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

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 (R) cherry SNP array. Two of the families were derived from self-pollination, which allowed construction of the first F-2 genetic maps in the species. The other map developed was from an interspecific cross of cultivars 'Vic' x '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.