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Genetic analysis of salt tolerance in a progeny derived from the citrus rootstocks Cleopatra mandarin and trifoliate orange

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A total of 60 traits that could be related to salt tolerance were genetically analyzed using nucellar plants as repetitions of apomictic hybrids in a reference population derived from two common citrus rootstocks, Cleopatra mandarin (salt tolerant) and trifoliate orange (salt sensitive), in two experiments differing in duration (1 versus 3 years) [NaCl] (30 versus 25 mM) and environmental control (greenhouse versus screenhouse). In both experiments, the trifoliate parent always showed less aerial vegetative growth than Cleopatra, and under salinity, the trifoliate parent showed higher Na+ and Cl leaf concentrations than the salt-tolerant parent. Salinity affected the relationships among traits, particularly those involving leaf water potential; leaf concentrations of Cl, K+, B and Fe; and root [Na+]. Most traits showed heritabilities below 0.6, and their quantitative trait locus (QTL) analyses were carried out using three mapping procedures to obtain complementary genetic information on trait inheritance. A total of 98 QTLs were detected by interval mapping and multiple QTL mapping procedures. Fresh and dried weights of the leaf, studied in both experiments, showed common QTLs, remarking their repeatability. A cluster of QTLs governing plant vigour and leaf boron concentration pointed a genomic region in linkage group 3 as the most relevant one to improve salt tolerance using the Cleopatra parent as donor. Besides, a QTL genotype in linkage group 7, associated with the smallest leaf water potential and defoliation index under salinity, corresponded to the highest leaf [Na+] and the largest leaf area, suggesting the presence of a putative tissue salt tolerance QTL.

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This work has been partially supported by grants AGL2008-00197/AGR, RTA2011-00132-C02 and AGL2014-56675-R from the Spanish Government (Ministerio de Economia y Competitividad) and Fondo Social Europeo (GPB). Authors thank Mr. J. Puchades and Dr. Alida Ballester for the technical assistance.

Data archiving statement

The SSR primer sequences are available upon request from http://www.ivia.es/deps/biot/labgen/request.html. The genetic linkage maps have been submitted to the Citrus Genome Database (https://www.citrusgenomedb.org/). Concerning markers derived from salt tolerance candidate genes, COR15 and Aquapor correspond to contig6158 (ATTATCAATT AATTTATAAA AGAAAATTAG TTTCTTTTTT TTTTTT) and contig2599 (TGGGGAAAAC TGCCTTGAAA GGAACCCCTT TTAATTCTT), respectively, from the KCl-salt1 library at Valencian Implemented Citrus EST and NucleoTide (VICENT sequences database). Mygbg2 and EREBP1 correspond to transcription factors from the NCBI database, accessions EF071983 and FJ544914, respectively. Marker 42C corresponds to a lectin gene obtained by PCR select and overexpressed in Cleopatra roots under salinity (forward primer: AGATCAAGCAGCAGATCC; reverse primer: AGCAAGCTCTTACTGTGACC). The parents of the progeny are kept at the Citrus Germplasm Bank, and the accession references are as follows: IVIA-385 (Cleopatra mandarin), IVIA-537 (Flying Dragon trifoliate orange) and IVIA-236 (Rich trifoliate orange).

Author information

Correspondence to M. J. Asins.

Additional information

Communicated by W.-W. Guo

Electronic supplementary material

Below is the link to the electronic supplementary material.


Online Resource 1- Pearson coefficients of significantly (p < 0.05) correlated traits (trait abbreviations in Table 1) under both control (Pears_C) and salinity (Pears_S). Common traits between experiments with yellow background. Traits whose correlation change from control to salinity are in bold. (PDF 61 kb)


Online Resource 2- Significant (p < 0.02) trait correlations under control (C) and salinity (S). Consistent trait correlations in bold. Trait abbreviations in Table 1 (PDF 98 kb)


Online Resource 3- List of significant trait-locus associations (the highest significant locus) and corresponding genotypic means depending on the genome where they were detected: Cleopatra mandarin (r: nn and np), trifoliate orange (p: ll and lm) or both parents (r + p: ac, ad, bc, and bd). K is the Kruskal-Wallis statistic provided by MapQTL 6 software. Trait abbreviations in Table 1. (PDF 60 kb)


Online Resource 4- Distributions of trait heritabilities (a) and total number of detected QTLs per trait (b). Absolute frequencies of each class is indicated at the Y axis. Control, or salinity, indicated by white or grey bars, respectively. (PDF 10 kb)

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Raga, V., Intrigliolo, D.S., Bernet, G.P. et al. Genetic analysis of salt tolerance in a progeny derived from the citrus rootstocks Cleopatra mandarin and trifoliate orange. Tree Genetics & Genomes 12, 34 (2016). https://doi.org/10.1007/s11295-016-0991-1

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  • QTL analysis
  • Plant vigour
  • Root
  • Leaf water potential
  • B nutrition
  • Leaf Fe
  • Candidate genes