Isolation and characterization of microsatellites in Bambusa arundinacea and cross species amplification in other bamboos

Abstract

Isolation and characterization of microsatellites was analysed in Bambusa arundinacea and cross species amplification studied in other bamboos. Microsatellites, tandem repeats of short nucleotide (1-6 bp) sequences, are the DNA marker of choice because of their highly polymorphic, ubiquitous distribution within the genome, ease of genotyping through Polymerase chain reaction, selectively neutral, codominant and multiallelic nature. Six microsatellites, three polymorphic and three monomorphic have been characterized for the first time in a bamboo species, Bambusa arundinacea belonging to the family Poaceae. The numbers of alleles per locus ranged from 2 to 13. Cross species amplification was tested in 18 other bamboo species. Monomorphic simple sequence repeats (SSRs) were found to be cross amplified in most of the species tested and polymorphic ones in only three to four species. The utility of SSR loci in a genetic diversity study of B. arundinacea and other cross-amplified bamboo species has been discussed. This study will help in population genetic studies in bamboo species.

Transferability of rice SSR markers to bamboo

“…Most of the strategies currently used to isolate SSR markers are both time-and cost-consuming, which limits the application of SSR in those genomes with less information (Zane et al 2002). To date, the only a limited number of SSR markers have been generated in bamboo species, namely, six SSR markers from Bambusa arundinacea (Nayak and Rout 2005), nine SSR markers from B. arnhemica (Kaneko et al 2008), and ten SSR markers from dwarf bamboo species (Kitamura et al 2009). One of the solutions to this dearth of SSR markers is cross-species amplification of SSR markers from a genome with abundant SSR markers in a target genome (Oliveira et al 2006).…”

“…These results suggest that cross-species amplification of SSR markers is an amenable and efficient procedure to generate new marker sources. In the grass family, this method has been used in both intrageneric (Hernandez et al 2001;Thiel et al 2003;Kuleung et al 2004;Nayak and Rout, 2005;Saha et al 2006) and intraspecies (Bandopadhyay et al 2004;Zhang et al 2007) studies. Barkley et al (2005) reported that they successfully transferred 25 expressed sequence tag (EST)-SSR markers from cereal crops into bamboo.…”

“…Bamboo is an economically valuable monocot (family Poaceae, subfamily Bambusoideae; Nayak and Rout 2005) in Asian countries where it is commonly used as a source of building materials (Das and Rout 1994) and paper fiber (Das et al 2005). It is also grown commercially for it shoots, which are a very popular vegetable in Asia .…”

Genetic Relationships Among 22 Taxa of Bamboo Revealed by ISSR and EST-Based Random Primers

“…AFLP has proved to be useful in diverse aspects of bamboo systematics, population structure, and diversity studies (Loh et al 2000;Marulanda et al 2002;Suyama et al 2000). The use of SSR markers is limited by their lack of availability in bamboo; nevertheless, they have been successfully applied to Phyllostachys (Lai and Hsiao 1997) and Bambusa (Nayak and Rout 2005). Polymorphic EST-SSR markers derived from major cereal crops have recently been used to assess phylogenetic and genetic diversity (Barkley et al 2005;Sharma et al 2008).…”

Identification and cross-species amplification of EST derived SSR markers in different bamboo species

“…Simple sequence repeat (SSR) markers have become the marker class of choice for genetic mapping, genotype fingerprinting and genetic diversity studies because they are mostly co-dominant, abundant in the genome, highly reproducible and some have high rate of transferability across species (Gaitán-Solís et al 2002;Saha et al 2004). The availability of SSR markers in bamboo is very limited and few genomic simple sequences repeat (SSR) markers have been developed for bamboo in recent years (Nayak and Rout 2005;Kaneko et al 2007). Nevertheless, the development of SSR markers has traditionally been limited by the time consuming and labor intensive methods of SSRs development (Edwards et al 1996).…”