Determining the genetic basis of hip set in diploid roses

Roses ( Rosa spp.) are globally valued for the ornamental, medicinal, culinary, and cosmetic applications of the flowers and hips. Rose hips hold significant economic value; however, the genetic basis of the rose hip set remains unexplored. This research sought to identify quantitative trait loci (QTLs) related to hip set and characterize hip set alleles using two multi-parental diploid rose populations evaluated over multiple years. Pedigree-based quantitative trait locus (QTL) mapping for rose hips has identified a significant QTL on linkage group (LG) 3, spanning from 23.0 to 34.0 Mbp on the Rosa chinensis genome. This QTL was consistently detected in both populations and various environments, accounting for 18–56 % of phenotypic variation. Additional QTLs with minor effects were detected across all linkage groups except for LG4. Single nucleotide polymorphism (SNP) haplotypes linked to higher or lower hip production were identified, with ‘Old Blush’ and the pollen parent of J14–3 (Texas A&M breeding line) being the sources of Q - and q -alleles, respectively. These findings contribute to a deeper understanding of genetic regulation in rose hip set. Additional research is needed to validate these findings. This study lays a foundation for developing tools to enhance rose hip production. It also has broader implications for other Rosaceae crops like blackberries, raspberries, and strawberries, where high fruit set is vital for yield. Validating these markers could improve breeding efficiency across important crops. • First QTL mapping study on hip set in roses using large multi-parental populations. • A major QTL for hip set was detected on LG3, stable across years and populations. • QTL on LG3 explains up to 56 % of the phenotypic variance in hip set. • SNP haplotypes associated with high hip set are traced to ‘Old Blush’ and the pollen parent of J14–3. • Study enables marker-assisted selection to breed roses with improved hip yield.