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Some lemon [Citrus limon (L.) Burm. f.] cultivars present compatibility problems with commonly used citrus rootstocks. Therefore, assessing trueness-to-type of lemon mother trees is needed by growers. Morphological differentiation of lemon cultivars is not precise because they present high phenotypic plasticity. The objective of this paper is to contrast the discriminatory ability of several molecular marker systems for lemon. Three marker types were used: randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR) and inter-retrotransposon amplified polymorphism (IRAP). The molecular variability found in C. limon is larger than that reported for C. clementina, another vegetatively propagated citrus species. This difference in variability content might be explained by differences in the distribution and age of both cultures. Similar to clementines, polymerase chain reaction (PCR) markers using primers anchored in copya-like retrotransposons resulted in a higher rate of polymorphisms (36.4%) than did primers of random sequence (27.3%) or those anchored at simple sequence repeats (0%), indicating a higher molecular variability at the locations where these retrotransposons inserted. Primers anchored in gypsy-like retroelements did not yield polymorphisms. Lemon cultivars from important groups such as `Eureka', `Fino', and `Verna' could be distinguished using all polymorphisms.
A seedling population from hybrids between ‘Volkamer’ lemon (Citrus volkameriana) and ‘Rubidoux’ trifoliate orange (Poncirus trifoliata) was grafted with ‘Hashimoto’ Satsuma mandarin (Citrus unshiu) to study the inheritance of rootstock effects on salt tolerance in terms of fruit yield. Trees were maintained in a screenhouse, and a salt treatment (25 mm NaCl) was applied to 32 genotypes from June to September every year for 5 years. Rootstocks were genotyped for five salt tolerance candidate genes. Significant effects of rootstock genotype (G) and treatment (E) were found for most traits. Salinity decreased yield and juice volume but improved soluble solids concentration (TSS) and rind thickness. Year effects were highly significant in most cases. G × E interactions were found for fruit weight, total fruit weight, juice volume (JV), leaf water content (LWC), and leaf [Na+]. Therefore, rootstocks that induce early fruit maturation under salinity (by increasing TSS and maintaining JV) can be selected to expand the harvesting calendar of mandarin cultivars. Salt tolerance candidate genes SOS1 and NHX1 were associated with fruit yield traits under normal conditions (1.4 dS·m−1), and SOS1 and CCC were associated with LWC under salinity conditions (4 dS·m−1). Only 5% progeny induced higher accumulated yield than ‘Volkamer’ lemon under salinity. Given the low heritability of rootstock effects on fruit yield under salinity conditions (0.18 at most), marker-assisted selection might be useful.