Isozymes and restriction fragment length polymorphisms were used as markers in the construction of a genetic map of the citrus nuclear genome. The map was based on the segregation of 8 isozyme, 1 protein, and 37 RFLP loci in 60 progeny of a cross of two intergeneric hybrids, 'Sacaton' citrumelo (Citrus paradisi Macf. x Poncirus trifoliata (L.) Raf.) and 'Troyer' citrange (C. sinensis (L.) Osbeck x P. trifoliata), often used as rootstocks. The map contains 38 of 46 studied loci distributed on ten linkage groups. A genome size of 1,700 cM was estimated from partial linkage data. Approximately 35% of the genome should be within 10 cM and 58% within 20 cM of the mapped markers. Eight loci in three linkage groups and 1 unlinked locus deviated significantly from Mendelian segregation.

Electrophoretic analysis of rootstock bark was used to identify citrus trees on zygotic rootstocks in five 9- to 19-year-old rootstock trials involving 24 rootstock cultivars, and in four additional 22- to 23-year-old rootstock trials involving 24 selections of trifoliate orange [Poncirus trifoliata (L.) Raf.]. The rootstock seedlings used to propagate the trees for these trials were rogued visually before budding. The theoretical probability of distinguishing between nucellar genotypes and zygotics resulting from self-pollination averaged ≈86% among the rootstocks studied. In cultivars other than trifoliate orange, only 17 of 899 rootstocks were detected to be zygotic: eight in Kikodaidai, four in H-56 tangor, two in C-32 citrange, and one each in three other rootstocks. Many of these zygotics resulted from cross-pollination. In trifoliate orange, 29 of 846 trees were identified to be on zygotic rootstocks, all apparently resulting from pollination by trifoliate orange. Some trees on zygotic rootstocks were smaller and lower-yielding than trees on nucellar genotypes of the same cultivar, but many were fairly similar to, and a few yielded significantly more than, trees on nucellars. Trees on zygotic rootstocks usually had bud unions that were either significantly more or less smooth than trees on nucellars of the same cultivar. Data from zygotics did not bias results of rootstock trials appreciably. Isozyme analysis of rootstocks in commercial groves or rootstock trials may allow preliminary identification of promising new genotypes resulting from open pollination.