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Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan

Abstract

The improvement of fruit quality is an important objective in citrus breeding. Using an F1 segregating population from a cross between citrus cultivars ‘Harehime’ (‘E647’—‘Kiyomi’ [Citrus unshiu Marcow. ‘Miyagawa Wase’ × Citrus sinensis (L.) Osbeck ‘Trovita’] × ‘Osceola’—a cultivar of clementine [Citrus clementina hort. ex Tanaka] × ‘Orland’ [Citrus paradisi Macfad. ‘Duncan’ × Citrus tangerina hort. ex Tanaka] × ‘Miyagawa Wase’) and ‘Yoshida’ ponkan (Citrus reticulata Blanco ‘Yoshida’), a SNP-based genetic linkage map was constructed and quantitative trait locus (QTL) mapping of four fruit-quality traits (fruit weight, sugar content, peel puffing, and water rot) was performed. The constructed genetic linkage map of ‘Harehime’ consisted of 442 single nucleotide polymorphisms (SNPs) on 9 linkage groups (LGs) and covered 635.8 cM of the genome, while that of ‘Yoshida’ ponkan consisted of 332 SNPs on 9 LGs and covered 892.9 cM of its genome. We identified four QTLs associated with fruit weight, one QTL associated with sugar content, three QTLs associated with peel puffing, and one QTL associated with water rot. For these QTL regions, we estimated the haplotypes of the crossed parents and verified the founding cultivars that these QTLs were originated from and their inheritance in descendant cultivars using pedigree information. QTLs identified in this study provide useful information for marker-assisted breeding of citrus in Japan.

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Acknowledgements

The authors thank Y. Yamamura and other staff members of agricultural field in Kuchinotsu Citrus Research Station, NARO for careful management of plant materials used in this study.

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Correspondence to T. Hayashi.

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The authors declare that they have no conflict of interest.

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All relevant data are within the paper and supplementary material files.

Additional information

Communicated by Y. Tsumura

Electronic supplementary material

Supplementary Table 1

(XLSX 38 kb)

Supplementary Table 2

(XLSX 32 kb)

Supplementary Fig. 1

Distribution of phenotypes in the ‘Harehime’ × ‘Yoshida’ ponkan mapping population. Frequency is shown on the vertical axes. White arrows, mean values for ‘Harehime’; black arrows, mean values for ‘Yoshida’ ponkan. The population mean and standard deviation are shown in each histogram (PPTX 94 kb)

Supplementary Fig. 2

The pedigree of ‘Harehime’ and the founder origin with inheritance of the FWq1 haplotype associated with fruit weight. The haplotype of a genomic region around the single nucleotide polymorphic site (ccsc3_7173412; in red) adjacent to the position of highest LOD score is shown. The figures following polymorphic sites are map distances (cM) between ccsc3_7173412 and the sites. Circles, seed parents; squares, pollen parents; diamond, a genotype with no offspring in this pedigree. Double horizontal lines indicate consanguinity. Black squares and circles, founding genotypes; red circle, ‘Harehime’. Haplotypes of founding genotypes are denoted by vertical columns of different colors, respectively. Haplotypes of the same column color within a founder have the same constitution of single nucleotide polymorphism in this region. The FWq1 haplotype associated with larger fruit weight in ‘Harehime’ is boxed (PPTX 73 kb)

Supplementary Fig. 3

The pedigree of ‘Harehime’ with the founder origin and inheritance of the FWq2 haplotype associated with fruit weight. The haplotype of a genomic region around the single nucleotide polymorphic site (ccsc3_46785655; in red) adjacent to the position of the highest LOD score is shown. The figures following polymorphic sites are map distances (cM) between ccsc3_46785655 and the sites. Circles, seed parents; squares, pollen parents; diamond, a genotype with no offspring in this pedigree. Double horizontal lines indicate consanguinity. Black squares and circles, founding genotypes; red circle, ‘Harehime’. Haplotypes of founding genotypes are denoted by vertical columns of different colors, respectively. Haplotypes of the same column color within a founder have the same constitution of single nucleotide polymorphism in this region. The FWq2 haplotype associated with the larger fruit weight in ‘Harehime’ is boxed (PPTX 83 kb)

