Development of gene-based identification markers for Phalaenopsis ‘KS Little Gem’ based on comparative genome analysis
Gene-based markers are useful tools for genetic background surveys and comparative genome analysis due to their ease of application across closely related species. We developed gene-based DNA markers for Phalaenopsis ‘KS Little Gem’, a new Phalaenopsis variety with excellent ornamental traits, based...
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Published in | Horticulture, environment and biotechnology Vol. 58; no. 2; pp. 162 - 169 |
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Main Authors | , , , , , |
Format | Journal Article |
Language | English |
Published |
Korea
Korean Society for Horticultural Science
01.04.2017
Springer Nature B.V 한국원예학회 |
Subjects | |
Online Access | Get full text |
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Summary: | Gene-based markers are useful tools for genetic background surveys and comparative genome analysis due to their ease of application across closely related species. We developed gene-based DNA markers for
Phalaenopsis
‘KS Little Gem’, a new
Phalaenopsis
variety with excellent ornamental traits, based on a genome-wide comparison of chloroplast and nuclear sequences with those of orchids as well as monocot species, including rice and banana, to establish a molecular basis for species identification. Sequence comparisons of chloroplast DNA from
P.
‘KS Little Gem’ with those of
P. aphrodite
and
P. equestris
identified six variable genic regions of the chloroplast genome in which an intron of
rpl16
was the most polymorphic between related orchid species. To develop conserved ortholog set (COS) markers, we compared transcriptome unigenes of
P.
‘KS Little Gem’ with the
P. equestris
, rice, and banana genomes and identified 582
Phalaenopsis
COS candidates with at least two exons. PCR application using primer sets targeting six variable regions of the chloroplast genome and introns of 45 randomly selected COS candidate genes showed 92-98% amplification in three
Phalaenopsis
species. Among the candidate genes, we developed
rpl16
and three COS genes as diagnostic cross-species markers for
P.
‘KS Little Gem’ and diverse, related orchids. The gene-based molecular markers developed in this study will play an important role in species identification to facilitate the protection of
P.
‘KS Little Gem’ variety rights, as well as breeding and genetic studies of
Phalaenopsis
orchids. |
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Bibliography: | G704-000103.2017.58.2.008 |
ISSN: | 2211-3452 2211-3460 |
DOI: | 10.1007/s13580-017-0189-y |