Molecular Genetics and Genomics

, Volume 272, Issue 3, pp 308–327 | Cite as

Genetic mapping of EST-derived microsatellites from the diploid Gossypium arboreum in allotetraploid cotton

  • Z.-G. Han
  • W.-Z. Guo
  • X.-L. Song
  • T.-Z. ZhangEmail author
Original Paper


To increase the numbers of microsatellites available for use in constructing a genetic map, and facilitate the use of functional genomics to elucidate fiber development and breeding in cotton, we sampled microsatellite sequences from expressed sequence tags (ESTs) transcribed during fiber elongation in the A-genome species Gossypium arboreum to evaluate their frequency of occurrence, level of polymorphism and distribution in the At and Dt subgenomes of tetraploid cotton. From among ESTs derived from G. arboreum fibers at 7–10 days post anthesis (dpa), 931 ESTs were found to contain simple sequence repeats (SSRs); 544 (58.4%) EST-SSR primer pairs were developed, and 468 (86%) amplified PCR products from allotetraploid cotton ( G. hirsutum cv. TM-1 and G. barbadense cv. Hai7124). However, only 99 (18.2%) of these were found to be polymorphic and segregating in our interspecific BC1 mapping population [(TM-1×Hai7124)×TM-1]. In these amplified and informative EST-SSRs, hexa- and tri-nucleotide repeat motifs were the most frequent, representing 40.1 and 30%, respectively, of the total. A total of 111 loci detected with these 99 EST-SSRs were integrated into our backbone map including 511 SSR loci. The distribution of the EST-SSRs appeared to be non-random, since 72 loci were anchored to the At and 37 to the Dt subgenome of allotetraploid cotton based on linkage tests. Interestingly, out of the 10 pairs of duplicate loci amplified, seven were mapped to the corresponding homeologous linkage groups and/or chromosomes. BLASTX analysis revealed that 69 of the 99 ESTs showed significant similarities to known genes. Some genes important for fiber development, such as sucrose synthase, were mapped to corresponding chromosomes. These EST-SSRs provide structural and functional genomic information that will be useful for understanding cotton fiber development.


Gossypium arboretum Expressed Sequecne Tag-Simple Sequence Repeats (EST-SSR) Genetic mapping Allotetraploid cotton 



This program was financially supported in part by The National High-Tech Program (2004AA211172), the State Key Basic Research and Development Plan of China (2002CB111301), the Key Project of Chinese Ministry of Education (10418) and Jiangsu High-Tech Project (BG2002306)


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Copyright information

© Springer-Verlag 2004

Authors and Affiliations

  1. 1.National Key Laboratory of Crop Genetics and Germplasm Enhancement, Cotton Research InstituteNanjing Agricultural UniversityNanjingChina

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