, Volume 161, Issue 3, pp 361–370 | Cite as

BAC-derived SSR markers chromosome locations in cotton

  • Yufang Guo
  • Sukumar Saha
  • John Z. Yu
  • Johnie N. Jenkins
  • Russell J. Kohel
  • Brian E. Scheffler
  • David M. Stelly


Bacterial artificial chromosome (BAC) libraries with large DNA fragment inserts have rapidly become the preferred choice for physical mapping. BAC-derived microsatellite or simple sequence repeats (SSRs) markers facilitate the integration of physical maps with genetic maps. The objective of this research was to identify chromosome locations of the BAC-derived SSR markers in tetraploid cotton. A total of 192 SSR primer pairs were derived from BAC clones of an Upland cotton genetic standard line TM-1 (Gossypium hirsutum L.). Metaphor agarose gel electrophoresis results revealed 76 and 59 polymorphic markers between TM-1 and 3–79 (G. barbadense) or G. tomentosum, respectively. Using deletion analysis method, we assigned 39 markers out of the 192 primer pairs to 17 different chromosomes or chromosome arms. Among them, 19 and 17 markers were localized to A-subgenomes (chromosome 1–13) and D-subgenomes (chromosome 14–26), respectively. The subgenome status for the remaining three markers remained unclear due to their two potential chromosome locations achieved by tertiary monosomic stocks deletion analysis. Chromosomal assignment of these BAC-derived SSR markers will help in integrating physical and cotton genetic linkage maps and thus facilitate positional candidate gene cloning, comparative genome analysis, and the coordination of chromosome-based genome sequencing project in cotton.


