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Fruit size QTL identification and the prediction of parental QTL genotypes and breeding values in multiple pedigreed populations of sweet cherry

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Abstract

Large fruit size is a critical trait for any new sweet cherry (Prunus avium L.) cultivar, as it is directly related to grower profitability. Therefore, determining the genetic control of fruit size in relevant breeding germplasm is a high priority. The objectives of this study were (1) to determine the number and positions of quantitative trait loci (QTL) for sweet cherry fruit size utilizing data simultaneously from multiple families and their pedigreed ancestors, and (2) to estimate fruit size QTL genotype probabilities and genomic breeding values for the plant materials. The sweet cherry material used was a five-generation pedigree consisting of 23 founders and parents and 424 progeny individuals from four full-sib families, which were phenotyped for fruit size and genotyped with 78 RosCOS single nucleotide polymorphism and 86 simple sequence repeat markers. These data were analyzed by a Bayesian approach implemented in FlexQTL™ software. Six QTL were identified: three on linkage group (G) 2 with one each on groups 1, 3, and 6. Of these QTL, the second G2 QTL and the G6 QTL were previously discovered while other QTL were novel. The predicted QTL genotypes show that some QTL were segregating in all families while other QTL were segregating in a subset of the families. The progeny varied for breeding value, with some progeny having higher breeding values than their parents. The results illustrate the use of multiple pedigree-linked families for integrated QTL mapping in an outbred crop to discover novel QTL and predict QTL genotypes and breeding values.

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Acknowledgments

This project was supported in part by two USDA grants, USDA-NRI NIFA 2008-02259 and USDA-SCRI Grant #2009 = 51181-05808 entitled ‘RosBREED: Enabling marker-assisted breeding in Rosaceae’.

Author information

Authors and Affiliations

  1. Department of Plant, Soil and Microbial Sciences, Michigan State University, East Lansing, MI, 48824, USA

    Umesh R. Rosyara, Guorong Zhang & Dechun Wang

  2. Department of Horticulture, Michigan State University, East Lansing, MI, 48824, USA

    Umesh R. Rosyara, Audrey Sebolt & Amy F. Iezzoni

  3. Biometris, Wageningen University and Research Centre, PO Box 100, 6700 AC, Wageningen, The Netherlands

    Marco C. A. M. Bink

  4. Plant Breeding, Wageningen-UR Plant Breeding, PO Box 16, 6700 AA, Wageningen, The Netherlands

    Eric van de Weg

  5. Agricultural Research Center-Hays, Kansas State University, 1232 240th Avenue, Hays, KS, 67601, USA

    Guorong Zhang

  6. INRA, UMR 1332 de Biologie du Fruit et Pathologie, 33140, Villenave d’Ornon, France

    Elisabeth Dirlewanger & Jose Quero-Garcia

  7. Université Bordeaux, UMR 1332 de Biologie du Fruit et Pathologie, 33140, Villenave d’Ornon, France

    Elisabeth Dirlewanger & Jose Quero-Garcia

  8. Julius Kühn-Institut, Federal Centre for Cultivated Plants, Pillnitzer Platz 3a, 01326, Dresden, Germany

    Mirko Schuster

Authors
  1. Umesh R. Rosyara
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  2. Marco C. A. M. Bink
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  5. Dechun Wang
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  6. Audrey Sebolt
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  7. Elisabeth Dirlewanger
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  8. Jose Quero-Garcia
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  9. Mirko Schuster
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  10. Amy F. Iezzoni
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Corresponding author

Correspondence to Amy F. Iezzoni.

Electronic supplementary material

Below is the link to the electronic supplementary material.

Supplementary Table S1

Populations, locations, and number of progeny individuals genotyped for 86 SSR and 78 RosCOS SNP markers. This plant material and genotyping is described in Cabrera et al (2012) (PPTX 99 kb)

Supplementary Table S2

Posterior probability for the fruit weight FW_G1, FW_G2a, FW_G2b, FW_G2c, FW_G3, and FW_G6 genotypes predicted by FlexQTL™, where Q is the positive QTL allele and q is negative QTL allele. Progeny from the bi-parental populations are identified by the combination of the first letter from both parents (PPTX 75 kb)

Supplementary Table S3

Estimated individual and genome-wide breeding values for the QTLs detected in this study. Progeny from the bi-parental populations are identified by the combination of the first letter from both parents (PPTX 67 kb)

Supplementary Figure S1

Full pedigree of the sweet cherry plant materials used in the study (PPTX 62 kb)

Supplementary Figure S2

Fruit weight (g) distributions of (1) all populations, (2) NY × EF (3) Regina × Lapins, (4) Namati × Krupnoplodnaya, and (5) Namati × Summit. n indicates number of individuals (PPTX 55 kb)

Supplementary Figure S3

Informative meioses at the first and second homologues across the eight sweet cherry linkage groups (PPTX 59 kb)

Supplementary Figure S4

Frequency of observed and expected double recombinants in the plant materials used in this study. The upper triangles indicate the first parent while the downward triangles indicate the second parent. The black and red colors are the expected and observed number of double recombinants, respectively. Stars result when the triangles from the first and second parent plot to the same position (DOCX 15 kb)

Supplementary Figure S5

QTL allele predictions (Q/q) and probabilities (QTL p) and breeding values (BV) for ‘Regina’ and ‘Lapins’ and two of their progeny individuals, RL0059 and RL0039, that have high and low breeding values, respectively. QTL genotypes predicted with a probability greater than 0.70 are in bold (XLSX 55 kb)

Supplementary Figure S6

Transmission for FW_G2b in progeny from the cross between ‘New York 54’ (New York) and ‘Emperor Francis’ (EF). The FW_G2b alleles are defined by the SSR marker BPPCT034. The predicted QTL genotypes are presented along with the fruit weight means for each of the four progeny genotypic classes. Fruit weigh means followed by the same letter are not significantly different (ANOVA, P > 0.05) (XLSX 167 kb)

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Rosyara, U.R., Bink, M.C.A.M., van de Weg, E. et al. Fruit size QTL identification and the prediction of parental QTL genotypes and breeding values in multiple pedigreed populations of sweet cherry. Mol Breeding 32, 875–887 (2013). https://doi.org/10.1007/s11032-013-9916-y

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