Table 1.
Summary of citrus samples used in this study.
Table 2.
Summary of DNA markers used in this study.
Table 3.
Parentage of hybrid varieties with their organellar genotypes and the LOD scores used for error checking of DNA markers.
Table 4.
List of varieties that hold identical genotypes to the representative variety.
Table 5.
Summary of genetic characteristics and deduced population structure.
A. Genetic characteristics for three sample categories.
Table 6.
Deduced F statistics and G''ST values among three sample categories.
Fig 1.
Principal coordinate analysis plot of 101 citrus indigenous varieties using genomic DNA markers.
The plot was produced from the dissimilarity index deduced from 169 genomic DNA markers.
Fig 2.
Phylogenetic tree of 101 citrus indigenous varieties estimated from genomic DNA markers.
The tree was produced using the neighbor-joining method from genetic distances by the simple matching method. Node labels show bootstrap support values larger than 20.
Fig 3.
Magnitude of ΔK deduced from structure analysis as a function of K.
Simulation runs were performed for K = 2 to 10 with 10 iterations for each K, and the mean values of ΔK are plotted against K.
Table 7.
Summary of ΔK estimation for Structure analysis.
Fig 4.
Inferred admixture populations (Q) of 101 indigenous citrus varieties for a K = 3 population model in STRUCTURE.
Three clusters correspond to the deduced basic taxa at K = 3 (pummelo, citron and mandarin).
Table 8.
SSR markers for the genotyping of organelle genomes.
Table 9.
Organellar genotype characteristics of plant samples observed using SSR markers.
Table 10.
Differences in genetic characteristics of organellar genotype among three sample categories.
Table 11.
The classes of citrus cytoplasmic genotype (cytotype) according to the nonredundant alleles of eight chloroplast and three mitochondrial SSR markers.
Table 12.
Summary of all plant samples and representative samples according to the organelle genotype classes.
Fig 5.
Organelle genome composition of the three sample categories.
Each pie chart shows the relative abundance of each cytotype within the three sample categories. C01: C. ichangensis type, C02: Mexican lime, C03: limonia type, C04: pummelo type, C05: hyuganatsu type, C06: lemon type, C07: sweet orange type, C08: Satsumakikoku type, C09: yuzu type, C10: Ichang lemon type, C11: kunenbo B type, C12: mandarin type, C13: sunki type, C14: tachibana type, C15: tachibana C type, C16: Ogimikugani type, C17: Cleopatra type, C18: koji type.
Fig 6.
Principal coordinate analysis plot of 18 representative organelle genomes observed within 101 citrus indigenous varieties.
The plot was produced from modalities by Rogers and Tanimoto’s coefficient estimated from 11 organellar DNA markers. Three groups of genomes that cluster together are circled (I, II and III).
Fig 7.
Estimated phylogenetic tree of the 18 representative organelle genomes observed in 101 citrus indigenous varieties.
The tree was produced using the neighbor-joining method. The three main clades observed are indicated by different colors (I, II and III). Node labels show bootstrap support values.
Table 13.
Summary of allele sharing test within the indigenous varieties for inferring parentage.
Table 14.
List of the inferred parentage in the indigenous varieties and orphan hybrid varieties.
Fig 8.
An inferred genealogy of citrus indigenous varieties, part 1.
The plot shows the pedigrees of Kishu, yuzu, lemon, sour orange and their inferred offspring. Codes in parentheses represent individual cytotypes, and the same color represents the same cytotype. Dashed boxes indicate postulated parents. Double-lined boxes correspond to key varieties in this plot.
Fig 9.
An inferred genealogy of citrus indigenous varieties, part 2.
A: The pedigree plot of sweet orange and its inferred offspring. B: The pedigree plot of three tachibanas and their inferred offspring with postulated parents. C: Various proposed pedigrees. Their codes, colors and lines are as described for Fig 8.
Table 15.
Inferred parent-to-child combinations in the indigenous varieties.