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Grape Phylloxera (Daktulosphaira vitifoliae) is a serious pest of commercial grapevines worldwide. These tiny sap-sucking aphidlike insects attack the roots of grapevines. The insects and secondary fungal infections can girdle roots, gradually cutting off the flow of nutrients and water to the vine. Nymphs also form protective galls on the undersides of grapevine leaves and overwinter under the bark or on the vine roots.

Inadvertently introduced in 1860 on imported American vinestocks, (it had already been introduced into California), Phylloxera wiped out a significant portion of European wine grapes in the mid-to-late 1800s. Phylloxera is native to the U.S., and native grape species there are at least partially resistant. The European wine grape Vitis vinifera is very susceptible, so when the pest was introduced in Europe it devastated the wine growing industry. Areas with sandy soils were spared, and the spread was slowed in dry climates, but gradually the louse was everywhere. A huge amount of research was devoted to finding a solution to the phylloxera problem, and two major solutions gradually emerged: hybridization and resistant rootstocks.

Hybridization was the breeding of vinifera with resistant species. Native American grapes are naturally phylloxera resistant but have aromas that are offputting to palates accustomed to European grapes. The intent of the cross was to generate a hybrid vine that was resistant to phylloxera but produced wine that did not taste like the native grape. Ironically, the hybrids tend not to be especially resistant to Phylloxera, although they are much more hardy with respect to climate and other vine diseases. The new varieties have never gained the popularity of the traditional ones, and in the EU are generally banned or at least strongly discouraged from use in quality wine.

Use of a resistant rootstock involves grafting a vinifera scion onto the roots of a resistant labrusca or other native species. This is the preferred method today, because the rootstock does not interfere with the development of the wine grapes, and it furthermore allows the customization of the rootstock to soil and weather conditions, as well as desired vigor. Unfortunately not all rootstocks are equally resistant. When phylloxera reached California, many growers used a rootstock called AXR-1 which was thought to be resistant. Sadly, it is not, and the replanting of afflicted vineyards continues today. Modern phylloxera infestation also occurs when wineries are in need of fruit immediately and cannot wait for grafted vines to be available.

The use of resistant American rootstock to guard against phylloxera also brought about a debate that remains unsettled to this day: whether self-rooted vines produce better wine than those that are grafted. So-called "pre-phylloxera" wines have a reputation for being ineffably better than those produced after grafting, and those that still survive are prized. Also much sought-after are wines made from self-rooted vines that have remained uninfected, such as Quinta do Noval's Nacional vineyard or Bollinger's "vignes francaises" bottling. However, all else being equal, it only seems logical that wines made from new, grafted vines would compare unfavorably with wines made from older, self-rooted vines. Also, rootstocks vary widely in quality, and a poor quality or poorly suited rootstock could produce poor wine.

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