BAC-derived SSR Chromosome location Cotton (GossypiumAneuploid lines 



Bacterial artificial chromosome


Expressed sequence tag


Fluorescence in situ hybridization


Quantitative trait locus


Sequence characterized amplified region


Simple sequence repeat


Single nucleotide polymorphisms




Tertiary monosomic cytogenetic stock


  1. Abdurakhmonov IY, Kushanov K, Djaniqulov1 F, Buriev Z, Pepper AE, Fayzieva N, Mavlonov G, Saha S, Jenkins JN, Abdukarimov A (2007) The role of induced mutation in conversion of photoperiod dependence in cotton. J Heredity 98(3):258–266CrossRefGoogle Scholar
  2. An C, Saha S, Jenkins JN, Scheffler BE, Wilkins TA, Stelly DM (2007) Transcriptome profiling, sequence characterization, and SNP-based chromosomal assignment of the EXPANSIN genes in cotton. Mol Gen Genomics 278:539–553CrossRefGoogle Scholar
  3. Blenda A, Scheffler J, Scheffler B, Palmer M, Lacape JM, Yu JZ, Jesudurai C, Jung S, Muthukumar S, Yellambalase P, Ficklin S, Staton M, Eshelman R, Ulloa M, Saha S, Burr B, Liu S, Zhang T, Fang D, Pepper A, Kumpatla S, Jacobs J, Tomkins J, Cantrell R, Main D (2006) CMD: a cotton microsatellite database resource for Gossypium genomics. BMC Genomics 7:132PubMedCrossRefGoogle Scholar
  4. Chen M, Presting G, Barbazuk WG, Goicoechea JL, Blackmon B, Fang G, Kim H, Frisch D, Yu Y, Sun S (2002) An integrated physical and genetic map of the rice genome. Plant Cell 14:537–545PubMedCrossRefGoogle Scholar
  5. Cregan PB, Mudge J, Fickus EW, Marek LF, Danish D, Denny R, Shoemaker RC, Matthews BF, Jarvik T, Young ND (1999) Targeted isolation of simple sequence repeat markers through the use of bacterial artificial chromosomes. Theor Appl Genet 98:919–928CrossRefGoogle Scholar
  6. Danesh D, Penuela S, Mudge J, Denny RL, Nordstrom H, Martinez JP, Young ND (1998) A bacterial artificial chromosome library for soybean and identification of clones near a major cyst nematode resistant gene. Theor Appl Genet 96:196–202CrossRefGoogle Scholar
  7. Frelichowski JE Jr, Palmer MB, Main D, Tomkins JP, Cantrell RG, Stelly DM, Yu J, Kohel RJ, Ulloa M (2006) Cotton genome mapping with new microsatellites from Acala ’Maxxa’ BAC-ends. Mol Gen Genomics 275:479–491CrossRefGoogle Scholar
  8. Guo W, Cai C, Wang C, Han Z, Song X, Wang K, Niu X, Wang C, Lu K, Shi B, Zhang T (2007) A microsatellite-based, gene-rich linkage map reveals genome structure, function and evolution in Gossypium. Genetics 176:527–541PubMedCrossRefGoogle Scholar
  9. Guo W, Zhang T, Shen X, Yu JZ, Kohell RJ (2003) Development of SCAR marker linked to a major QTL for high fiber strength and its usage in molecular-marker assisted selection in Upland cotton. Crop Sci 43:2252–2256CrossRefGoogle Scholar
  10. Han Z, Wang C, Song X, Guo W, Gou J, Li C, Chen X, Zhang T (2006) Characteristics, development and mapping of Gossypium hirsutum derived EST-SSRs in allotetraploid cotton. Theor Appl Genet 112:430–439PubMedCrossRefGoogle Scholar
  11. Han ZG, Guo WZ, Song XL, Zhang TZ (2004) Genetic mapping of EST-derived microsatellites from the diploid Gossypium aboreum in allotetraploid cotton. Mol Gen Genomics 272:308–327CrossRefGoogle Scholar
  12. Hanson RE, Zwick MS, Choi S, Islam-Faridi MN, McKnight TD, Wing RA, Price HJ, Stelly DM (1995) Fluorescent in situ hybridization of a bacterial artificial chromosome. Genome 38:646–651PubMedCrossRefGoogle Scholar
  13. Kohel RJ, Stelly DM, Yu J (2002) Tests of six cotton (Gossypium hirsutum L.) mutants for association with aneuploids. J Hered 93:130–132PubMedCrossRefGoogle Scholar
  14. Lacape JM, Nguyen TB, Courtois B, Belot JL, Giband M, Gourlot JP, Gawryziak G, Roques S, Hau B (2005) QTL analysis of cotton fiber quality using multiple Gossypium hirsutum  ×  Gossypium barbadense backcross generations. Crop Sci 45:123–140Google Scholar
  15. Lacape JM, Nguyen TB, Thibivilliers S, Bojinov B, Courtois B, Cantrell RG, Burr B, Hau B (2003) A combined RFLP-SSR-AFLP map of tetraploid cotton based on a Gossypium hirsutum  ×  Gossypium barbadense backcross population. Genome 46:612–626PubMedCrossRefGoogle Scholar
  16. Lichtenzveig J, Scheuring C, Dodge J, Abbo S, Zhang HB (2005) Construction of BAC and BIBAC libraries and their applications for generation of SSR markers for genome analysis of chickpea, Cicer arietinum L. Theor Appl Genet 110:492–510PubMedCrossRefGoogle Scholar
  17. Liu S, Saha S, Stelly DM, Burr B, Cantrell RG (2000) Chromosomal assignment of microsatellite loci in cotton. J Hered 91:326–332PubMedCrossRefGoogle Scholar
  18. Nguyen TB, Giband M, Brottier P, Risterucci AM, Lacape JM (2004) Wide coverage of the tetraploid cotton genome using newly developed microsatellite markers. Theor Appl Genet 109:167–176PubMedCrossRefGoogle Scholar