Supplementary Fig. 4

The pedigree of ‘Harehime’ with the founder origin and inheritance of the FWq4 haplotype associated with fruit weight. The haplotype of a genomic region around the single nucleotide polymorphic site (ccsc7_4531969; in red) adjacent to the position of the highest LOD score is shown. The figures following polymorphic sites are map distances (cM) between ccsc7_4531969 and the sites. Circles, seed parents; squares, pollen parents; diamond, a genotype with no offspring in this pedigree. Double horizontal lines indicate consanguinity. Black squares and circles, founding genotypes; red circle, ‘Harehime’. Haplotypes of founding genotypes are denoted by vertical columns of different colors, respectively. Haplotypes originated by recombination are shown by two or three-colored columns. The FWq4 haplotype associated with larger fruit weight in ‘Harehime’ is boxed (PPTX 75 kb)

Supplementary Fig. 5

The pedigree of ‘Harehime’ with the founder origin and inheritance of the SCq1 haplotypes associated with fruit sugar content. The haplotype of a genomic region around the single nucleotide polymorphic site (ccsc5_39529280; in red) adjacent to the position of the highest LOD score is shown. The figures following polymorphic sites are map distances (cM) between ccsc5_39529280 and the sites. Circles, seed parents; squares, pollen parents; diamond, a genotype with no offspring in this pedigree. Double horizontal lines indicate consanguinity. Black squares and circles, founding genotypes; red circle, ‘Harehime’. Haplotypes of founding genotypes are denoted by vertical columns of different colors, respectively. The haplotype of ‘031045’ originated by recombination is shown by two-colored column. The SCq1 haplotype associated with higher sugar content in ‘Harehime’ is boxed (PPTX 89 kb)

Supplementary Fig. 6

The pedigree of ‘Harehime’ with the founder origin and inheritance of the PPq2 haplotypes associated with peel puffing. The haplotype of a genomic region around the single nucleotide polymorphic site (ccsc5_35985465; in red) adjacent to the position of the highest LOD score is shown. The figures following polymorphic sites are map distances (cM) between ccsc5_35985465 and the sites. Circles, seed parents; squares, pollen parents; diamond, a genotype with no offspring in this pedigree. Double horizontal lines indicate consanguinity. Black squares and circles, founding genotypes; red circle, ‘Harehime’. Haplotypes of founding genotypes are denoted by vertical columns of different colors, respectively. Haplotypes of the same column color within a founder have the same constitution of single nucleotide polymorphism in this region. The haplotypes of ‘Osceola’ and ‘E647’ that are not determined to a single origin are indicated with two or three-colored vertical column. Haplotypes originated by recombination are shown by two-colored columns. The PPq2 haplotype associated with a higher degree of peel puffing in ‘Harehime’ is boxed (PPTX 52 kb)

Supplementary Fig. 7

The pedigree of ‘Harehime’ with the founder origin and inheritance of the PPq3 haplotypes associated with peel puffing. The haplotype of a genomic region around the single nucleotide polymorphic site (ccsc7_5847448; in red) adjacent to the position of the highest LOD score is shown. The figures following polymorphic sites are map distances (cM) between ccsc7_5847448 and the sites. Circles, seed parents; squares, pollen parents; diamond, a genotype with no offspring in this pedigree. Double horizontal lines indicate consanguinity. Black squares and circles, founding genotypes; red circle, ‘Harehime’. Haplotypes of founding genotypes are denoted by vertical columns of different colors, respectively. The PPq3 haplotype associated with a higher degree of peel puffing in ‘Harehime’ is boxed (PPTX 80 kb)

Supplementary Fig. 8

The pedigree of ponkan with the inheritance of the WRq1 haplotypes associated with the occurrence of water rot. The haplotype of a genomic region around the single nucleotide polymorphic site (ccsc2_31345168; in red) adjacent to the position of the highest LOD score is shown. The figures following polymorphic sites are map distances (cM) between ccsc2_31345168 and the sites. Circles, seed parents; squares, pollen parents; diamond, a genotype with no offspring in this pedigree. Double horizontal lines indicate consanguinity. Red squares, ponkan; black squares and circles, other founding genotypes. Haplotypes of founding genotypes are denoted by vertical columns of different colors, respectively. Haplotypes of the same column color within a founder have the same constitution of single nucleotide polymorphism in this region. Haplotypes originated by recombination are shown by two-colored columns. The WRq1 haplotype associated with a higher proportion of water rot in ponkan is boxed (PPTX 86 kb)

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Imai, A., Yoshioka, T. & Hayashi, T. Quantitative trait locus (QTL) analysis of fruit-quality traits for mandarin breeding in Japan. Tree Genetics & Genomes 13, 79 (2017). https://doi.org/10.1007/s11295-017-1162-8

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Keywords

  • Citrus
  • QTL mapping
  • Pedigree
  • Fruit-quality traits