Development and Characterization of EST-SSR Markers for Juniperus squamata (Cupressaceae), an ecologically important conifer in Asian mountains

Abstract

Juniperus squamata, an endemic conifer of Asia, is an important shrub ecologically and economically. Yet little is known about its genetic diversity and population structure due to lacking of highly polymorphic molecular markers. In this study, expressed sequence tag microsatellite markers (EST-SSR) were developed for Juniperus squamata. Illumina HiSeq data were used to reconstruct the transcriptome of this species by de novo assembly. Based on this transcriptome, 18 SSR markers were designed and successfully amplified. Just one locus was eliminated due to its detection of null alleles and the remaining 17 loci were polymorphic, generating five to 14 alleles per locus in J. squamata. Markers cross-amplification tests were successful in two closely related species of J. squamata. These markers will serve as a basis for further studies to assess the genetic diversity and population structure of J. squamata. As well, they could be useful in promoting sustainable forest management strategies for this species in the face of global climate change.

Reproduction and genetic diversity of Juniperus squamata along an elevational gradient in the Hengduan Mountains

“…To identify the number of individuals in one shrub patch, we used microsatellite genotypes as DNA markers. DNA was extracted from leaf tissue using a modified Cetyltrimethylammonium Bromide protocol (CTAB; Doyle and Doyle, 1987 ), followed by the amplification and sequencing of 18 microsatellite markers (for details of DNA extraction and amplification, see Ju et al., 2020 ). Microsatellites were scored using GeneMarker v.2.4.0 (Soft Genetics, State College, PA, USA) and automatically binned by the software FlexiBin ( Amos et al., 2007 ).…”