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

Beyond bloom: validated marker-trait discovery for polyploid roses via GWAS

Introduction

Breeding roses with ideal ornamental characteristics such as beautiful flowers, a pleasant fragrance, and attractive growth habits is complex and time-consuming. This process can be improved and accelerated through the use of molecular markers.

Methods

We conducted a genome-wide association study on nine ornamental traits in roses using the RhWagSNP chip across a panel of 285 cultivars and varieties. Significant marker-trait associations found for major quantitative trait loci were further validated using single-marker analyses with PACE technology in independent panels of up to 182 genotypes.

Results

For six traits- 'Young shoot: intensity of anthocyanin coloration', 'Stem: number of prickles', 'Leaf: glossiness of upper side', 'Flower: number of petals', 'Flower: fragrance', and 'Petal: length'-we identified and validated marker-trait associations for major QTLs. Conversely, we were unable to validate associations for 'Leaf: anthocyanin coloration' and 'Leaf: intensity of green color on the upper side', and found no significant associations in the GWAS for 'Leaf: size'. Loci that affect petal size, petal number and fragrance have been previously studied. We were able to detect associated markers with increased effect sizes for all three traits. Even greater effects were observed when we combined markers from independent loci for petal number and fragrance.

Discussion

Associated markers for some of the analysed traits largely colocalise with markers previously identified in QTL analyses of biparental populations. Our validation strategy using PACE as an alternative marker technology in independent panels and different environments supports the robustness of our data, irrespective of our limited panel sizes. For the six traits for which we could validate marker-trait associations, our data can be interpreted cautiously as indicating high complexity of inheritance, with few large-effect QTLs influencing the traits. For the other four traits, either greater genetic complexity and/or stronger environmental effects may have confounded our analyses. We believe that the markers presented here can serve as valuable tools for marker-assisted selection and for further genetic analysis of the traits we have analysed.

Development of a robust SNP marker set for genotyping diverse gene bank collections of polyploid roses

BACKGROUND

Due to genetic depletion in nature, gene banks play a critical role in the long-term conservation of plant genetic resources and the provision of a wide range of plant genetic diversity for research and breeding programs. Genetic information on accessions facilitates gene bank management and can help to conserve limited resources and to identify taxonomic misclassifications or mislabelling. Here, we developed SNP markers for genotyping 4,187 mostly polyploid rose accessions from large rose collections, including the German Genebank for Roses.

RESULTS

We filtered SNP marker information from the RhWag68k Axiom SNP array using call rates, uniformity of the four allelic dosage groups and chromosomal position to improve genotyping efficiency. After conversion to individual PACE® markers and further filtering, we selected markers with high discriminatory power. These markers were used to analyse 4,187 accessions with a mean call rate of 91.4%. By combining two evaluation methods, the mean call rate was increased to 95.2%. Additionally, the robustness against the genotypic groups used for calling was evaluated, resulting in a final set of 18 markers. Analyses of 94 pairs of assumed duplicate accessions included as controls revealed unexpected differences for eight pairs, which were confirmed using SSR markers. After removing the duplicates and filtering for accessions that were robustly called with all 18 markers, 141 out of the 1,957 accessions showed unexpected identical marker profiles with at least one other accession in our PACE® and SSR analysis. Given the attractiveness of NGS technologies, 13 SNPs from the marker set were also analysed using amplicon sequencing, with 76% agreement observed between PACE® and amplicon markers.

CONCLUSIONS

Although sampling error cannot be completely excluded, this is an indication that mislabelling occurs in rose collections and that molecular markers may be able to detect these cases. In future applications, our marker set could be used to develop a core reference set of representative accessions, and thus optimise the selection of gene bank accessions.

