Molecular Breeding

, 37:85 | Cite as

Genetic structure of a QTL hotspot on chromosome 2 in sweet cherry indicates positive selection for favorable haplotypes

  • Lichun Cai
  • Roeland E. Voorrips
  • Eric van de Weg
  • Cameron Peace
  • Amy IezzoniEmail author


A genomic region of particular interest for sweet cherry (Prunus avium L.) breeding is a quantitative trait locus (QTL) “hotspot” on chromosome 2. QTLs for fruit size, firmness, sweetness, and flowering time are reported to map to this region. An understanding of genetic diversity, allele sources, linkage relationships, and historical recombinations is critical to enable the combining of favorable alleles at multiple loci. The objectives of this study were to characterize, visualize, and interpret the genetic structure of this previously identified QTL hotspot within North American sweet cherry breeding germplasm, using a pedigree-based haploblocking approach. Across the 29.4 cM (6.3 Mbp) region defined by single nucleotide polymorphism (SNP) information from the RosBREED cherry 6K SNP array v1, a total of 12 recombination events falling into six inter-marker regions were traced within the pedigree of elite and wild germplasm (n = 55). These recombinations defined five haploblocks containing 5–15 markers and exhibiting 7–11 haplotypes each. Over the entire QTL hotspot, 30 extended haplotypes were identified for which parental gametes could be determined. When the haploblocks and their haplotypes were used to explore genetic diversity, ancestry, and recombination patterns, and then integrated with previous QTL results for fruit size, the results indicated that favorable alleles at this QTL hotspot are under positive selection in breeding. The genetic framework provided by a haploblock approach and knowledge of haplotype-level diversity sets the stage for assigning breeding utility to these haplotypes.


Prunus avium Haplotype SNP QTL hotspot 



This work was supported by USDA’s National Institute of Food and Agriculture-Specialty Crop Research Initiative project, “RosBREED: Combining Disease Resistance and Horticultural Quality in New Rosaceous Cultivars” (2014-51181-22378).

Supplementary material

11032_2017_689_MOESM1_ESM.xlsx (16 kb)
Supplementary Table S1 Sweet cherry plant materials and their parentage information. (XLSX 15 kb)
11032_2017_689_MOESM2_ESM.xlsx (11 kb)
Supplementary Table S2 Descriptions of locations (cM, bp) and lengths (cM, Mbp) of the haploblocks and gaps between sweet cherry haploblocks identified for a QTL hotspot on chromosome 2 in the sweet cherry breeding germplasm listed in Table S1. (XLSX 10 kb)
11032_2017_689_MOESM3_ESM.xlsx (12 kb)
Supplementary Table S3 Frequencies and founder contributors of haplotypes identified for five haploblocks spanning a QTL hotspot on chromosome 2, calculated for elite and wild germplasm only. (XLSX 11 kb)
11032_2017_689_MOESM4_ESM.xlsx (15 kb)
Supplementary Table S4 Haplotypes observed across five haploblocks for a QTL hotspot on chromosome 2 in U.S. elite and wild sweet cherry breeding germplasm for which parental gametes could be determined (n=55). (XLSX 14 kb)
11032_2017_689_MOESM5_ESM.docx (1 mb)
Supplementary Fig. S1 (A) Recombination sites identified for determining haploblock boundaries of a QTL hotspot on chromosome 2, illustrated using the Segregation Indicator Pattern and Recombination Sequence parameters of FlexQTL™. Phased marker genotype data for a maternal parent (‘Van’) – paternal parent (‘Lapins’) – child (‘Sweetheart’) combination is shown. For each individual, alleles in the left column were inherited from the maternal parent and alleles on the right column were from the paternal parent. ‘0’ or ‘1’ indicates the grandparental origin of alleles (maternal or paternal, respectively). Recombination Sequences are marked by black line boxes. Recombination sites are highlighted by red lines. Six recombination sites used for delimiting the QTL hotspot’s five haploblocks were identified from elite germplasm including EE, ‘Sweetheart’, ‘Lapins’, and ‘Stella’. Examples of within-haploblock recombination are illustrated with five unselected offspring from different families. For example, offspring 4 was determined to have inherited a gamete with a recombination within HB-E between the SNPs located at 19,200,549 and 19,324,328. (B) Pedigree of individuals presented in Supplementary Fig. S1 (A). (DOCX 1054 kb)
11032_2017_689_MOESM6_ESM.docx (276 kb)
Supplementary Fig. S2 Marker allele composition of each haplotype across five haploblocks for the sweet cherry QTL hotspot on chromosome 2. SSR alleles are recorded as fragment sizes in base pairs. The smallest subset of markers needed to differentiate the haplotypes within each haploblock are highlighted in red font. Haplotypes were assigned by the PediHaplotyper software (Voorrips et al. 2016). Haplotypes containing missing marker scores were omitted from the table. (DOCX 275 kb)


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Copyright information

© Springer Science+Business Media B.V. 2017

Authors and Affiliations

  • Lichun Cai
    • 1
  • Roeland E. Voorrips
    • 2
  • Eric van de Weg
    • 2
  • Cameron Peace
    • 3
  • Amy Iezzoni
    • 1
    Email author
  1. 1.Department of HorticultureMichigan State UniversityEast LansingUSA
  2. 2.Plant BreedingWageningen University and ResearchWageningenThe Netherlands
  3. 3.Department of HorticultureWashington State UniversityPullmanUSA

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