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Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine

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Abstract

Genomic DNA sequence databases are a potential and growing resource for simple sequence repeat (SSR) marker development in loblolly pine (Pinus taeda L.). Loblolly pine also has many expressed sequence tags (ESTs) available for microsatellite (SSR) marker development. We compared loblolly pine SSR densities in genome survey sequences (GSSs) to those in non-redundant EST and cDNA sequences (UniGenes) and designed SSR primer pairs from both sequence types. Overall SSR densities were 96 SSR/Mb in GSSs and 38 SSR/Mb in UniGenes. Loblolly pine had the lowest transcriptome SSR density when compared to 49 other species in the NCBI UniGene database. Among the five different GSS genome fractions of loblolly pine analyzed, methylation-filtered DNA had the highest SSR density at 145 SSR/Mb. The most abundant loblolly pine SSR motif was AT in both GSSs (34 SSR/Mb) and UniGenes (7.6 SSR/Mb). Among the trinucleotide SSR motifs, the most abundant was AAT (9.5 SSR/Mb) in GSSs and AGC (4.9 SSR/Mb) in UniGenes. We designed PCR primer pairs for 120 genomic SSRs and 315 EST-SSRs and evaluated PCR amplification for 108 (25%). We identified 21 primer pairs that reliably amplified polymorphic loci from 31 loblolly pine individuals and estimated that at least 60 additional polymorphic marker loci could be developed from available P. taeda GSS and UniGene resources.

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Abbreviations

EST:

Expressed sequence tag

GSS:

Genome survey sequence

NCBI:

National Center for Biotechnology Information

Mb:

Megabase

SSR:

Simple sequence repeat

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Acknowledgments

We thank Jim Roberds for his helpful discussions during the preparation of this manuscript and thank Tom Kubisiak, Ross Whetten, and an anonymous reviewer for their insightful comments on previous versions.

Author information

Authors and Affiliations

  1. Southern Institute of Forest Genetics, Southern Research Station U.S. Forest Service, Saucier, MS, 39574, USA

    Craig S. Echt, Dennis L. Deemer & C. Dana Nelson

  2. Mississippi Genome Exploration Laboratory, Mississippi State University, Mississippi State, MS, 39762, USA

    Surya Saha

  3. Department of Computer Science and Engineering, Mississippi State University, Mississippi State, MS, 39762, USA

    Surya Saha

  4. Department of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY, 14853, USA

    Surya Saha

Authors
  1. Craig S. Echt
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  2. Surya Saha
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  4. C. Dana Nelson
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Corresponding author

Correspondence to Craig S. Echt.

Additional information

Communicated by S. González-Martínez

Electronic supplementary materials

All supplementary files are data tables that conform to the XHTML 1.1 standard of the World Wide Web Consortium (W3C), as determined at http://validator.w3.org, and can be viewed with any web browser, as well as with Microsoft Excel or Word.

Supplementary Table S1

Summary and detailed SSR statistics from 5,393 Pinus taeda GSSs (.htm, 92 KB) (HTM 91 kb)

Supplementary Table S2

Summary and detailed SSR statistics from 18,079 Pinus taeda UniGenes (.htm, 209 KB) (HTM 209 kb)

Supplementary Table S3

Comparison of SSR densities, by motif, of NBCI UniGenes for 50 plant species from the NCBI UniGene database (.htm, 15 KB) (HTM 15 kb)

Supplementary Table S4

SSR marker and primer data derived from Pinus taeda GSS (PtSIFG_5000 series) and UniGenes (PtSIFG_6000 series); marker polymorphism evaluations were with 31 diverse P. taeda samples (.htm, 195 KB) (HTM 193 kb)

Supplementary Table S5

SSR allele genotypes from Pinus taeda samples 7-56, B-145-L, 11-1060, 20-1010, 6-1031, and 8-1070 (.htm, 16 KB) (HTM 6 kb)

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Echt, C.S., Saha, S., Deemer, D.L. et al. Microsatellite DNA in genomic survey sequences and UniGenes of loblolly pine. Tree Genetics & Genomes 7, 773–780 (2011). https://doi.org/10.1007/s11295-011-0373-7

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