Genome-wide association study (GWAS) analyses of early anatomical changes in rose adventitious root formation

Adventitious root (AR) formation is a genetically complex trait with high genotypic variability. Therefore, only a limited range of cultivars are currently propagated by cuttings in rose. In this study, we analysed the anatomy of in vitro shoots, the early formation of root primordia (RP) and the formation of ARs in a diverse set of 106 rose genotypes. Correlation analysis indicated that the growth in shoot diameter and the vasculature dimensions after 1 week of rooting contributed to successful AR formation. Using phenotypic data for genome-wide association studies (GWAS) analyses, nine significantly associated single nucleotide polymorphisms (SNPs) and genomic regions contributing to various RP and AR formation traits were identified. The contribution of genomic regions to trait variation was notably greater for traits associated with earlier processes than for traits associated with later developmental stages. The combination of RP and AR data allowed the detection of regions by GWAS that contain factors that potentially limit RP emergence. Homologues of 47 genes known to be involved in AR formation from the literature could be assigned to the identified peaks. Further studies are needed to investigate the suitability of SNPs exhibiting strong effects as allele-specific PCR markers for use in breeding.

Backcrossing Modulates the Metabolic Profiles of Anthocyanin-Pigmented 'Vitamaize' Lines Derived from Elite Maize Lines

Vitamaize lines (VMLs) were created by backcrossing the pigmented aleurone trait into Centro Internacional de Mejoramiento de Maíz y Trigo (CIMMYT) maize lines (CMLs). This study evaluates metabolic differences between the VMLs and their original CMLs. Direct infusion mass spectrometry (DIMS) analyses, carotenoid profiling, total anthocyanins content (TAC) determination, and biochemical evaluation of the quality protein maize (QPM) endosperm trait allowed a comprehensive chemical characterization of the maize lines. DIMS data indicate higher hexoses and trigonelline content for most VMLs; the carotenoid profile revealed a decrease in β-cryptoxanthin to less than half of the original parent content for two VMLs but an augmentation for one VML. The pigmented aleurone VMLs did not inherit the complex QPM endosperm trait of the QPM CMLs. Except for anthocyanin accumulation, no other metabolites were consistently modified across all the backcross-generated maize lines with a pigmented aleurone trait. These findings suggest using genetic or metabolic markers rather than morphological or visual traits for future breeding programs.

Pigment Diversity in Leaves of Caladium × hortulanum Birdsey and Transcriptomic and Metabolic Comparisons between Red and White Leaves

Leaf color is a key ornamental characteristic of cultivated caladium (Caladium × hortulanum Birdsey), a plant with diverse leaf colors. However, the genetic improvement of leaf color in cultivated caladium is hindered by the limited understanding of leaf color diversity and regulation. In this study, the chlorophyll and anthocyanin content of 137 germplasm resources were measured to explore the diversity and mechanism of leaf color formation in cultivated caladium. Association analysis of EST-SSR markers and pigment traits was performed, as well as metabolomics and transcriptomics analysis of a red leaf variety and its white leaf mutant. We found significant differences in chlorophyll and anthocyanin content among different color groups of cultivated caladium, and identified three, eight, three, and seven EST-SSR loci significantly associated with chlorophyll-a, chlorophyll-b, total chlorophyll and total anthocyanins content, respectively. The results further revealed that the white leaf mutation was caused by the down-regulation of various anthocyanins (such as cyanidin-3-O-rutinoside, quercetin-3-O-glucoside, and others). This change in concentration is likely due to the down-regulation of key genes (four PAL, four CHS, six CHI, eight F3H, one F3'H, one FLS, one LAR, four DFR, one ANS and two UFGT) involved in anthocyanin biosynthesis. Concurrently, the up-regulation of certain genes (one FLS and one LAR) that divert the anthocyanin precursors to other pathways was noted. Additionally, a significant change in the expression of numerous transcription factors (12 NAC, 12 bZIP, 23 ERF, 23 bHLH, 19 MYB_related, etc.) was observed. These results revealed the genetic and metabolic basis of leaf color diversity and change in cultivated caladium, and provided valuable information for molecular marker-assisted selection and breeding of leaf color in this ornamental plant.

Robust markers associated with floral traits in roses are suitable for marker-assisted selection across gene pools

We investigated the potential of markers associated with floral traits for parental selection in a cut rose breeding program. We analysed six Kompetitive Allele Specific PCR (KASP) markers for three important floral traits, petal length, petal number and scent, derived from experiments in a garden rose population. The six markers were applied to genotype a collection of 384 parental genotypes used for commercial cut rose breeding. We phenotyped a selection of progeny derived from pairs of parents having either high or low dosages of (contrasting) marker alleles associated with these traits. Significant differences were found between the contrasting progeny groups for each of the traits, although parents with the optimal allele dosage combinations could not always be used for the crosses. This not only supports the robustness of these marker‒trait associations but also demonstrates their potential for commercial rose breeding. It also demonstrates the use of marker information generated in garden rose populations for cut rose breeding.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-023-01438-5.

