Isolation and characterization of microsatellite markers for Achyranthes bidentata (Amaranthaceae) using next-generation sequencing platform |
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| Institution: | 1. College of Forestry, Henan Agricultural University, Zhengzhou 450002, PR China;2. College of Life Sciences, Xinyang Normal University, Xinyang 464000, PR China;1. School of Chemistry and Chemical Engineering, University of Jinan, Jinan 250022, China;2. School of Biological Science and Technology, University of Jinan, Jinan 250022, China;1. Departamento de Química, Universidade Federal de Viçosa, 36570-000 Viçosa, MG, Brazil;2. Department of Chemistry, Ripon College, Ripon, WI 54971, USA;1. Rzhanov Institute of Semiconductor Physics, 630090 Novosibirsk, Russia;2. Novosibirsk State University, 630090 Novosibirsk, Russia;1. Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science and Technology, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan;2. Department of Biology, Faculty of Science and Technology, Uttaradit Rajabhat University, Uttaradit 53000, Thailand;3. Osaka Museum of Natural History, 1-23, Nagai-koen, Higashisumiyoshi-ku, Osaka, Osaka, 546-0034, Japan;4. Biology Programme, Faculty of Science, Nakhon Phanom University, 167 Naratchakouy Sub-District, Muang District, Nakhon Phanom, 48000, Thailand;5. Laboratory of Forest Botany, Graduate School of Agricultural and Life Sciences, The University of Tokyo, 1-1-1 Yayoi, Bunkyo-ku, Tokyo 113-8657, Japan;6. Department of Bioscience and Biotechnology, Faculty of Agriculture, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan;7. Division of Terrestrial Ecosystem, Institute of Mountain Science, Shinshu University, 8304, Minami-minowa, Nagano, 399-4598, Japan |
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| Abstract: | Achyranthes bidentata Blume (Amaranthaceae) is a perennial herb that is widely distributed in India, Java, China, and Japan. The natural resources of A. bidentata in its geo-authentic product area have rapidly declined in recent years because of the over-collection of its roots. To devise adequate conservation and management strategies for this species, its genetic diversity and population structure should be characterized. Roche 454 pyrosequencing combined with magnetic bead enrichment was used to develop microsatellite markers for A. bidentata. A total of 903 microsatellite loci were identified from 42,004 individual sequence reads. One hundred microsatellite loci were selected to test the primer amplification efficiency across 16 individuals from two A. bidentata populations. Of these tested markers, 8 yielded polymorphic amplification products, 29 yielded single alleles. For polymorphic primer pairs, the number of alleles per locus ranged from 2 to 4, with an average of 2.75. The observed and expected heterozygosities ranged from 0.353 to 0.671 and 0.250 to 0.938, respectively. The inbreeding coefficient varied from ?0.692 to 0.627. This set of markers will provide useful tools for examining genetic diversity and population structure, and aid in better understanding of the conservation of A. bidentata. |
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| Keywords: | Microsatellite markers Genetic diversity Population structure 454 pyrosequencing |
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