Isolation and characterization of SSR and EST‐SSR loci in Chamaecyparis formosensis (Cupressaceae)

Abstract

Premise of the StudySimple sequence repeat (SSR) and expressed sequence tag (EST)–SSR markers were developed as tools for marker‐assisted selection of Chamaecyparis formosensis and for the molecular differentiation of cypress species.Methods and ResultsBased on the SSR‐enriched genomic libraries and transcriptome data of C. formosensis, 300 primer pairs were selected for initial confirmation, of which 19 polymorphic SSR and eight polymorphic EST‐SSR loci were chosen after testing in 92 individuals. The number of alleles observed for these 27 loci ranged from one to 17. The levels of observed and expected heterozygosity ranged from 0.000 to 1.000 and from 0.000 to 0.903, respectively. Most markers also amplified in C. obtusa var. formosana.ConclusionsThe developed SSR and EST‐SSR sequences are the first reported markers specific to C. formosensis. These markers will be useful for individual identification of C. formosensis and to distinguish cypress species such as C. obtusa var. formosana.

Development and technical application of SSR-based individual identification system for Chamaecyparis taiwanensis against illegal logging convictions

“…1 , Tables 1 , 2 ), and the success rate for gSSR and EST-SSR marker was found to be 5.82% and 11.42%, respectively. Our data showed that it is easier to select SSR markers from the RNA library than from the DNA library, which is akin to previous studies 4 , 32 , 33 . Other reports 24 , 34 , 35 suggest that SSR occurs more frequently in EST sequence than in the genome.…”

“…A total of 75 markers including 23 gSSR and 12 EST-SSR markers newly designed in this study, and 40 published SSR 4 , 53 , 54 (Supplementary Sect. 2 ) were subjected to validation test on 96 samples from four C. taiwanensis populations (TP, SY, DS and FR, see Supplementary Sect.…”

“…Illegal felling remains a persistent problem in the timber producing countries all over the world. For decades, illegal logging endangered precious and valuable tree species such as cypress 4 , ash 5 , mahogany tree 6 , and Brazilian rosewood 7 all over the world. In some cases, the law enforcement authorities, such as forestry police, arrest the suspects in time.…”

“…EST-SSRs are markers mined from EST sequence collections. gSSR markers have been reported to be more polymorphic when compared with EST-SSR in gymnosperms 4 and crops 25 , 26 because of a more diversified nucleotide sequence. Since the development of high-throughput sequencing technology, the marker development technique has been continuously advanced.…”

Developing SSR Individual Identification System and Tracking the Geographical Origin of Timber for the Endangered Species Chamaecyparis Formosensis

“…Therefore, SSR is the most commonly used method for individual identi cation systems 15,16 . In order to protect our precious cypress resources in Taiwan, we have developed and adapted several polymorphic SSR markers 17 for individual identi cation.…”