title: Hybrid Origins of Citrus Varieties Inferred from DNA Marker Analysis of Nuclear and Organelle Genomes.
abstract: 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.
authors.affiliation: Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan.
authors.forename: Tokurou
authors.identifier: http://orcid.org/0000-0003-3554-3964
authors.initials: T
authors.lastname: Shimizu
authors.affiliation: Experimental Farm, Graduate School of Agriculture, Kyoto University, Kizugawa, Kyoto, Japan.
authors.forename: Akira
authors.initials: A
authors.lastname: Kitajima
authors.affiliation: Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan.
authors.forename: Keisuke
authors.initials: K
authors.lastname: Nonaka
authors.affiliation: Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan.
authors.forename: Terutaka
authors.initials: T
authors.lastname: Yoshioka
authors.affiliation: Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan.
authors.forename: Satoshi
authors.initials: S
authors.lastname: Ohta
authors.affiliation: Division of Citrus Research, Institute of Fruit Tree and Tea Science, NARO, Shimizu, Shizuoka, Japan.
authors.forename: Shingo
authors.initials: S
authors.lastname: Goto
authors.affiliation: National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Atsushi
authors.initials: A
authors.lastname: Toyoda
authors.affiliation: National Institute of Genetics, Comparative Genomics laboratory, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Asao
authors.initials: A
authors.lastname: Fujiyama
authors.affiliation: National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Takako
authors.initials: T
authors.lastname: Mochizuki
authors.affiliation: National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Hideki
authors.initials: H
authors.lastname: Nagasaki
authors.affiliation: National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Eli
authors.initials: E
authors.lastname: Kaminuma
authors.affiliation: National Institute of Genetics, Center for Information Biology, National Institute of Genetics, Mishima, Shizuoka, Japan.
authors.forename: Yasukazu
authors.initials: Y
authors.lastname: Nakamura
mesh_terms: D002467:Cell Nucleus / Q000235:genetics*; D002736:Chloroplasts / Q000235:genetics*; D002957:Citrus / Q000145:classification / Q000235:genetics*; D018744:DNA, Plant / Q000235:genetics*; D005819:Genetic Markers / Q000235:genetics; D014644:Genetic Variation; D054629:Genome, Mitochondrial / Q000235:genetics*; D018745:Genome, Plant / Q000235:genetics; D023281:Genomics; D060005:Genotyping Techniques; D010802:Phylogeny
chemical_list: D018744:DNA, Plant; D005819:Genetic Markers