Table 1.
Accession list.
Fig 1.
Distribution of read numbers per fragment.
Table 2.
Average SNP diversity by chromosome.
Table 3.
SNP diversity of horticultural groups.
Fig 2.
Neighbour-joining analysis (NJA) of representative of the four basic taxa based on the 1,053 SNPs found in all gene fragments.
Table 4.
Intra- and inter-horticultural group dissimilarities (Average SNP/kb between two varieties).
Fig 3.
Factorial analysis and accession heterozygosity reveal C. reticulata/C. maxima heterozygosity of four mandarins for the C2P27 gene fragment.
Fig 4.
Distribution of SNP GST values for the four basic taxa from estimated ancestral taxa allelic frequencies after removal of genotypes with interspecific heterozygosity at the gene fragment level.
Table 5.
Screening of SNP markers in different citrus species and subtribes of the Aurantioideae subfamily.
Fig 5.
Location of all KASPar SNP markers used.
105 markers; position in kb according to reference sequence of the haploid clementine (Wu et al. [20]; Phytozome.net).
Fig 6.
Distribution of individual diagnostic marker GST values for the four basic taxa through consideration of representatives of the four basic horticultural groups as subpopulations.
Table 6.
Diversity of secondary species and modern hybrid varieties assessed using 105 SNP markers.
Fig 7.
PCA distribution of 70 Citrus cultivars from 105 SNP marker genotyping.
First three axes. Individual heterozygosity is provided in parentheses after the variety name in the F1/F2 plan. a. F1/F2; b. F1/F3.
Fig 8.
Frequency of specific alleles of the four basic taxa in homozygosity and heterozygosity for 70 Citrus accessions analysed with 103 species diagnostic markers.
Taxon DM: diagnostic markers for the considered taxon; FMHom, FMHet, FMabs, FPHom, FPHet, FPAbs, FCHom, FCHet, FCAbs, FMicHom, FMicHet, and FMicAbs are, respectively, the frequency of homozygous, heterozygous, and absent specific alleles for C. reticulata, C. maxima, C. medica, and C. micrantha.