Evaluation of rice and sugarcane SSR markers for phylogenetic and genetic diversity analyses in bambooIHBT Publication No. 0732.

Abstract

Simple sequence repeat (SSR) markers are valuable tools for many purposes such as phylogenetic, fingerprinting, and molecular breeding studies. However, only a few SSR markers are known and available in bamboo species of the tropics (Bambusa spp.). Considering that grass genomes have co-evolved and share large-scale synteny, theoretically it should be possible to use the genome sequence based SSR markers of field crops such as rice (Oryza sativa) and sugarcane (Saccharum spp.) for genome analysis in bamboo. To test this, 98 mapped SSR primers representing 12 linkage groups of rice and 20 EST-derived sugarcane SSR primers were evaluated for transferability to 23 bamboo species. Of the tested markers, 44 (44.9%) rice and 15 (75%) sugarcane SSR primers showed repeatable amplification in at least one species of bamboo and thus were successfully utilized for phylogenetic and genetic diversity analyses. Transferred SSR primers revealed complex amplification patterns in bamboo, with an average of 9.62 fragments per primer, indicating a high level of polyploidy and genetic variability in bamboo. Forty-two of these primers (34 rice and 8 sugarcane SSR primers) detected an average of 2.12 unique fragments per primer and thus could be exploited for species identification. Six bamboo SSR primers exhibited cross transferability, to varying degrees, to different bamboo species. The genetic similarity coefficient indicated a high level of divergence at the species level (73%). However, a relatively low level of diversity was observed within species (25% in 20 accessions of Dendrocalamus hamiltonii). Further, cluster analysis revealed that the major grouping was in accordance with the taxonomical classification of bamboo. Thus, the rice and sugarcane SSRs can be utilized for phylogenetic and genetic diversity studies in bamboo.

The draft genome of the fast-growing non-timber forest species moso bamboo (Phyllostachys heterocycla)

“…Recent genomic studies in bamboo have included genome-wide full-length cDNA sequencing 2 , chloroplast genome sequencing 3 , identification of syntenic genes between bamboo and other grasses 4 and phylogenetic analysis of Bambusoideae subspecies 5 . Fifty-nine simple sequence repeat markers from rice and sugarcane were used in the genetic diversity analyses of 23 bamboo species 6 , and 2 species-specific sequence-characterized amplified region markers were developed in the identification of different bamboo species 7 .…”

Transferability of Sorghum Microsatellite Markers to Bamboo and Detection of Polymorphic Markers

“…Percentage of transferability was computed by dividing the number of the SSR markers amplified in non-donor (bamboo) species to the total number of tested SSRs. Fragments in base pair were converted to binary data because of the complex amplification pattern in bamboo genome [27]. The level of polymorphism of the entire markers across the selected bamboo species was computed.…”

“…Several studies have been conducted on the transferability of SSR markers across species or genera of several cereal crops which belong to grass family such as rice [16], wheat [17], wheat, rye and triticale [18], barley [19], sugar cane [20,21], sorghum [22,23] major cereal to minor grass [24] and pearl millet [25]. There are also reports about transferability of SSRs from cereals such as rice and sugar cane to bamboo species [26,27]. Sharma et al [15] also conducted an experiment on identification and amplification of EST-SSR markers in different bamboo species.…”

DNA Barcoding: An Alternative for the Identification of the Medicinal Plants Employed in Mexico

“…Some molecular techniques currently employed for the identification of medicinal plants are amplified fragment length polymorphism (Passinho-Soares et al, 2006), Restriction Fragment J. Plant Sci., 10 (4): 116-127, 2015 Length Polymorphism (RFLP) (Diao et al, 2009), random amplification of polymorphic DNA (Cao et al, 2010), Inter-simple sequence repeat (Tamhankar et al, 2009), Simple Sequence Repeat (SSR) (Sharma et al, 2008) and through microarray design (Carles et al, 2005;Jayasinghe et al, 2007;Zhu et al, 2008), which determine the variations of nucleotides in a DNA sequence belonging to the genome of plants, in particular of conserved sequences of genes present in the nucleus, mitochondria or chloroplast (Hao et al, 2008(Hao et al, , 2010a. These genomic fingerprints can differentiate between genera and species, demonstrating its usefulness for characterizing plants of medicinal interest and in consequence, the detection of possible adulterants.…”