Research Article: Construction and Comparative Analyses of Highly Dense Linkage Maps of Two Sweet Cherry Intra-Specific Progenies of Commercial Cultivars

Date Published: January 31, 2013

Publisher: Public Library of Science

Author(s): Carolina Klagges, José Antonio Campoy, José Quero-García, Alejandra Guzmán, Levi Mansur, Eduardo Gratacós, Herman Silva, Umesh R. Rosyara, Amy Iezzoni, Lee A. Meisel, Elisabeth Dirlewanger, Jean-Marc Lacape.


Despite the agronomical importance and high synteny with other Prunus species, breeding improvements for cherry have been slow compared to other temperate fruits, such as apple or peach. However, the recent release of the peach genome v1.0 by the International Peach Genome Initiative and the sequencing of cherry accessions to identify Single Nucleotide Polymorphisms (SNPs) provide an excellent basis for the advancement of cherry genetic and genomic studies. The availability of dense genetic linkage maps in phenotyped segregating progenies would be a valuable tool for breeders and geneticists. Using two sweet cherry (Prunus avium L.) intra-specific progenies derived from crosses between ‘Black Tartarian’ × ‘Kordia’ (BT×K) and ‘Regina’ × ‘Lapins’(R×L), high-density genetic maps of the four parental lines and the two segregating populations were constructed. For BT×K and R×L, 89 and 121 F1 plants were used for linkage mapping, respectively. A total of 5,696 SNP markers were tested in each progeny. As a result of these analyses, 723 and 687 markers were mapped into eight linkage groups (LGs) in BT×K and R×L, respectively. The resulting maps spanned 752.9 and 639.9 cM with an average distance of 1.1 and 0.9 cM between adjacent markers in BT×K and R×L, respectively. The maps displayed high synteny and co-linearity between each other, with the Prunus bin map, and with the peach genome v1.0 for all eight LGs (LG1–LG8). These maps provide a useful tool for investigating traits of interest in sweet cherry and represent a qualitative advance in the understanding of the cherry genome and its synteny with other members of the Rosaceae family.

Partial Text

All cherry species belong to the Cerasus subgenus of the Prunus genus, within the Rosaceae family. Sweet cherry (Prunus avium L.) is an economically important crop that includes cherry trees cultivated for human consumption and wild cherry trees used for their wood, also called mazzards [1]; [2]. The majority of cultivated cherry trees belongs to the diploid (2n = 2x = 16) sweet cherry and allotetraploid (2n = 4x = 32) sour cherry (P. cerasus L.) species. Sweet cherry and the tetraploid ground cherry (P. fruticosa Pall., 2n = 4x = 32) are believed to be the parental species that gave rise to sour cherry [1]; [2]; [3]; [4].

The number of heterozygous markers observed using the RosBREED cherry 6K SNP array v1 in each of the four parents (515–634, Table 2) represent 9–11% of all SNPs on the array (28–35% of 1,825 SNPs reported to be polymorphic among the 269 sweet cherry accessions evaluated by Peace et al. [23]). These results are consistent with the heterozygosity estimation of 400–700 markers for any given sweet cherry cultivar suggested by Peace et al. [23]. The majority of these heterozygous SNPs were SNPs that would more likely be heterozygous given that the MAFs for the majority of these SNPs were >0.2. Additionally, these results sustain the choice of the accessions used for the detection panel in the RosBREED cherry 6K SNP array v1 to efficiently represent cherry breeding germplasm from different origins (Table 1). The common gaps on chromosome 1 (∼21.0 Mb), chromosome 2 (∼8.5 Mb), chromosome 3 (∼12.0 Mb), chromosome 4 (∼24.5 Mb), chromosome 5 (∼7.0 Mb), chromosome 6 (∼15.0 Mb), chromosome 7 (∼5.0 Mb), and chromosome 8 (∼10.0 Mb), may represent putative centromeric regions (S. Scalabrin, personal communication) as it was already reported for peach [21]. These regions correspond to low recombination frequency as shown in Figure S1; S2.