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    Author(s): Mengmeng Lu; Konstantin V. Krutovsky; C. Dana Nelson; Tomasz E. Koralewski; Thomas D. Byram; Carol A. Loopstra
    Date: 2016
    Source: BMC Genomics
    Publication Series: Scientific Journal (JRNL)
    Station: Southern Research Station
    PDF: View PDF  (1.0 MB)

    Description

    Background: Loblolly pine (Pinus taeda L.) is one of the most widely planted and commercially important forest
    tree species in the USA and worldwide, and is an object of intense genomic research. However, whole genome
    resequencing in loblolly pine is hampered by its large size and complexity and a lack of a good reference. As a
    valid and more feasible alternative, entire exome sequencing was hence employed to identify the gene-associated
    single nucleotide polymorphisms (SNPs) and to genotype the sampled trees.

    Results: The exons were captured in the ADEPT2 association mapping population of 375 clonally-propagated loblolly
    pine trees using NimbleGen oligonucleotide hybridization probes, and then exome-enriched genomic DNA fragments
    were sequenced using the Illumina HiSeq 2500 platform. Oligonucleotide probes were designed based on 199,723
    exons (≈49 Mbp) partitioned from the loblolly pine reference genome (PineRefSeq v. 1.01). The probes covered 90.2 %
    of the target regions. Capture efficiency was high; on average, 67 % of the sequence reads generated for each tree
    could be mapped to the capture target regions, and more than 70 % of the captured target bases had at least 10X
    sequencing depth per tree. A total of 972,720 high quality SNPs were identified after filtering. Among them, 53 % were
    located in coding regions (CDS), 5 % in 5’ or 3’ untranslated regions (UTRs) and 42 % in non-target and non-coding
    regions, such as introns and adjacent intergenic regions collaterally captured. We found that linkage disequilibrium (LD)
    decayed very rapidly, with the correlation coefficient (r2) between pairs of SNPs linked within single scaffolds decaying
    to half maximum (r2 = 0.22) within 55 bp, to r2 = 0.1 within 192 bp, and to r2 = 0.05 within 451 bp. Population structure
    analysis using unlinked SNPs demonstrated the presence of two main distinct clusters representing western and
    eastern parts of the loblolly pine range included in our sample of trees.

    Conclusions: The obtained results demonstrated the efficiency of exome capture for genotyping species such as
    loblolly pine with a large and complex genome. The highly diverse genetic variation reported in this study will be a
    valuable resource for future genetic and genomic research in loblolly pine.

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    Citation

    Lu, Mengmeng; Krutovsky, Konstantin V.; Nelson, C. Dana; Koralewski, Tomasz E.; Byram, Thomas D.; Loopstra, Carol A. 2016.Exome genotyping, linkage disequilibrium and population structure in loblolly pine (Pinus taeda L.). BMC Genomics. 17(1): 421-. https://doi.org/10.1186/s12864-016-3081-8.

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    Keywords

    Loblolly pine, Exome sequence capture, Target enrichment, Genotyping by sequencing, Linkage disequilibrium, Population structure, SNPs

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