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QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers


Seedlessness, flavor, and color are top priorities for mandarin (Citrus reticulata Blanco) cultivar improvement. Given long juvenility, large tree size, and high breeding cost, marker-assisted selection (MAS) may be an expeditious and economical approach to these challenges. The objectives of this study were to construct high-density mandarin genetic maps and to identify single nucleotide polymorphism (SNP) markers associated with fruit quality traits. Two parental genetic maps were constructed from an F1 population derived from ‘Fortune’ × ‘Murcott’, two mandarin cultivars with distinct fruit characters, using a 1536-SNP Illumina GoldenGate assay. The map for ‘Fortune’ (FOR) consisted of 189 SNPs spanning 681.07 cM and for ‘Murcott’ (MUR) consisted of 106 SNPs spanning 395.25 cM. Alignment of the SNP sequences to the Clementine (Citrus clementina) genome showed highly conserved synteny between the genetic maps and the genome. A total of 48 fruit quality quantitative trait loci (QTLs) were identified, and ten of them stable over two or more samplings were considered as major QTLs. A cluster of QTLs for flavedo color space values L, a, b, and a/b and juice color space values a and a/b were detected in a single genomic region on linkage group 4. Two carotenoid biosynthetic pathway genes, pds1 and ccd4, were found within this QTL interval. Several SNPs were potentially useful in MAS for these fruit characteristics. QTLs were validated in 13 citrus selections, which may be useful in further validation and tentative MAS in mandarin fruit quality improvement.

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This work was partly funded by New Varieties Development & Management Corporation, Citrus Research and Development Foundation, and the University of Florida Plant Molecular Breeding Initiative. The authors thank Yanzi Zhang, Marjorie Wendell, Xu Wei, Qibin Yu, and Misty Holt for technical assistance, as well as Sanghamitra Das for help with editing and Harry Klee for critical reading of the manuscript.

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Correspondence to Frederick G. Gmitter Jr..

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The authors declare that they have no conflicts of interest.

Author’s contributions

FGG and CC conceived and designed the study; the mapping population was developed within the breeding program of FGG. YY carried out the work, analyzed the data, and wrote the manuscript. CC developed the GoldenGate array and read SNP genotyping data. CC and FGG critically read and revised the manuscript. All authors read and approved the final manuscript.

Data archiving statement

The SNPs, genetic maps, and QTL data reported in this manuscript will be made publicly available through the Citrus Genome Database (www.citrusgenomedb.org).

Additional information

Communicated by W.-W. Guo

Electronic supplementary material


Frequency distributions of mandarin quality traits for the F1 population in three samplings (January and February in 2012 and February in 2013). (PPTX 90 kb)


Phenotypic variation of 15 fruit quality traits evaluated in ‘Fortune’, ‘Murcott’ and the F1 population in four samplings (January and February in 2012 and 2013). (XLSX 15 kb)


Phenotypic correlations among 15 fruit quality traits measured in the ‘Fortune’ x ‘Murcott’ F1 progeny in four samplings (January and February in 2012 and 2013). (XLSX 13 kb)


Two-factor (Genotype, sampling date) ANOVA for mandarin fruit quality traits in four samplings (January and February in 2012 and 2013). Fruit diameter (FD), fruit weight (FW), juice percentage (JP), seed number (SD), soluble solids content (SSC), titratable acidity (TA), SSC over TA ratio (ST), flavedo color space value L (FCL), a (FCA), b (FCB), a over b ratio (FCAB), juice color space value L (JCL), a (JCA), b (JCB), a over b ratio (JCAB). (XLSX 11 kb)


SNP-based markers and genetic position on the linkage groups. The maternal parent is ‘Fortune’ (FOR), and the paternal parent is ‘Murcott’ (MUR). (XLSX 67 kb)


Validation of QTLs in the 13 citrus selections. (XLSX 11 kb)

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Yu, Y., Chen, C. & Gmitter, F.G. QTL mapping of mandarin (Citrus reticulata) fruit characters using high-throughput SNP markers. Tree Genetics & Genomes 12, 77 (2016). https://doi.org/10.1007/s11295-016-1034-7

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  • Mapping
  • Fruit quality
  • Mandarin
  • Breeding