  19. Park YH, Alabady MS, Ulloa M, Sickler B, Wilkins TA, Yu J, Stelly DM, Kohel RJ, El-Shihy OM, Cantrell RG (2005) Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol Gen Genomics 274:428–441CrossRefGoogle Scholar
  20. Rong J, 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 166:389–417PubMedCrossRefGoogle Scholar
  21. Saha S, Stelly DM (1994) Chromosomal location of phosphoglucomutase7 locus in Gossypium hirsutum. J Hered 85:35–40Google Scholar
  22. Song X, Wang K, Guo W, Zhang J, Zhang T (2005) A comparison of genetic maps constructed from haploid and BC1 mapping populations from the same crossing between Gossypium hirsutum L. and Gossypium barbadense L. Genome 48:378–390PubMedCrossRefGoogle Scholar
  23. Ulloa M, Saha S, Jenkins JN, Meredith WR, McCarty JC, Stelly DM (2005) Chromosomal assignment of RFLP linkage groups harboring important QTLs on an intraspecific cotton (Gossypium hirsutum L.) joinmap. J Hered 96:132–144PubMedCrossRefGoogle Scholar
  24. Wang K, Guo W, Zhang T (2007) Development of one set of chromosome-specific microsatellite-containing BACs and their physical mapping in Gossypium hirsutum L. Theor Appl Genet 115:675–682PubMedCrossRefGoogle Scholar
  25. Wang K, Song X, Han Z, Guo W, Yu JZ, Sun J, Pan J, Kohel RJ, Zhang T (2006) Complete assignment of the chromosomes of Gossypium hirsutum L. by translocation and fluorescence in situ hybridization mapping. Theor Appl Genet 113:73–80PubMedCrossRefGoogle Scholar
  26. Wendel JF, Albert VA (1992) Phylogenetics of the cotton genus (Gossypium): character-state weighted parsimony analysis of chloroplast-DNA restriction site data and its systematic and biogeographic implications. Sys Bot 17:115–143CrossRefGoogle Scholar
  27. Werner-Fraczek JE, Close TJ (1998) Genetic studies of Triticeae dehydrins: assignment of seed proteins and a regulatory factor to map positions. Theor Appl Genet 97:220–226CrossRefGoogle Scholar
  28. Wu C, Sun S, Nimmakayala P, Santos F, Meksem K, Springman R, Ding K, Lightfoot DA, Zhang HB (2004) A BAC- and BIBAC-based physical map of the soybean genome. Genome Res 14:319–326PubMedCrossRefGoogle Scholar
  29. Yin J, Guo W, Yang L, Liu L, Zhang T (2006) Physical mapping of the Rf 1 fertility-restoring gene to a 100 kb region in cotton. Theor Appl Genet 112:1318–1325PubMedCrossRefGoogle Scholar
  30. Yu JZ, Kohel RJ, Dong J (2002a) Development of integrative SSR markers from TM-1 BACs. Proceeding of Beltwide cotton improvement conference, Atlanta, GA, January 8–12, 2002. CD-Rom Published by National Cotton Council of AmericaGoogle Scholar
  31. Yu JZ, Kohel RJ, Zhang HB, Dong J, Sun S, Steele NL (2002b) Toward development of a whole-genome, BAC/BIBAC-based integrated physical/genetic map of the cotton genome using the Upland genetic standard TM-1: BAC and BIBAC library construction, SSR marker development, and physical/genetic map integration. The third international cotton genome initiative workshop, Nanjing, China, June 3–6, 2002. Cotton Sci 14(S):32Google Scholar
  32. Yu JZ, Kohel RJ, Zhang HB, Stelly D M, Xu Z, Dong J, Covaleda L, Lee MK, Cui P, Lazo GR, Gupta P, Ding K (2004a) Toward an integrative physical and genetic map of the cultivated allotetraploid cotton genome. Proceedings of the 12th International Conference on Plant and Animal Genome, San Diego, CA, January 10–16, 2004. P. No. W147 Cited 25 Oct 2007
  33. Yu JZ, Kohel RJ, Zhang HB, Xu Z, Dong J (2004b) Integrated physical mapping of the cotton genome. Proceedings of the fourth International Cotton Genome Initiative (ICGI) Workshop, Hyderabad, India, October 10–13, 2004. Books of Abstracts, Published by CIRCOT, Mumbai, India. P. 2Google Scholar
  34. Zhang P, Li W, John F, Bernd F, Bikram SG (2004) BAC-FISH in wheat identifies chromosome landmarkers consisting of different types of transposable elements. Chromosoma 112:288–299PubMedCrossRefGoogle Scholar

Copyright information

© GovernmentEmployee: U. S. Department of Agriculture, Agricultural Research Service 2007

Authors and Affiliations

  • Yufang Guo
    • 1
  • Sukumar Saha
    • 2
  • John Z. Yu
    • 3
  • Johnie N. Jenkins
    • 2
  • Russell J. Kohel
    • 3
  • Brian E. Scheffler
    • 4
  • David M. Stelly
    • 5
  1. 1.Department of Plant and Soil SciencesMississippi State UniversityMississippi StateUSA
  2. 2.USDA-ARS, Crop Science Research LaboratoryMississippi StateUSA
  3. 3.USDA-ARS, Crop Germplasm Research UnitCollege StationUSA
  4. 4.USDA-ARS-CGRUStonevilleUSA
  5. 5.Department of Soil and Crop SciencesTexas A&M UniversityCollege StationUSA

Personalised recommendations