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The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny

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Biologia Plantarum

Abstract

Moth orchids (Phalaenopsis) are among the top-traded blooming potted plants in the world. To explore mitochondrial DNA (mtDNA) markers for species identification, we located simple sequence repeats in the mtDNA of Phalaenopsis aphrodite subsp. formosana and then pre-screened them for polymorphic markers by their comparison with corresponding mtDNA regions of P. equestris. The combination of 13 selected markers located in intergenic spacers could unambiguously distinguish 15 endemic moth orchids. Five most variable markers with polymorphic information content (PIC) ≥ 0.7 could be combined to classify 18 of 19 endemic moth orchids including parental strains most commonly used in breeding programs. The sequences of four selected mtDNA regions were highly variable, and one region (MT2) could be used to completely distinguish 19 endemic moth orchids. Though mitochondrial introns were highly conserved among moth orchids, evolutionary hotspots, such as variable simple sequence repeats and minisatellite repeats, were identified as useful markers. Furthermore, a marker technology was applied to reveal the maternal inheritance mode of mtDNA in the moth orchids. Moreover, phylogenetic analysis indicates that the mtDNA was nonmonophyletic below the Phalaenopsis genus. In summary, we have revealed a set of mtDNA markers that could be used for identification and phylogenetic study of Phalaenopsis orchids.

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Abbreviations

AFLP:

amplified fragment length polymorphism

CAPS:

cleaved amplified polymorphic sequence

cpDNA:

chloroplast DNA

InDel:

insertion and deletion

ML:

maximum likelihood

mtDNA:

mitochondrial DNA

NGS:

next generation sequencing

nrITS:

internal transcribed spacers of nuclear ribosomal DNA

PAGE:

polyacrylamide gel electrophoresis

PCR:

polymerase chain reaction

PIC:

polymorphic information content

RAPD:

random amplified polymorphic DNA

RHS:

Royal Horticultural Society

SNP:

single nucleotide polymorphism

SSR:

simple sequence repeat

STR:

sequence tandem repeat

UPGMA:

unweighed pair-group method with arithmetic mean

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Authors and Affiliations

  1. Institute of Biotechnology, National Cheng Kung University, Tainan, 701, Taiwan

    B. -Y. Lin, L. L. H. Huang, Y. -C. Liu, Y. -Y. Su, T. -C. Chen & C. -C. Chang

  2. Department of Veterinary Medicine, National Pingtung University of Science and Technology, Pingtung, 912, Taiwan

    C. -D. Chang

  3. Institute of Tropical Plant Sciences, National Cheng Kung University, Tainan, 701, Taiwan

    R. -H. Lee

  4. Department of Life Sciences, National Cheng Kung University, Tainan, 701, Taiwan

    H. -J. Huang & W. -L. Wu

Authors
  1. B. -Y. Lin
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  2. C. -D. Chang
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  3. L. L. H. Huang
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  4. Y. -C. Liu
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  5. Y. -Y. Su
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  6. T. -C. Chen
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  7. R. -H. Lee
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  8. H. -J. Huang
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  9. W. -L. Wu
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  10. C. -C. Chang
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Corresponding authors

Correspondence to W. -L. Wu or C. -C. Chang.

Additional information

Acknowledgements: We thank Dr. Chi-Chu Tsai for sparing the moth orchids. We are also grateful to the anonymous reviewers for their comments that helped to improve the quality of this manuscript. This work was financially supported by the grant (MOST 102-2321-B-006-017 and 103-2321-B-006-009) from the Ministry of Science and Technology to C.-C. Chang.

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Lin, B.Y., Chang, C.D., Huang, L.L.H. et al. The mitochondrial DNA markers for distinguishing Phalaenopsis species and revealing maternal phylogeny. Biol Plant 60, 68–78 (2016). https://doi.org/10.1007/s10535-015-0566-2

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  • DOI: https://doi.org/10.1007/s10535-015-0566-2

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