Simple sequence repeats as useful resources to study transcribed genes of cotton

• Published in: Euphytica 2003-01, Vol.130 (3), p.355-364
• Main Authors: SAHA, Sukumar, KARACA, Mehmet, JENKINS, Johnie N, ZIPF, Allan E, REDDY, O. Umesh K, KANTETY, Ramesh V
• Format: Article
• Language: English
• Subjects: Agronomy. Soil science and plant productions; Amplification; Biological and medical sciences; Classical and quantitative genetics. Population genetics. Molecular genetics; Cotton; Data mining; Fundamental and applied biological sciences. Psychology; Gene mapping; Generalities. Genetics. Plant material; Genes; Genetic markers; Genetics; Genetics and breeding of economic plants; Genomes; Markers; Microsatellites; Molecular genetics; Plant species; Sequence analysis; Simple sequence repeats; Species
• ISSN: 0014-2336; 1573-5060
• DOI: 10.1023/A:1023077209170

Microsatellites or Simple Sequence Repeats(SSRs) are informative molecular genetic markers in many crop species. SSRs are PCR-based, highly polymorphic, abundant, widely distributed throughout the genome and inherited in a co-dominant manner in most cases. Here we describe the presence of SSRs in cDNAs of cotton. Thirty one SSR primer pairs of 220 (∼14%) tested led to PCR amplification of discrete fragments using cotton leaf cDNA as template. Sequence analysis showed 25% of 24randomly selected cDNA clones amplified with different SSR primer pairs contained repeat motifs. We further showed that sequences from the SSR-containing cDNAs were conserved across G. barbadense and G. hirsutum, revealing the importance of the SSR markers for comparative mapping of transcribed genes. Data mining for plant SSR-ESTs from the publicly available databases identified SSRs motifs in many plant species,including cotton, in a range of 1.1 to4.8% of the submitted ESTs for a given species.