Transferability of rice SSR markers to bamboo

Abstract

Simple sequence repeat (SSR) markers are widely applied in studies of plant molecular genetics due to their abundance in the genome, codominant nature, high repeatability, and transferability in cross-species applications. To investigate the possibility of applying rice SSR markers in bamboo, we selected 120 rice SSR markers that are evenly distributed on rice chromosomes and assessed these for their transferability to 21 different bamboo species. A total of 4847 bands of 2196 alleles were obtained from 82 SSR markers that were able to amplify products in the bamboo genome; the transferability was 68.3%. Seven markers specifically amplified individual bamboo species and are consequently valuable markers for species identification. SSR markers located on rice chromosome 7 and 1 showed the highest and lowest transferability, respectively to the bamboo genome. SSR markers located on some regions of the rice chromosomes could not be amplified in bamboo, suggesting that regional divergence occurred between rice and bamboo during evolution. A dendrogram was constructed. The dendrogram classified bamboo species into two major groups which coincided with rhizome type, runner, and clumper. The results of this study demonstrate that rice SSR markers can be a valuable source of markers for those genomes lacking useful marker systems

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

“…Most of these fragments were amplified higher than the size of the donor fragment, which is in agreement with the previous study implying that the amplified fragments from the selected species have different allele sizes than those of the donor species [26,24,27].…”

“…Markers such as Xiabtp424, Xise0443 and Xisep0648 did not score any amplification in either of the bamboo species. The transferability rate obtained in this study is higher than the one reported for various grass family species including bamboo using [18,26,27]. However, the rate is slightly lower than the rice SSR transferability to bamboo that was reported to be 68% [26].…”

“…The transferability rate obtained in this study is higher than the one reported for various grass family species including bamboo using [18,26,27]. However, the rate is slightly lower than the rice SSR transferability to bamboo that was reported to be 68% [26]. It is possible to improve the transferability rate of markers by using markers that were developed from expressed sequences [18].…”

“…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.…”

Microsatellites grant more stable flanking genes

“…The stability of the SSR flanking regions was investigated in different organisms; three Phytophthora species (algae) [13]; rice and bamboo [14]; cotton [15]; Brassica rapa and Arabidopsis thaliana [16]; cowpea, mung bean and adzuki bean [17]; Castanea spp. [18]; Carya [19] and wheat [20].…”