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Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes

Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence...

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Autores principales: Shimizu, Tokurou, Kitajima, Akira, Nonaka, Keisuke, Yoshioka, Terutaka, Ohta, Satoshi, Goto, Shingo, Toyoda, Atsushi, Fujiyama, Asao, Mochizuki, Takako, Nagasaki, Hideki, Kaminuma, Eli, Nakamura, Yasukazu
Formato: Online Artículo Texto
Lenguaje:English
Publicado: Public Library of Science 2016
Materias:
Acceso en línea:https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130255/
https://www.ncbi.nlm.nih.gov/pubmed/27902727
http://dx.doi.org/10.1371/journal.pone.0166969
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author Shimizu, Tokurou
Kitajima, Akira
Nonaka, Keisuke
Yoshioka, Terutaka
Ohta, Satoshi
Goto, Shingo
Toyoda, Atsushi
Fujiyama, Asao
Mochizuki, Takako
Nagasaki, Hideki
Kaminuma, Eli
Nakamura, Yasukazu
author_facet Shimizu, Tokurou
Kitajima, Akira
Nonaka, Keisuke
Yoshioka, Terutaka
Ohta, Satoshi
Goto, Shingo
Toyoda, Atsushi
Fujiyama, Asao
Mochizuki, Takako
Nagasaki, Hideki
Kaminuma, Eli
Nakamura, Yasukazu
author_sort Shimizu, Tokurou
collection PubMed
description Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies.
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spelling pubmed-51302552016-12-15 Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes Shimizu, Tokurou Kitajima, Akira Nonaka, Keisuke Yoshioka, Terutaka Ohta, Satoshi Goto, Shingo Toyoda, Atsushi Fujiyama, Asao Mochizuki, Takako Nagasaki, Hideki Kaminuma, Eli Nakamura, Yasukazu PLoS One Research Article Most indigenous citrus varieties are assumed to be natural hybrids, but their parentage has so far been determined in only a few cases because of their wide genetic diversity and the low transferability of DNA markers. Here we infer the parentage of indigenous citrus varieties using simple sequence repeat and indel markers developed from various citrus genome sequence resources. Parentage tests with 122 known hybrids using the selected DNA markers certify their transferability among those hybrids. Identity tests confirm that most variant strains are selected mutants, but we find four types of kunenbo (Citrus nobilis) and three types of tachibana (Citrus tachibana) for which we suggest different origins. Structure analysis with DNA markers that are in Hardy–Weinberg equilibrium deduce three basic taxa coinciding with the current understanding of citrus ancestors. Genotyping analysis of 101 indigenous citrus varieties with 123 selected DNA markers infers the parentages of 22 indigenous citrus varieties including Satsuma, Temple, and iyo, and single parents of 45 indigenous citrus varieties, including kunenbo, C. ichangensis, and Ichang lemon by allele-sharing and parentage tests. Genotyping analysis of chloroplast and mitochondrial genomes using 11 DNA markers classifies their cytoplasmic genotypes into 18 categories and deduces the combination of seed and pollen parents. Likelihood ratio analysis verifies the inferred parentages with significant scores. The reconstructed genealogy identifies 12 types of varieties consisting of Kishu, kunenbo, yuzu, koji, sour orange, dancy, kobeni mikan, sweet orange, tachibana, Cleopatra, willowleaf mandarin, and pummelo, which have played pivotal roles in the occurrence of these indigenous varieties. The inferred parentage of the indigenous varieties confirms their hybrid origins, as found by recent studies. Public Library of Science 2016-11-30 /pmc/articles/PMC5130255/ /pubmed/27902727 http://dx.doi.org/10.1371/journal.pone.0166969 Text en © 2016 Shimizu et al http://creativecommons.org/licenses/by/4.0/ This is an open access article distributed under the terms of the Creative Commons Attribution License (http://creativecommons.org/licenses/by/4.0/) , which permits unrestricted use, distribution, and reproduction in any medium, provided the original author and source are credited.
spellingShingle Research Article
Shimizu, Tokurou
Kitajima, Akira
Nonaka, Keisuke
Yoshioka, Terutaka
Ohta, Satoshi
Goto, Shingo
Toyoda, Atsushi
Fujiyama, Asao
Mochizuki, Takako
Nagasaki, Hideki
Kaminuma, Eli
Nakamura, Yasukazu
Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes
title Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes
title_full Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes
title_fullStr Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes
title_full_unstemmed Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes
title_short Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes
title_sort hybrid origins of citrus varieties inferred from dna marker analysis of nuclear and organelle genomes
topic Research Article
url https://www.ncbi.nlm.nih.gov/pmc/articles/PMC5130255/
https://www.ncbi.nlm.nih.gov/pubmed/27902727
http://dx.doi.org/10.1371/journal.pone.0166969
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