GWAS of adventitious root formation in roses identifies a putative phosphoinositide phosphatase (SAC9) for marker-assisted selection

Rose propagation by cuttings is limited by substantial genotypic differences in adventitious root formation. To identify possible genetic factors causing these differences and to develop a marker for marker-assisted selection for high rooting ability, we phenotyped 95 cut and 95 garden rose genotypes in a hydroponic rooting system over 6 weeks. Data on rooting percentage after 3 to 6 weeks, root number, and root fresh mass were highly variable among genotypes and used in association mappings performed on genotypic information from the WagRhSNP 68 K Axiom SNP array for roses. GWAS analyses revealed only one significantly associated SNP for rooting percentage after 3 weeks. Nevertheless, prominent genomic regions/peaks were observed and further analysed for rooting percentage after 6 weeks, root number and root fresh mass. Some of the SNPs in these peak regions were associated with large effects on adventitious root formation traits. Very prominent were ten SNPs, which were all located in a putative phosphoinositide phosphatase SAC9 on chromosome 2 and showed very high effects on rooting percentage after 6 weeks of more than 40% difference between nulliplex and quadruplex genotypes. SAC9 was reported to be involved in the regulation of endocytosis and in combination with other members of the SAC gene family to regulate the translocation of auxin-efflux PIN proteins via the dephosphorylation of phosphoinositides. For one SNP within SAC9, a KASP marker was successfully derived and used to select genotypes with a homozygous allele configuration. Phenotyping these homozygous genotypes for adventitious root formation verified the SNP allele dosage effect on rooting. Hence, the presented KASP derived from a SNP located in SAC9 can be used for marker-assisted selection in breeding programs for high rooting ability in the future.

Potential regulatory genes of light induced anthocyanin accumulation in sweet cherry identified by combining transcriptome and metabolome analysis

Anthocyanins exist widely in various plant tissues and organs, and they play an important role in plant reproduction, disease resistance, stress resistance, and protection of human vision. Most fruit anthocyanins can be induced to accumulate by light. Here, we shaded the "Hong Deng" sweet cherry and performed an integrated analysis of its transcriptome and metabolome to explore the role of light in anthocyanin accumulation. The total anthocyanin content of the fruit and two of its anthocyanin components were significantly reduced after the shading. Transcriptome and metabolomics analysis revealed that PAL, 4CL, HCT, ANS and other structural genes of the anthocyanin pathway and cyanidin 3-O-glucoside, cyanidin 3-O-rutinoside, and other metabolites were significantly affected by shading. Weighted total gene network analysis and correlation analysis showed that the upstream and middle structural genes 4CL2, 4CL3, and HCT2 of anthocyanin biosynthesis may be the key genes affecting the anthocyanin content variations in fruits after light shading. Their expression levels may be regulated by transcription factors such as LBD, ERF4, NAC2, NAC3, FKF1, LHY, RVE1, and RVE2. This study revealed for the first time the possible role of LBD, FKF1, and other transcription factors in the light-induced anthocyanin accumulation of sweet cherry, thereby laying a preliminary foundation for further research on the role of light in anthocyanin accumulation of deep red fruit varieties and the genetic breeding of sweet cherry.

Pedigree-based QTL analysis of flower size traits in two multi-parental diploid rose populations

