Abstract
Bamboo are woody grass species containing important economic and ecological values. Lei bamboo (Phyllostachys violascens) is a kind of shoot-producing bamboo species with the highest economic yield per unit area. However, identifying different varieties of Lei bamboo based on morphological characteristics is difficult. Microsatellites play an important role in plant identification and genetic diversity analysis and are superior to other molecular markers. In this study, we identified 18,356 expressed sequence tag-simple sequence repeat (EST-SSR) loci in Lei bamboo transcriptome data. A total of 11,264 primer pairs were successfully designed from unigenes of all EST-SSR loci, and 96 primer pairs were randomly selected and synthesized. A total of 54 primer pairs were used for classifying 16 Lei bamboo varieties and 10 different Phyllostachys species. The number of polymorphism alleles among the 54 primer pairs ranged from 3 to 12 for P. violascens varieties and 3 to 20 for Phyllostachys. The phylogenetic tree based on polymorphism alleles successfully distinguished 16 P. violascens varieties and 10 Phyllostachys species. Our study provides abundant EST-SSR resources that are useful for genetic diversity analysis and molecular verification of bamboo and suggests that SSR markers developed from Lei bamboo are more efficient and reliable than ISSR, SRAP or AFLP markers.
Highlights
Bamboo is an economically important member of the woody grasses
We identified expressed sequence tag-simple sequence repeat (EST-SSR) loci as well as primer pairs based on these data
A total of 132,678 transcriptome sequences were examined by MISA software, and 18,356 EST-SSRs loci were identified in P. violascens
Summary
Bamboo is an economically important member of the woody grasses. It includes 88 genera and more than 1,400 species worldwide; 34 genera and 534 species are in China (Wu and Raven, 2006). Given the considerably fast growth, strong carbon fixation capability and edible shoots, bamboo has worldwide ecological and economic value. The classification and nomenclature of plants are mainly based on morphological characteristics, such as roots, stems, leaves and flowers (Lichtenthaler, 1987). Flower morphology is the most important (PDCress and Staden, 1998). Morphological characteristics sometimes are not very reliable because they are affected by ecological
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