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High-density linkage maps constructed in sweet cherry (Prunus avium L.) using cross- and self-pollination populations reveal chromosomal homozygosity in inbred families and non-syntenic regions with the peach genome

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Abstract

The landrace sweet cherry (Prunus avium L.) cultivar ‘Cristobalina’ is a useful resource for sweet cherry breeding due to several important traits, including low chilling requirement, early maturity date, and self-compatibility. In this work, three families (N = 325), derived from ‘Cristobalina’, were used to develop high-density genetic maps using the RosBREED 6K Illumina Infinium® cherry SNP array. Two of the families were derived from self-pollination, which allowed construction of the first F2 genetic maps in the species. The other map developed was from an interspecific cross of cultivars ‘Vic’ × ‘Cristobalina’. The maps developed include 511 to 816 mapped SNPs covering 622.4 to 726.0 cM. Mapped SNP marker order and position were compared to the sweet cherry and peach genome sequences, and a high degree of synteny was observed. However, inverted and small translocated regions between peach and sweet cherry genomes were observed with the most noticeable inversion at the top of LG5. The progeny resulting from self-pollination also revealed a high level of homozygosity, as large presumably homozygous regions as well as entire homozygous LGs were observed. These maps will be used for genetic analysis of relevant traits in sweet cherry breeding by QTL analysis, and self-pollination populations will be useful for investigating inbreeding depression in a naturally outbreeding species.

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Acknowledgments

This work was funded by the Spanish Government INIA research projects RTA2012-00103-00-00, RTA2015-00027-00-00, RFP2015-00015-00-00, and FEDER funds. A. Calle was funded by the Departamento de Industria e Innovación (Gobierno de Aragón) “Subvenciones destinadas a la contratación de personal investigador en formación 2015–2019.” L. Cai was supported by the USDA-NIFA-Specialty Crop Research Initiative project, RosBREED: Enabling marker-assisted breeding in Rosaceae (2009-51181-05808) and RosBREED 2: Combining disease resistance with horticultural quality in new rosaceous cultivars (2014-51181-22378). The genotyping service was carried out at CEGEN-PRB2-ISCIII; it is supported by grant PT13/0001, ISCIII-SGEFI/FEDER.

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Correspondence to Ana Wünsch.

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Communicated by E. Dirlewanger

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Genetic linkage maps will be submitted to the Genome Database for Rosaceae (www.rosaceae.org).

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Online Resource 3

Comparison of the genetic map and physical map constructed using all the SNPs placed on the linkage maps constructed. The SNPs were ordered according to their position in the peach genome v2.0.a1. (GIF 7528 kb)

High-Resolution Image (TIFF 527 kb)

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Online Resource 5

Comparison of physical positions of RosBREED cherry 6K SNP array v1 markers on the peach genome v2.0.a1 (PGv2) with the genetic maps of sweet cherry. ‘Vic’ (V), ‘Cristobalina’ (C), C × C and B × C2 (this work), ‘Black Tartarian’ (BT), ‘Kordia’ (K), ‘Lapins’ (L), and ‘Regina’ (R) (Klagges et al., 2013). (GIF 80 kb)

High-Resolution Image (EPS 189 kb)

Online Resource 6

Distribution of homozygous linkage groups (LGs) identified in self-pollinated families C × C and B × C2. (GIF 26 kb)

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Calle, A., Cai, L., Iezzoni, A. et al. High-density linkage maps constructed in sweet cherry (Prunus avium L.) using cross- and self-pollination populations reveal chromosomal homozygosity in inbred families and non-syntenic regions with the peach genome. Tree Genetics & Genomes 14, 37 (2018). https://doi.org/10.1007/s11295-018-1252-2

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