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Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.).
Genes (Basel). 2017 Jul 07; 8(7)G

Abstract

Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-five primers were verified as polymorphic, with clear bands. The polymorphism information content values were 0.033-0.765, the number of alleles per locus ranged from 2 to 10, and the observed and expected heterozygosities were 0.000-0.931 and 0.035-0.810, respectively, indicating a high level of informativeness. Subsequently, 45 polymorphic EST-SSR loci were tested for amplification efficiency, using the verified primers, in an additional nine species of Leguminosae, 23 loci were amplified in more than three species, of which two loci were amplified successfully in all species. These EST-SSR markers provide a valuable tool for investigating the genetic diversity and population structure of R. pseudoacacia, constructing a DNA fingerprint database, performing quantitative trait locus mapping, and preserving genetic information.

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Authors+Show Affiliations

Guo Q
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. Guoqi0529@126.com.
Wang JX
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. Xing521-zi@126.com.
Su LZ
State-owned Linghai Hongqi Forest, Jinzhou 121228, China. 18037935780@163.com.
Lv W
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. sunyuhan@bjfu.edu.cn.
Sun YH
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. scarlett-2@163.com.
Li Y
Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing 100083, China. yunli@bjfu.edu.cn.

Pub Type(s)

Journal Article

Language

eng

PubMed ID

28686183

Citation

Guo, Qi, et al. "Development and Evaluation of a Novel Set of EST-SSR Markers Based On Transcriptome Sequences of Black Locust (Robinia Pseudoacacia L.)." Genes, vol. 8, no. 7, 2017.
Guo Q, Wang JX, Su LZ, et al. Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.). Genes (Basel). 2017;8(7).
Guo, Q., Wang, J. X., Su, L. Z., Lv, W., Sun, Y. H., & Li, Y. (2017). Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.). Genes, 8(7). https://doi.org/10.3390/genes8070177
Guo Q, et al. Development and Evaluation of a Novel Set of EST-SSR Markers Based On Transcriptome Sequences of Black Locust (Robinia Pseudoacacia L.). Genes (Basel). 2017 Jul 7;8(7) PubMed PMID: 28686183.
* Article titles in AMA citation format should be in sentence-case
TY - JOUR T1 - Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.). AU - Guo,Qi, AU - Wang,Jin-Xing, AU - Su,Li-Zhuo, AU - Lv,Wei, AU - Sun,Yu-Han, AU - Li,Yun, Y1 - 2017/07/07/ PY - 2017/05/04/received PY - 2017/07/03/revised PY - 2017/07/04/accepted PY - 2017/7/8/entrez PY - 2017/7/8/pubmed PY - 2017/7/8/medline KW - EST-SSR markers KW - Illumina sequencing KW - Robinia pseudoacacia KW - polymorphism JF - Genes JO - Genes (Basel) VL - 8 IS - 7 N2 - Black locust (Robinia pseudoacacia L. of the family Fabaceae) is an ecologically and economically important deciduous tree. However, few genomic resources are available for this forest species, and few effective expressed sequence tag-derived simple sequence repeat (EST-SSR) markers have been developed to date. In this study, paired-end sequencing was used to sequence transcriptomes of R. pseudoacacia by the Illumina HiSeq TM2000 platform, and EST-SSR loci were identified by de novo assembly. Furthermore, a total of 1697 primer pairs were successfully designed, from which 286 primers met the selection screening criteria; 94 pairs were randomly selected and tested for validation using polymerase chain reaction amplification. Forty-five primers were verified as polymorphic, with clear bands. The polymorphism information content values were 0.033-0.765, the number of alleles per locus ranged from 2 to 10, and the observed and expected heterozygosities were 0.000-0.931 and 0.035-0.810, respectively, indicating a high level of informativeness. Subsequently, 45 polymorphic EST-SSR loci were tested for amplification efficiency, using the verified primers, in an additional nine species of Leguminosae, 23 loci were amplified in more than three species, of which two loci were amplified successfully in all species. These EST-SSR markers provide a valuable tool for investigating the genetic diversity and population structure of R. pseudoacacia, constructing a DNA fingerprint database, performing quantitative trait locus mapping, and preserving genetic information. SN - 2073-4425 UR - https://www.unboundmedicine.com/medline/citation/28686183/Development_and_Evaluation_of_a_Novel_Set_of_EST_SSR_Markers_Based_on_Transcriptome_Sequences_of_Black_Locust__Robinia_pseudoacacia_L___ L2 - https://www.mdpi.com/resolver?pii=genes8070177 DB - PRIME DP - Unbound Medicine ER -