Isolation and characterization of microsatellite markers for Achyranthes bidentata (Amaranthaceae) using next-generation sequencing platform. (August 2015)

• Record Type: Journal Article
• Authors: Li, Yong; Zhang, Wei; Fu, Zizhen; Wang, Wei; Li, Yonghua
• Is Part Of: Biochemical systematics and ecology. Volume 61(2015)
• Page Start: 437
• Page End: 440
• Publication Date: 2015-08
• Subjects: Microsatellite markers -- Genetic diversity -- Population structure -- 454 pyrosequencing -- Achyranthes bidentata; Chemotaxonomy -- Periodicals; Biochemical variation -- Periodicals; Ecology -- Periodicals; Biochemistry -- Periodicals; Ecology -- Periodicals; Chimiotaxinomie -- Périodiques; Variation biochimique -- Périodiques; Écologie -- Périodiques; 578.012
• DOI: 10.1016/j.bse.2015.06.032
• Languages: English
• ISSNs: 0305-1978

Abstract

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 . Highlights: 903 microsatellite loci were developed for Achyranthes bidentata . This marker set is the first one described for an Achyranthes species. These markers may help guide future conservation studies.