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Our comparison of repeat masking methods revealed that more stringent masking criteria should be avoided in the case of grapevine.
This approach has been shown to be effective, and the gain in power has been proven, as in the case of grapevine [ 28, 29].
Nevertheless, the other physical maps constructed on heterozygous genomes show important differences with respect to the case of grapevine and therefore they can only partially be taken as a comparison.
This is especially important in the case of grapevine where many varieties have been under cultivation for centuries, and some molecular markers have been shown not to be fully stable in certain old varieties, due to somatic mutation [ 2].
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This was observed in the case of grapevines cultivated in North Italy and Tunisia where R, S, and B fractions tended to cluster together according to the PCA).
In the case of the grapevine, the availability of a reference genome based on a wine-derived genotype (line PN40024) has not been as effective for table grape genetic studies as it would have been expected.
However, while all combinations of Y and/or Yh are lethal in Papaya, in Vitis HH genotypes do strive and set seeds, as in the case of certain domesticated grapevines such as Chardonnay, Muscat de Hambourg, Riesling or Cardinal (Truel pers. comm., Vassal INRA), which produce 100% hermaphrodite progenies.
In this case, the single-copy ubiquitin gene of grapevine (GenBank:FQ378362.1) was used instead of the 18S rDNA gene.
In some cases, it could even reduce an excessive vegetative vigour of grapevine.
Viroids sometimes infect crops asymptomatically, as in the case of the hop stunt viroid in grapevines and citrus.
In grapevine, phytoplasma cause grapevine yellows (GY) diseases, which were identified in the majority of grapevine growing countries worldwide.
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