Molecular investigation of the progenitors, origin, and domestication patterns of diploid Chinese old garden roses.

Background and aims: Chinese old garden roses are major contributors in the genetic development of modern roses. The RoKSN gene is associated with continuous flowering in roses and is proposed to have originated from Chinese wild roses. However, the wild roses that are implicated in the breeding of Chinese old garden roses and the origin of the RoKSN locus remain unidentified. We collected 25 of the most renowned and classic diploid Chinese old garden roses along with all related wild roses from East Asia. These roses were analyzed with the aim of identifying the wild species that contributed to genetic composition of Chinese old garden roses. In addition, we aimed to infer the geographical origin of the RoKSN gene and to develop a schematic overview of hybrid domestication of Chinese old garden roses.

Methods: We compared the haplotypes of internal transcribed spacers (nrITS), six nuclear single-copy genes, and three chloroplast genes between Chinese old garden roses and wild roses. Additionally, we assessed genetic organization using 21 Expressed Sequence Tag-Simple Sequence Repeats to identify potential donor species that contributed to the emergence of these cultivars. Primers were designed for RoKSN to allow comparison of the gene across the entire distribution range of Rosa sect. Chinenses.

Key results: Our findings confirmed that the majority of rose cultivars are descendants of early hybridization events. Rosa chinensis var. spontanea, R. odorata var. gigantea, and R. multiflora var. cathayensis were the primary donors for the 25 cultivar roses. Chinese old garden roses were categorized into four groups. Ten cultivars were hybrids between R. chinensis var. spontanea and R. multiflora var. cathayensis, thereby forming the 'Old Blush' group. Five cultivars were hybrids between 'Old Blush' and R. kwangtungensis species complex, thereby forming the 'Slater's crimson' group. Six cultivars were hybrids between 'Old Blush' and R. odorata var. gigantea, thereby forming the 'Tea Rose' group, and three cultivars were hybrids that evolved from more than three donors. Moreover, we observed relatively close genetic proximity among Chinese old garden roses with an identical RoKSN-copia gene that is responsible for continuous flowering which indicates a single origin for this retrotransposon-containing allele. Additionally, we determined that the haplotypes of the RoKSN-copia gene predominantly occurred in the Sichuan Basin region. In contrast, R. chinensis cultivated in the Ya'an region showed no markers of hybridization and displayed a genetic composition that was close to that of the wild species R. chinensis var. spontanea. This cultivar may represent the earliest mutated individual that bears the RoKSN-copia gene and may have served as a bridge from wild species to continuous flowering old rose cultivars.

Conclusions: The study provides crucial evidence that elucidates the origin of cultivated roses and lays the groundwork for further analysis of the breeding history of Chinese old garden roses using genomic data.