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The IUP Journal of Genetics and Evolution
Identification of Simple Sequence Repeats in Casuarina equisetifolia
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Casuarinas are one of the popular and fast growing hardwood trees planted widely for multiple purposes in the tropical regions. C. equisetifolia has been identified as one of the suitable species for farm forestry and it is used as the source of paper pulp, fuel wood, poles and timber. This species is targeted for the genetic improvement through conventional breeding approaches. Simple Sequence Repeats (SSRs) are considered to be the best choice of DNA markers in tree genome analysis; however, these single locus markers require isolation of specific repeat sequences and development of specific primer pairs that involve laborious techniques. The aim of this study is to develop a cost-effective strategy for species_specific SSR markers in Casuarina and to investigate their utility in fingerprinting. Cross amplification approach was utilized, where SSRs of Eucalyptus species were amplified with Casuarina genomic DNA, an enriched SSR library was generated and sequenced for the rapid characterization of SSR motifs in Casuarina equisetifolia. Dinucleotide repeat (GA)n ((GA)n/(CT)n/(AG)n /(TC)n) was more common. Gen Bank sequence comparison analysis showed significant homology with SSRs of other plant species. Transferability and allelic variation of the SSRs to its close relative C. junhuhniana were observed.

 
 
 

Casuarinas are one of the popular and fast growing hardwood trees planted widely for multiple purposes in the tropical regions. They are actinorhizal plants which can form endosymbiotic associations with species of Frankia, an actinomycete able to fix atmospheric nitrogen (Diem et al., 2000). In coastal areas, casuarinas are planted for protection against wind, tsunami (Zucchi et al., 2003) and stabilization of sand dunes. In India, the species C. equisetifolia has been identified as one of the suitable species for farm forestry and it is used as the source of paper pulp, fuel wood, poles and timber.

Utility value and growth performance of C. equisetifolia led to the initiation of genetic improvement programs in the form of provenance trials and clonal selection (Pinyopusarerk et al., 2004). Genetic improvement and domestication of casuarinas has been supplemented with molecular markers like allozymes, which are used to estimate genetic relationships existing among the populations of casuarinas (Moore and Moran, 1989; and Moran et al., 1989). Genome size of the members of Casuarinaceae has been determined (Van der Nest et al., 2000), followed by the use of dominant DNA markers like RAPD, ISSR and FISSR markers to study the genetic diversity within and between species and to differentiate the species and clones (Leroy et al., 2001; Kantety et al., 2002; and Yasodha et al., 2004). However, advanced molecular genetic improvement programs require codominant and multi-allelic markers such as Simple Sequence Repeats (SSRs) or microsatellites for the development of high resolution linkage maps and in marker assisted selection/breeding (Brondani et al., 1998; and Gupta and Varshney, 2000). The presence of abundant repeat regions in tropical tree genomes was described by Condit and Hubbell (1991); since then several reports have been published on isolation and characterization of microsatellites.

 
 
 

Identification of Simple Sequence Repeats in Casuarina equisetifolia, Microsatellites, Cross-amplification, Eucalyptus, C. equisetifolia, C. junhuhniana, microsatellites, RAPD, ISSR, FISSR, clonal selection, endosymbiotic, codominant and multi-allelic, actinorhizal plants.