The objective of this study is to explore rootstock genetic effects on salt tolerance in terms of fruit yield. A seedling population from hybrids between Citrus volkameriana (V) and Poncirus trifoliata (P), and itsgrandparents (V and P) were grafted with ‘Hashimoto’ mandarin. Trees were maintained in a screenhouse andsalt treatment (25 mM NaCl) was applied from June to September for 5 years (2004-2008) to 32 genotypesand 18 controls. Rootstocks were genotyped for 5 salt tolerance candidate genes. Alleles of 96 and 73 markerssegregating at the V and P genomes, respectively, in the VxP nucellar seedlings were studied for marker-traitassociations. Significant effects for rootstock genotype (G) and treatment (E) were found for most traits. Salinity decreased yield and juice volume, but improved total soluble solids and rind thickness. Year effectswere highly significant in most cases. GxE interaction was found for fruit weight, total fruit weight, leaf watercontent and leaf [Na]. Trait heritabilities of rootstock effects ranged from low to very low and no fruit yieldtrait had consistent, significant correlations through years with any non-fruit trait. Two salt tolerant candidateswere associated with fruit yield traits, but only under control conditions. Segregations at 8 and 9 loci on the Vand P genomes, respectively, were highly associated with fruit yield under the salinity treatment. Therefore,phenotypic selection assisted by markers linked to these QTL is more efficient than just phenotypic selectionto obtain rootstocks that confer salt tolerance to the grafted mandarin.

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