Dataset Information

Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.).

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.

SUBMITTER: Guo Q

PROVIDER: S-EPMC5541310 | biostudies-literature | 2017 Jul

REPOSITORIES: biostudies-literature

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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.).

Guo Qi Q Wang Jin-Xing JX Su Li-Zhuo LZ Lv Wei W Sun Yu-Han YH Li Yun Y

Genes 20170707 7

Black locust (<i>Robinia pseudoacacia</i> 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 assem ...[more]

PMID: 28686183

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Project description:Robinia pseudoacacia, invaded many countries a long time ago and is now a common part of the Central European landscape. Positive economic but negative environmental impacts of Robinia result in conflicts of interest between nature conservation, forestry, urban landscaping, beekeepers and the public when defining management priorities. Because current legislation will determine the future distribution of Robinia in the landscape, a comprehensive view of this species is necessary. Although this species is well studied, most of the scientific papers deal with the economic aspects. Other information is published in local journals or reports. Therefore we reviewed the ecological and socio-economic impact of Robinia placing particular emphasis on the species' history, vegetation ecology, invasiveness and management. In Central Europe, Robinia is limited climatically by late spring frost combined with a short vegetation period, soil hypoxia, shade and frequent major disturbances. The long historical tradition of using Robinia for afforestation has resulted in its popularity as a widespread forest tree and it being an important part of the economy in some countries. The main reasons are its fast growth, valuable and resistant wood, suitability for amelioration, reclamation of disturbed sites and erosion control, honey-making and recently dendromass production. On the other hand, a side-effect of planting this nitrogen-fixing pioneer tree, very tolerant of the nature of the substrate, is its propagation and spread, which pose a problem for nature conservation. Robinia is considered invasive, threatening especially dry and semi-dry grasslands, some of the most species-rich and endangered types of habitat in the region, causing extinction of many endangered light-demanding plants and invertebrates due to changes in light regime, microclimate and soil conditions. Other often invaded habitats include open dry forests and shrubland, alluvial habitats, agrarian landscapes, urban and industrial environments and disturbed sites, e.g. post-fire sites, forest clearings or degraded forestry plantations. Without forestry, black locust abundance would decrease during succession in forests with highly competitive and shade tolerant trees and in mature forests it occurs only as admixture of climax trees. The limited pool of native woody species, lack of serious natural enemies and a dense cover of grasses and sedges can suppress forest succession and favour the development of Robinia monodominant stands over 70 years old. A stratified approach, which combines both tolerance in some areas and strict eradication at valuable sites, provides the best option for achieving a sustainable coexistence of Robinia with people and nature.

Project description:BackgroundElymus L. is the largest genus in the Triticeae tribe. Most species in this genus are highly stress resistant, with excellent forage value. Elymus breviaristatus, a rare species endemic to the Qinghai-Tibet Plateau (QTP), is declining due to habitat fragmentation. However, genetic data for E. breviaristatus are limited, with expressed sequence tag (EST) markers being particularly rare, hampering genetic studies and protection measures.ResultsWe obtained 9.06 Gb clean sequences from the transcriptome of E. breviaristatus, generating 171,522 unigenes, which were assembled and functionally annotated against five public databases. We identified 30,668 SSRs in the E. breviaristatus transcriptome, from which 103 EST-SSR primer pairs were randomly selected. Of these, 58 pairs of amplified products of the expected size, and 18 of the amplified products were polymorphic. Model-based Bayesian clustering, the unweighted pair group method with arithmetic average (UPGMA), and principal coordinate analysis (PCoA) of 179 wild E. breviaristatus in 12 populations using these EST-SSRs were generally consistent, grouping the 12 populations into two major clades. Analysis of molecular variance (AMOVA) found 70% of the genetic variation among the 12 populations and 30% within the populations, indicating a high level of genetic differentiation (or low gene exchange) among the 12 populations. The transferability of the 58 successful EST-SSR primers to 22 related hexaploid species was 86.2-98.3%. UPGMA analysis generally grouped species with similar genome types together.ConclusionsHere, we developed EST-SSR markers from the transcriptome of E. breviaristatus. The transferability of these markers was evaluated, and the genetic structure and diversity of E. breviaristatus were explored. Our results provide a basis for the conservation and management of this endangered species, and the obtained molecular markers represent valuable resources for the exploration of genetic relationships among species in the Elymus genus.

Dataset Information

Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.).

Publications

Development and Evaluation of a Novel Set of EST-SSR Markers Based on Transcriptome Sequences of Black Locust (Robinia pseudoacacia L.).

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