Towards a unified genetic map for diploid roses

Abstract

We have constructed the Wrst integrated consensus map (ICM) for rose, based on the information of four diploid populations and more than 1,000 initial markers. The single population maps are linked via 59 bridge markers, on average 8.4 per linkage group (LG). The integrated map comprises 597 markers, 206 of which are sequence-based, distributed over a length of 530 cM on seven LGs. By using a larger eVective population size and therefore higher marker density, the marker order in the ICM is more reliable than in the single population maps. This is supported by a more even marker distribution and a decrease in gap sizes in the consensus map as compared to the single population maps. This uniWed map establishes a standard nomenclature for rose LGs, and presents the location of important ornamental traits, such as self-incompatibility, black spot resistance (Rdr1), scent production and recurrent blooming. In total, the consensus map includes locations for 10 phenotypic single loci, QTLs for 7 diVerent traits and 51 ESTs or gene-based molecular markers. This consensus map combines for the Wrst time the information for traits with high relevance for rose variety development. It will serve as a tool for selective breeding and marker assisted selection. It will beneWt future eVorts of the rose community to sequence the whole rose genome and will be useful for synteny studies in the Rosaceae family and especially in the section Rosoideae.

New genetic maps for globe artichoke and wild cardoon and their alignment with an SSR-based consensus map

“…Such minor differences may be due to mapping imprecisions (Lombard and Delourme 2001), to differences in recombination frequencies of marker pairs in different populations (Studer et al 2010) or might be attributed to different population sizes (Spiller et al 2011). Other potential sources of variation are genotyping errors, an excess of missing values and the mapping of distorted markers (Hackett and Broadfoot 2003).…”

Genetic mapping in polyploids

“…Tetrasomic inheritance is generally assumed for Rosa hybrida (Gar et al, 2011) with the possibility of some preferential pairing (KoningBoucoiran et al, 2012) although this has never been quantified. A large number of publications have studied linkage mapping in Rosa, including an integrated map at the diploid level (Spiller et al, 2011) and maps at the tetraploid level (Gar et al, 2011;Koning-Boucoiran et al, 2012;Vukosavljev et al, 2016), but none have taken full account of its pairing behaviour. An initiative is underway to sequence the genome of the diploid species Rosa chinensis (Bendahmane et al, 2016), for which ultra-high density genetic linkage maps will likely provide useful information for connecting and orientating scaffolds (Bartholomé et al, 2015).…”

“…we missed one P2 homologue). Chromosomes were re-numbered according to the ICM numbering previously introduced (Spiller et al, 2011), through linkage with SSR markers from a previous study (Koning-Boucoiran et al, 2012). All other marker segregation types were subsequently assigned to both chromosomes and homologues based on their linkage to SxN markers (LOD > 3).…”

“…Fifty-five of the expected 56 homologues were identified, following which we assigned every other marker type to both its most probable linkage group (chromosomes, termed integrated consensus map (ICM) groups 1 to 7, c.f. Spiller et al (2011)) and homologue(s) using a linkage logarithm of odds (LOD) threshold of 3.…”

“…The final integrated map positions of 25,695 markers, using the corrections for ICM 1, 3 and 4 are provided in Table S4. The closest-linked SxN marker positions on the SNP map to a set of previously-mapped 1:1 segregating SSR and AFLP markers (Koning-Boucoiran et al, 2012) are provided in Table S5, which facilitated numbering the linkage groups according to the ICM numbering (Spiller et al, 2011 …”