Rose (Rosa spp.) is one of the most economically important ornamental species worldwide. Flower diameter, flower weight, and the number of petals and petaloids are key flower-size parameters and attractive targets for DNA-informed breeding. Pedigree-based analysis (PBA) using FlexQTL software was conducted using two sets of multi-parental diploid rose populations. Phenotypic data for flower diameter (Diam), flower weight (fresh (FWT)/dry (DWT)), number of petals (NP), and number of petaloids (PD) were collected over six environments (seasons) at two locations in Texas. The objectives of this study were to 1) identify new and/or validate previously reported QTL(s); 2) identify SNP haplotypes associated with QTL alleles (Q-/q-) of a trait and their sources; and 3) determine QTL genotypes for important rose breeding parents. Several new and previously reported QTLs for NP and Diam traits were identified. In addition, QTLs associated with flower weight and PD were identified for the first time. Two major QTLs with large effects were mapped for all traits. The first QTL was at the distal end of LG1 (60.44-60.95 Mbp) and was associated with Diam and DWT in the TX2WOB populations. The second QTL was consistently mapped in the middle region on LG3 (30.15-39.34 Mbp) and associated with NP, PD, and flower weight across two multi-parent populations (TX2WOB and TX2WSE). Haplotype results revealed a series of QTL alleles with differing effects at important loci for most traits. This work is distinct from previous studies by conducting co-factor analysis to account for the DOUBLE FLOWER locus while mapping QTL for NP. Sources of high-value (Q) alleles were identified, namely, 'Old Blush' and Rosa wichuraiana from J14-3 for Diam, while 'Violette' and PP-J14-3 were sources for other traits. In addition, the source of the low-value (q) alleles for Diam was 'Little Chief', and Rosa wichuraiana through J14-3 was the source for the remaining traits. Hence, our results can potentially inform parental/seedling selections as means to improve ornamental quality in roses and a step towards implementing DNA-informed techniques for use in rose breeding programs.

Genome-Wide Association Study of Phenolic Content and Antioxidant Properties in Eggplant Germplasm

The phenolic compounds in eggplant offer potential natural antioxidants for improved health. A large number of samples were examined in order to find eggplant germplasm with a high potential for health promotion. A genome-wide association study (GWAS) was conducted to identify single nucleotide polymorphisms (SNPs) associated with variations in total phenolic content (TPC) and antioxidant activity in eggplants, including ABTS (2,2'-azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)) scavenging activity and ferric reducing antioxidant power (FRAP). TPC values varied from 14.19 to 842.90 mg gallic acid equivalent (GAE)/100 g of dry weight of eggplant fruit powder. TPC showed a strong positive correlation with both FRAP and ABTS (r = 0.89 *** and 0.77 ***, respectively). The GWAS identified 20 SNPs that were significantly associated out of 29,183 SNPs. Out of the 20 significant SNPs, 11 showed associations with TPC, 4 with ABTS activity, and 5 with FRAP. Among the SNPs associated with TPC, one SNP was found on each of Chromosomes 3, 4, 7, and 12. In contrast, Chromosome 5 comprised two SNPs associated to TPC. Furthermore, the gene encoding IRX12 laccase-4 on Chromosome 10 was found to contain five SNPs associated with TPC. Four significantly linked SNPs on Chromosomes 1 (1 SNP), 4 (2 SNPs), and 10 (1 SNP) were found to be related to ABTS activity. The identified SNPs will be further examined as markers for selecting desirable eggplant varieties and exploring the links between candidate genes, phenolic content, and antioxidant activity. The findings of this study could assist in further study and the development of eggplants with improved health advantages through targeted breeding.

Genome-Wide association analysis of phenotypic traits in Bambara groundnut under drought-stressed and non-stressed conditions based on DArTseq SNP

INTRODUCTION

Bambara groundnut (BG) (Vigna subterranea [L.] Verdc) is an indigenous, resilient, but underutilized leguminous crop that occurs mostly as genetically heterogeneous landraces with limited information on the drought tolerant attributes. This study elucidates the associations between sequencing-based diversity array technology (DArTseq) and phenotypic character as well as differing indices related to drought tolerance in one hundred accessions of Bambara groundnut.

METHODS

The field experiments were conducted at IITA research stations in Kano and Ibadan between 2016 and 2018 planting seasons. The experiments were arranged in randomised complete block design with three replications, under the different water regimes. The phenotypic traits evaluated was further to construct the dendrogram. Genome-wide association mapping was conducted based on 5927 DArTs loci with < 20% missing data.

