Genetic analysis of the flowering date and number of petals in rose

Roman, Hanaé; Rapicault, M.; Miclot, Anne-Sophie; Larenaudie, Magali; Kawamura, Kôji; Thouroude, Tatiana; Chastellier, Annie; Lemarquand, Arnaud; Dupuis, Fabrice; Foucher, Fabrice; Loustau, Sébastien; Oyant, Laurence Hibrand‐Saint

doi:10.1007/s11295-015-0906-6

Cited by 32 publications

(23 citation statements)

References 54 publications

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“…All of the QTLs studied to date in rose have been mapped in biparental populations (Crespel et al, 2002; Linde et al, 2006; Spiller et al, 2011; Moghaddam et al, 2012; Roman et al, 2015) using AFLP and microsatellite markers. Tetraploid populations derived from crosses between ornamental varieties display complex patterns of inheritance that complicate not only genetic analysis but also map construction and require many more markers (Bourke et al, 2015).…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

et al. 2016

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Petal color is one of the key characteristics determining the attractiveness and therefore the commercial value of an ornamental crop. Here, we present the first genome-wide association study for the important ornamental crop rose, focusing on the anthocyanin and carotenoid contents in petals of 96 diverse tetraploid garden rose genotypes. Cultivated roses display a vast phenotypic and genetic diversity and are therefore ideal targets for association genetics. For marker analysis, we used a recently designed Axiom SNP chip comprising 68,000 SNPs with additionally 281 SSRs, 400 AFLPs and 246 markers from candidate genes. An analysis of the structure of the rose population revealed three subpopulations with most of the genetic variation between individual genotypes rather than between clusters and with a high average proportion of heterozygous loci. The mapping of markers significantly associated with anthocyanin and carotenoid content to the related Fragaria and Prunus genomes revealed clusters of associated markers indicating five genomic regions associated with the total anthocyanin content and two large clusters associated with the carotenoid content. Among the marker clusters associated with the phenotypes, we found several candidate genes with known functions in either the anthocyanin or the carotenoid biosynthesis pathways. Among others, we identified a glutathione-S-transferase, 4CL, an auxin response factor and F3'H as candidate genes affecting anthocyanin concentration, and CCD4 and Zeaxanthine epoxidase as candidates affecting the concentration of carotenoids. These markers are starting points for future validation experiments in independent populations as well as for functional genomic studies to identify the causal factors for the observed color phenotypes. Furthermore, validated markers may be interesting tools for marker-assisted selection in commercial breeding programmes in that they provide the tools to identify superior parental combinations that combine several associated markers in higher dosages.

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Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

et al. 2016

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“…It was previously shown that the genetic basis of the double flower trait in rose is complex, with a dominant gene ( DOUBLE FLOWER ) controlling simple versus double flower phenotypes and two QTLs controlling the number of petals on double flowers [33]. Here, we combined the genome sequence with segregation data of four different F1 progenies to confine the putative location of the DOUBLE FLOWER locus (Supplementary Table 6) to a region of 293 kbp (between position 33.24 Mbp and 33.53 Mbp, Figure 4a).…”

Section: Resultsmentioning

confidence: 99%

A high-quality sequence ofRosa chinensisto elucidate genome structure and ornamental traits

Hibrand

Ruttink

Hamama

et al. 2018

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Rose is the world’s most important ornamental plant with economic, cultural and symbolic value. Roses are cultivated worldwide and sold as garden roses, cut flowers and potted plants. Rose has a complex genome with high heterozygosity and various ploidy levels. Our objectives were (i) to develop the first high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short read sequencing, and anchoring to a high-density genetic map and (ii) to study the genome structure and the genetic basis of major ornamental traits.We produced a haploid rose line from R. chinensis ‘Old Blush’ and generated the first rose genome sequence at the pseudo-molecule scale (512 Mbp with N50 of 3.4 Mb and L75 of 97). The sequence was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features including the pericentromeric regions through annotation of TE families and positioned centromeric repeats using FISH. Genetic diversity was analysed by resequencing eight Rosa species. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and number of flower petals. A rose APETALA2 homologue is proposed to be the major regulator of petals number in rose. This reference sequence is an important resource for studying polyploidisation, meiosis and developmental processes as we demonstrated for flower and prickle development. This reference sequence will also accelerate breeding through the development of molecular markers linked to traits, the identification of the genes underlying them and the exploitation of synteny across Rosaceae.

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“…Genotyping analysis revealed a complex allele–dosage effect on average petal number in homozygous ΔCter ( Di2/Di2 ) individuals of the WP 2 progeny. Additional modulating factor(s) could be at work in determining petal number in these individuals, in agreement with what has been described in rose, where a major QTL associated with flower traits was mapped in proximity of Blfo (Hibrand‐Saint Oyant et al ., ; Roman et al ., ). Environmental factors are likely to play an important role as well, and it was recently reported that in double‐flower R. chinensis , RcAP2 (an AP2 type, identical to Rc_XP_024182693 in Figure ) is involved in the conversion of stamens into petals in response to temperature (Han et al ., ).…”

Section: Discussionmentioning

confidence: 97%

Deletion of the miR172 target site in a TOE‐type gene is a strong candidate variant for dominant double‐flower trait in Rosaceae

et al. 2018

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Double flowers with supernumerary petals have been selected by humans for their attractive appearance and commercial value in several ornamental plants, including Prunus persica (peach), a recognized model for Rosaceae genetics and genomics. Despite the relevance of this trait, knowledge of the underlying genes is limited. Of two distinct loci controlling the double-flower phenotype in peach, we focused on the dominant Di2 locus. High-resolution linkage mapping in five segregating progenies delimited Di2 to an interval spanning 150 858 bp and 22 genes, including Prupe.6G242400 encoding an euAP2 transcription factor. Analyzing genomic resequencing data from single- and double-flower accessions, we identified a deletion spanning the binding site for miR172 in Prupe.6G242400 as a candidate variant for the double-flower trait, and we showed transcript expression for both wild-type and deleted alleles. Consistent with the proposed role in controlling petal number, Prupe.6G242400 is expressed in buds at critical times for floral development. The indelDi2 molecular marker designed on this sequence variant co-segregated with the phenotype in 621 progenies, accounting for the dominant inheritance of the Di2 locus. Further corroborating the results in peach, we identified a distinct but similar mutation in the ortholog of Prupe.6G242400 in double-flower roses. Phylogenetic analysis showed that these two genes belong to a TARGET OF EAT (TOE)-type clade not represented in Arabidopsis, indicating a divergence of gene functions between AP2-type and TOE-type factors in Arabidopsis and other species. The identification of orthologous candidate genes for the double-flower phenotype in two important Rosaceae species provides valuable information to understand the genetic control of this trait in other major ornamental plants.

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Genetic analysis of the flowering date and number of petals in rose

Cited by 32 publications

References 54 publications

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

Genome-Wide Association Analysis of the Anthocyanin and Carotenoid Contents of Rose Petals

A high-quality sequence ofRosa chinensisto elucidate genome structure and ornamental traits

Deletion of the miR172 target site in a TOE‐type gene is a strong candidate variant for dominant double‐flower trait in Rosaceae

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