Evidence map›Paper›PMID 28789702›Full record

ArticleBMC research notes2017

Development of novel genic microsatellite markers from transcriptome sequencing in sugar maple (Acer saccharum Marsh.).

Monica Harmon, Thomas Lane, Margaret Staton, Mark V Coggeshall, Teodora Best, Chien-Chih Chen, Haiying Liang, Nicole Zembower, Daniela I Drautz-Moses, Yap Zhei Hwee and 4 more

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in BMC research notes, 2017. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 2 papers.

0numbers the graph read from it
0cells of the map it votes in
2citing papers in PubMed
0.9field-weighted citation impact, top 30% of its field
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

2 citing papers in PubMed, 14 citations in OpenAlex.

  1. Article
  2. Article
4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

14 authors at 7 institutions in 4 countries.

Monica HarmonSchool of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA.
Thomas LaneDepartment of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, 37996, USA.
Margaret StatonDepartment of Entomology and Plant Pathology, The University of Tennessee, Knoxville, TN, 37996, USA.
Mark V CoggeshallDepartment of Forestry, University of Missouri, Columbia, MO, 65274, USA.
Teodora BestDepartment of Ecosystem Science and Management and Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
Chien-Chih ChenDepartment of Genetics and Biochemistry, Clemson University, Clemson, SC, 29630, USA.
Haiying LiangDepartment of Genetics and Biochemistry, Clemson University, Clemson, SC, 29630, USA.
Nicole ZembowerDepartment of Ecosystem Science and Management and Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
Daniela I Drautz-MosesSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
Yap Zhei HweeSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
Stephan C SchusterSingapore Centre for Environmental Life Sciences Engineering, Nanyang Technological University, Singapore, 637551, Singapore.
Scott E SchlarbaumDepartment of Forestry, Wildlife & Fisheries, The University of Tennessee, Knoxville, TN, 37996-4563, USA.
John E CarlsonDepartment of Ecosystem Science and Management and Department of Plant Science, The Pennsylvania State University, University Park, PA, 16802, USA.
Oliver GailingSchool of Forest Resources and Environmental Science, Michigan Technological University, 1400 Townsend Drive, Houghton, MI, 49931, USA. ogailing@mtu.edu.ORCID http://orcid.org/0000-0002-1839-6694
Nanyang Technological University · SGPennsylvania State University · USUniversity of Tennessee at Knoxville · USMichigan Technological University · USClemson University · USFiji National University · FJUniversity of Missouri · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

backgroundSugar maple (Acer saccharum Marsh.) is a hardwood tree species native to northeastern North America and economically valued for its wood and sap. Yet, few molecular genetic resources have been developed for this species to date. Microsatellite markers have been a useful tool in population genetics, e.g., to monitor genetic variation and to analyze gene flow patterns. The objective of this study is to develop a reference transcriptome and microsatellite markers in sugar maple.

findingsA set of 117,861 putative unique transcripts were assembled using 29.2 Gb of RNA sequencing data derived from different tissues and stress treatments. From this set of sequences a total of 1068 microsatellite motifs were identified. Out of 58 genic microsatellite markers tested on a population of 47 sugar maple trees in upper Michigan, 22 amplified well, of which 16 were polymorphic and 6 were monomorphic. Values for expected heterozygosity varied from 0.224 to 0.726 for individual loci. Of the 16 polymorphic markers, 15 exhibited transferability to other Acer L. species.

conclusionsGenic microsatellite markers can be applied to analyze genetic variation in potentially adaptive genes relative to genomic reference markers as a basis for the management of sugar maple genetic resources in the face of climate change.

Indexed as

Genome, PlantMicrosatellite RepeatsTranscriptomeAcerClimate ChangeGene FlowGenetic VariationHeterozygoteHigh-Throughput Nucleotide SequencingPlant LeavesTreesAcer saccharumEST-SSRsNext-generation sequencingTransferability

Identifiers

PMID28789702
PMCPMC5549316
OpenAlexW2743207042

What OpenQuestion holds

Textmetadata
LicenceCC BY
Read underepoch 390

Registered trials

None linked

Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.