Mapped SSR markers unevenly distributed on the cotton chromosomes
- 45 Downloads
In the past 15 years, more than 9000 SSR markers have been developed, which are a valuable resource for cotton genetics and breeding. Many of them have been mapped in cotton, and several high-density genetic maps have been constructed. In this paper, we jointly analyzed the mapped SSRs to characterize their motifs on cotton chromosomes. The results showed that SSR loci were distributed unevenly on cotton chromosomes with more on C11 and C19 and less on C02 and C04. Different sources of SSRs contributed different predominant SSR types, which were also distributed unequally on cotton chromosomes. Compared to SSRs derived from enriched libraries and BAC end sequences, EST-SSRs could generate novel SSR motifs especially for AT/TA of di-, tetra-, penta- and hexanucleotide. SSR motifs showed a biased distribution on cotton chromosomes with more on C05, C11, and C19, and less on C02 and C04. The uneven distribution of SSRs on cotton chromosomes would help us to enrich the cotton genetic map by motif-specific SSRs. This analysis gave us new knowledge on the architecture of the cotton genome.
Keywordscotton SSR motif genetic linkage map
Unable to display preview. Download preview PDF.
- Blenda A, Scheffer J, Scheffer 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, 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: 132CrossRefPubMedGoogle Scholar
- Fryxell P A (1992). A revised taxonomic interpretation of Gossypium L. (Malvaceae). Rheedea, 2: 108–165Google Scholar
- Park Y H, Alabady M S, Ulloa M, Sickler B, Wilkins T A, Yu J, Stelly D M, Kohel R J, El-Shihy O M, Cantrell R G (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
- Qureshi S N, Saha S, Kantety R V, Jenkins J N (2004). EST-SSR: A new class of genetic markers in cotton. J Cotton Sci, 8: 112–123Google Scholar
- Reddy O K, Pepper A E, Abdurakhmonov I, Saha S, Jenkins J N, Brooks T, Bolek Y, El-Zik K M (2001). New dinucleotide and trinucleotide microsatellite marker resources for cotton genome research. J Cotton Sci, 5: 103–113Google Scholar
- Rong J K, Abbey C, Bowers J E, Brubaker C L, Chang C, Peng W C, Delmonte T A, Ding X L, Garza J J, Marler B S, Park C, Pierce G J, Rainey K M, Rastogi V K, Schulz S R, Trolinder N L, Wendel J F, Wilkins T A, Williams-Coplin T D, Wing R A, Wrigh R J, Zhao X P, Zhu L H, Paterson A H (2004). A 3347-locus genetic recombination map of sequence-tagged sites reveals features of genome organization, transmission and evolution of cotton (Gossypium). Genetics, 166: 389–417CrossRefPubMedGoogle Scholar
- Scott K D (2001). Microsatellites derived from ESTs, and their comparison with those derived by other methods. In plant genotyping: the DNA fingerprinting of plants. CAB International, Wellingford, 255–237Google Scholar
- Taliercio E, Allen R D, Essenberg M, Klueva N, Nguyen H, Patil M A, Payton P, Millena A C M, Phillips A L, Pierce M L, Scheffler B, Turley R, Wang J, Zhang D, Scheffler J (2006). Analysis of ESTs from multiple Gossypium hirsutum tissues and identification of SSRs. Genome, 49: 306–319CrossRefPubMedGoogle Scholar
- Zhang H B, Li Y N, Wang B H, Chee P W (2008a). Recent Advances in Cotton Genomics. Int J Plant Genomics, Volume 2008: Article ID 742304, 20 pages, doi:10.1155/2008/742304Google Scholar