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ARS Home » Southeast Area » Mississippi State, Mississippi » Crop Science Research Laboratory » Genetics and Sustainable Agriculture Research » Research » Publications at this Location » Publication #94005
Title: DNA FINGERPRINTING IN COTTON USING SSR PRIMERS FROM DIVERSE PLANT SPECIES

Author
item AGRAWAL, DINESH - NAT CHEMICAL LAB, INDIA
item Saha, Sukumar
item Jenkins, Johnie
item ZIPF, ALLAN - ALABAMA A&M UNIVERSITY
item May Iii, Oscar

Submitted to: Journal of Cotton Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 11/3/1998
Publication Date: N/A
Citation: N/A

Interpretive Summary: Use of DNA markers for molecular genetic analysis of plants and other organisms is routine and geneticists may choose among many techniques. Each approach has merits and disadvantages. Simple sequence repeats (SSRs) have been used because of their potential for identifying polymorphic DNA markers in plant genomes. The SSRs are tandemly repeated di-, tri-, or tetra-nucleotide units in the genome. Development of SSR markers specific to a plant species is time consuming and involves high costs associated with DNA isolation, sequencing, and production of primers. In the present study, commercially available SSR markers developed for other species were tested for use in detecting genetic differences in cotton. Selected SSR primers from soybean, banana, sweet potato, conifer, and hard pine were used to detect differences in cotton at the intra- and inter-specific levels. The use of existing SSR primers from other plant species saved time and money otherwise required for development of SSR markers specific to cotton. The technique also had advantages common to PCR-based methods, in that it did not use radioactive materials, used simple DNA amplification technology, and was overall relatively simple and rapid.

Technical Abstract: The use of simple sequence repeat (SSR) DNA markers for genetic analysis of plants and other organisms is on the increase. Development of SSR markers specific to a particular species, however, is time-consuming and costly. The present study was conducted to determine whether SSR primers from other species could be used to detect polymorphisms in cotton. Forty-four SSR primers from cotton, soybean, sweet potato, banana, conifer, and hard pine, and 10 random amplified polymorphic DNA (RAPD) primer pairs were examined. Polymerase chain reaction (PCR) amplification, agarose gel electrophoresis and ethidium bromide staining were used to generate DNA fingerprints. The size range of DNA markers varied from 40 bp to more than 1000 bp. Band separation of as low as 20 bp was achieved by use of high resolution agarose. Numbers of bands per primer combination and percentages of polymorphic bands at inter- and intra-specific levels varied widely. The SSR markers from primer combinations specific to cotton produced the least number of bands (2.2 and 2.6 at inter- and intra-specific levels, respectively). The SSR primers from sweet potato produced the highest number of bands per primer combination (20.5 and 19.5 at inter- and intra-specific levels, respectively). Polymorphic markers generated by SSR primers from species other than cotton were dominant, while SSR primers specific to cotton produced both co-dominant and dominant markers. This study demonstrated the use of SSR primers from diverse species in the genetic analysis of cotton.