High-density SNP-based genetic maps for the parents of an outcrossed and a selfed tetraploid garden rose cross, inferred from admixed progeny using the 68k rose SNP array.
Dense genetic maps create a base for QTL analysis of important traits and future implementation of marker-assisted breeding. In tetraploid rose, the existing linkage maps include <300 markers to cover 28 linkage groups (4 homologous sets of 7 chromosomes). Here we used the 68k WagRhSNP Axiom single-nucleotide polymorphism (SNP) array for rose, in combination with SNP dosage calling at the tetraploid level, to genotype offspring from the garden rose cultivar 'Red New Dawn'. The offspring proved to be not from a single bi-parental cross. In rose breeding, crosses with unintended parents occur regularly. We developed a strategy to separate progeny into putative populations, even while one of the parents was unknown, using principle component analysis on pairwise genetic distances based on sets of selected SNP markers that were homozygous, and therefore uninformative for one parent. One of the inferred populations was consistent with self-fertilization of 'Red New Dawn'. Subsequently, linkage maps were generated for a bi-parental and a self-pollinated population with 'Red New Dawn' as the common maternal parent. The densest map, for the selfed parent, had 1929 SNP markers on 25 linkage groups, covering 1765.5 cM at an average marker distance of 0.9 cM. Synteny with the strawberry (Fragaria vesca) genome was extensive. Rose ICM1 corresponded toF. vescapseudochromosome 7 (Fv7), ICM4 to Fv4, ICM5 to Fv3, ICM6 to Fv2 and ICM7 to Fv5. Rose ICM2 corresponded to parts ofF. vescapseudochromosomes 1 and 6, whereas ICM3 is syntenic to the remainder of Fv6.
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Mirjana
M
Vukosavljev
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Paul
P
Arens
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Roeland E
RE
Voorrips
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Wendy Pc
WP
van 't Westende
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
G D
GD
Esselink
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Peter M
PM
Bourke
Roath BV , Eindhoven, The Netherlands.
Peter
P
Cox
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
W Eric
WE
van de Weg
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Richard Gf
RG
Visser
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Chris
C
Maliepaard
Wageningen UR Plant Breeding, Wageningen University & Research , NL-6700 AJ Wageningen, The Netherlands.
Marinus Jm
0000-0002-8549-6046
MJ
Smulders