<abstract xmlns="http://www.w3.org/1999/xhtml"><p> The Chinese fir (Cunninghamia lanceolata) is a very important plantation species that is mainly distributed in Southern China. However, genomic analyses of C. lanceolata have lagged significantly behind those of other conifer species due to a lack of suitable markers. To address this issue, we examined 27,666,670 reads from C. lanceolata transcriptome sequences recorded in the SRA database. Assembly produced 35,633 contigs, 1,822 (5.11%) of which contained one or more SSRs. In total, 2,156 SSRs were identified, giving an average SSR density of 68.4 SSRs/Mb. The most common SSR types were tri-SSRs (41.7%), followed by hexa-(29.8%), penta- (12.7%), di-(11.1%) and tetra-(4.7%) SSRs. EST-SSR markers based on the 1,822 SSR-containing contigs were developed using the CMiB pipeline and primer pairs were designed to target 35 loci. Polymorphism was observed in 28 of these loci, for which the number of alleles per locus ranged from 3 to 12 over 16 plus-tree individuals. The observed heterozygosity (Ho), expected heterozygosity (He) and fixation index (F<sub>IS</sub>) values for the targeted loci ranged from 0.125 to 0.938, 0.225 to 0.891 and -0.368 to 0.456, respectively. The corres - ponding PIC values ranged from 0.210 to 0.881, with an average of 0.573. Some of these markers have since been used in our ongoing genetic diversity analyses of C. lanceolata. To our knowledge, this is the first analysis of SSRs and EST-SSR markers in C. lanceolata, and the identified EST-SSR markers will be useful in future genetic analyses of C. lanceolata and related species.</p></abstract>

The Chinese fir (Cunninghamia lanceolata) is a very important plantation species that is mainly distributed in Southern China. However, genomic analyses of C. lanceolata have lagged significantly behind those of other conifer species due to a lack of suitable markers. To address this issue, we examined 27,666,670 reads from C. lanceolata transcriptome sequences recorded in the SRA database. Assembly produced 35,633 contigs, 1,822 (5.11%) of which contained one or more SSRs. In total, 2,156 SSRs were identified, giving an average SSR density of 68.4 SSRs/Mb. The most common SSR types were tri-SSRs (41.7%), followed by hexa-(29.8%), penta- (12.7%), di-(11.1%) and tetra-(4.7%) SSRs. EST-SSR markers based on the 1,822 SSR-containing contigs were developed using the CMiB pipeline and primer pairs were designed to target 35 loci. Polymorphism was observed in 28 of these loci, for which the number of alleles per locus ranged from 3 to 12 over 16 plus-tree individuals. The observed heterozygosity (Ho), expected heterozygosity (He) and fixation index (FIS) values for the targeted loci ranged from 0.125 to 0.938, 0.225 to 0.891 and -0.368 to 0.456, respectively. The corres - ponding PIC values ranged from 0.210 to 0.881, with an average of 0.573. Some of these markers have since been used in our ongoing genetic diversity analyses of C. lanceolata. To our knowledge, this is the first analysis of SSRs and EST-SSR markers in C. lanceolata, and the identified EST-SSR markers will be useful in future genetic analyses of C. lanceolata and related species.

Development and characterization of 28 polymorphic EST-SSR markers for Cunninghamia lanceolata (Taxodiaceae) based on transcriptome sequences

Silvae Genetica

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

The Chinese fir (Cunninghamia lanceolata) is a very important plantation species that is mainly distributed in Southern China. However, genomic analyses of C....

Development and characterization of 28 polymorphic EST-SSR markers for Cunninghamia lanceolata (Taxodiaceae) based on transcriptome sequences

Published Online: Jul 01, 2017

Page range: 137 - 141

Received: Nov 09, 2012

DOI: https://doi.org/10.1515/sg-2013-0018

Keywords
Cunninghamia lanceolata, expressed sequence tag, microsatellite markers, de novo assembly, transcriptome sequences

© 2017

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Development and characterization of 28 polymorphic EST-SSR markers for Cunninghamia lanceolata (Taxodiaceae) based on transcriptome sequences

Published Online: Jul 01, 2017

Page range: 137 - 141

Received: Nov 09, 2012

DOI: https://doi.org/10.1515/sg-2013-0018

KeywordsCunninghamia lanceolata, expressed sequence tag, microsatellite markers, de novo assembly, transcriptome sequences

© 2017

This work is licensed under the Creative Commons Attribution-NonCommercial-NoDerivatives 4.0 License.

Keywords
Cunninghamia lanceolata, expressed sequence tag, microsatellite markers, de novo assembly, transcriptome sequences