu Y, Jiang W, Fang L, Guan X, Chen J, Zhang J, Saski CA, Scheffler BE, Stelly DM, Hulse-Kemp AM, Wan Q, Liu B, Liu C, Wang S, Pan M, Wang Y, Wang D, Ye W, Chang L, Zhang W, Song Q, Kirkbride RC, Chen X, Dennis E, Llewellyn DJ, Peterson DG, Thaxton P, Jones DC, Wang Q, Xu X, Zhang H, Wu H, Zhou L, Mei G, Chen S, Tian Y, Xiang D, Li X, Ding J, Zuo Q, Tao L, Liu Y, Li J, Lin Y, Hui Y, Cao Z, Cai C, Zhu X, Jiang Z, Zhou B, Guo W, Li R, Chen ZJ (2015) Sequencing of allotetraploid cotton (Gossypium hirsutum L. acc. TM-1) provides a resource for fiber improvement. Nat Biotechnol 33:531–537CrossRefGoogle Scholar

Copyright information

© This is a U.S. government work and not under copyright protection in the U.S.; foreign copyright protection may apply 2019

Authors and Affiliations

  1. 1.Southern Plains Agricultural Research Center, Crop Germplasm Research UnitUSDA-ARSCollege StationUSA
  2. 2.Department of Botany and Plant PathologyOregon State UniversityCorvallisUSA

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