Development and characterization of genomic and expressed SSRs for levant cotton (Gossypium herbaceum L.)
Four microsatellite-enriched genomic libraries for CA(15), GA(15), AAG(8) and ATG(8) repeats and transcriptome sequences of five cDNA libraries of Gossypium herbaceum were explored to develop simple sequence repeat (SSR) markers. A total of 428 unique clones from repeat enriched genomic libraries were mined for 584 genomic SSRs (gSSRs). In addition, 99,780 unigenes from transcriptome sequencing were explored for 8,900 SSR containing sequences with 12,471 expressed SSRs. The present study adds 1,970 expressed SSRs and 263 gSSRs to the public domain for the use of genetic studies of cotton. When 150 gSSRs and 50 expressed SSRs were tested on a panel of four species of cotton, 68 gSSRs and 12 expressed SSRs revealed polymorphism. These 200 SSRs were further deployed on 15 genotypes of levant cotton for the genetic diversity assessment. This is the first report on the successful use of repeat enriched genomic library and expressed sequence database for microsatellite markers development in G. herbaceum.
KeywordsSimple Sequence Repeat Marker Polymorphism Information Content Repeat Motif Genomic SSRs Simple Sequence Repeat Motif
The present work was financially supported by the Council of Scientific and Industrial Research, New Delhi (CSIR under NMITLI, SIP 005).
- 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 7:132–142Google Scholar
- Gupta PK, Balyan HS, Sharma PC, Ramesh B (1996) Microsatellites in plants: a new class of molecular markers. Curr Sci 70:45–54Google Scholar
- Hartl D, Clark A (1989) Principles of population genetics, 2nd edn. Sinauer Associates, SunderlandGoogle Scholar
- Jarvie T, Harkins T (2008) Transcriptome sequencing with the Genome Sequencer FLX system. Nat Methods 5:6–8Google Scholar
- Jones KC, Levine KF, Banks JD (2000) DNA-based genetic markers in black-tailed and mule deer for forensic applications. Calif Fish Game 86:115–126Google Scholar
- Morgante M, Hanafey M, Powell W (2002) Microsatellites are preferentially associated with non repetitive DNA in plant genomes. Nat Genet 30:194–200Google Scholar
- Qureshi SN, Saha S, Kantety RV, Jenkins JN (2004) EST–SSR: a new class of genetic markers in cotton. J Cotton Sci 8:112–123Google Scholar
- Rong J, Abbey C, Bowers JE, Brubaker CL, Chang C, Chee PW, Delmonte TA, Ding X, Garza JJ, Marler BS (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
- Sefc KM, Steinkellner H, Wagner HW, Glössl J, Regner F (1997) Application of microsatellite markers to parentage studies in grapevine. Vitis 36:179–183Google Scholar
- Shannon CE, Weaver W (1949) A mathematical model of communication. University of Illinois Press, ChampaignGoogle Scholar
- Xiao J, Wu K, Fang DD, Stelly DM, Yu J, Cantrell RG (2009) New SSR markers for use in cotton (Gossypium spp.) improvement. J Cotton Sci 13:75–157Google Scholar