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According to their supposed origin (see below), the heterozygosity of C. limon and C. aurantifolia is based on the interspecific differentiation between the basic taxa.
The first is the differentiation between the basic taxa that appears to be underestimated with CHet loci when compared with CHom loci.
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Secondary species arose from the hybridization of the basic taxa.
(lemon) originated later through hybridization and a limited number of sexual recombination events among the basic taxa.
For the secondary species resulting from hybridization between the C. reticulata gene pool and the other basic taxa, the WNA loci present the advantage of frequent recessivity for the other parental gene pools.
The analysis of Fstat parameters on the subset of the genotypes of the three basic taxa (C. reticulata, C. medica, C. maxima) with a non-significant Fis value but high Fit and Fst values confirms this important organization of the allelic diversity between these taxa.
As these markers were identified from the Clementine BES and GoldenGate primers defined from Clementine sequences, these results are reasonable based on the strong genetic relationship between Clementine and C. reticulata and the important inter-specific differentiation between C. reticulata and the others basic taxa [ 28].
Data sets derived from different molecules and different morphological character systems rarely included the same basic taxa, thus they couldn't be compared.
As a result, a very low rate of EST-SSR markers is usable to make comparative genetic mapping between these three basic taxa: it is only 3% for Citron/Pummelo, 3% for Citron/Mandarin (cv Cleopatra) and around 9% for Pummelo (cv Pink)/Mandarin (cv Cleopatra).
This view is further supported by limited data on mitochondrial DNA differences between the three taxa.
The resulted dendrogram interpreted the similarities and dissimilarities between the investigated taxa.
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