RESULTS AND DISCUSSIONS

The genome wide association study predicted drought tolerance in Bambara accessions for geometric mean productivity (GMP) and stress tolerance index (STI). TVSu-423 had the highest GMP and STI values (28.50, 2.40), while TVSu-2017 had the lowest at GMP (1.74) and STI (0.01) respectively. The relative water content (%) was significantly higher for accessions; TVSu-266 (60.35, 61.49), TVSu-2 (58.29, 53.94), and TVSu-411 (55.17, 58.92) in 2016/2017 and 2017/2018, respectively. The phenotypic characters studied delineated the accessions into two major clusters and five distinct sub-clusters, indicating variations across all the geographical locations. The 5,927 DArTseq genomic markers in association with STI further grouped the 100 accessions into two main clusters. TVSu-1897 from Botswana (Southern Africa) was in the first cluster, while the remaining 99 accessions from Western, Central, and Eastern Africa made up the second cluster. The eight significant Quantitative Trait Loci (QTLs) (24346377|F|0-22:A>G-22:A>G, 24384105|F|0-56:A>G33 :A> G, 24385643|F|0-53:G>C-53:G>C, 24385696|F|0-43:A>G-43:A>G, 4177257|F|0-44:A>T-44:A>T, 4182070|F|0-66:G>A-66:G>A, 4183483|F|0-24:G>A-24:G>A, 4183904|F|0-11:C>T-11:C>T) identified with Bonferroni threshold was in association with STI, indicative of variations under the drought-stressed condition. The observation of consistent SNPs in the 2016 and 2017 planting seasons, as well as in combination with the 2016 and 2017 planting seasons, led to the designation of these QTLs as significant. The drought selected accessions could form basis for hybridization breeding. The identified quantitative trait loci could be useful in marker-assisted selection in drought molecular breeding programs.

Diversity, classification, and EST-SSR-based association analysis of caladium ornamental traits

Caladium (Caladium × Hortulanum Birdsey) is a popular ornamental plant with a wide range of vibrant leaf color among Araceae. Even after years of breeding, creating new caladium leaf color variations is extremely difficult. Molecular marker-assisted selection is an effective approach for accelerating breeding, but few studies on the molecular markers associated with caladium traits have been performed. In the current study, 144 caladium accessions were used to examine 12 phenotypic characteristics. The coefficient of variation for four numerical characters ranged from 23.94% to 43.22%, and the Shannon-Wiener indexes for eight descriptive characters ranged from 0.13 to 1.52. Based on L*, a*, b*, C, h^° values determined by a colorimeter and hierarchical cluster analysis, the leaf color can be divided into four groups: pale green, green, light pink, and red. Furthermore, 7708 new SSR loci were identified by transcriptome sequencing, and 26 SSR markers with high polymorphism and reproducibility were screened. Genetic structure, NJ clustering, and PCoA analysis revealed that 144 accessions could be divided into three clusters, with genetic structure being closely related to germplasm origin. An association analysis revealed that the SSR markers 2, 1, 1, 1, 1, and 1 were mainly associated with petiole color, main vein color, blade upperside glossiness, and C, b*, and L* of leaf color (p < 0.01). These findings will serve as a valuable reference for evaluating germplasm resources and caladium molecular marker-assisted breeding.

Genome-wide association study of traits in sacred lotus uncovers MITE-associated variants underlying stamen petaloid and petal number variations

Understanding the genetic variants responsible for floral trait diversity is important for the molecular breeding of ornamental flowers. Widely used in water gardening for thousands of years, the sacred lotus exhibits a wide range of diversity in floral organs. Nevertheless, the genetic variations underlying various morphological characteristics in lotus remain largely unclear. Here, we performed a genome-wide association study of sacred lotus for 12 well-recorded ornamental traits. Given a moderate linkage disequilibrium level of 32.9 kb, we successfully identified 149 candidate genes responsible for seven flower traits and plant size variations, including many pleiotropic genes affecting multiple floral-organ-related traits, such as NnKUP2. Notably, we found a 2.75-kb presence-and-absence genomic fragment significantly associated with stamen petaloid and petal number variations, which was further confirmed by re-examining another independent population dataset with petal number records. Intriguingly, this fragment carries MITE transposons bound by siRNAs and is related to the expression differentiation of a nearby candidate gene between few-petalled and double-petalled lotuses. Overall, these genetic variations and candidate genes responsible for diverse lotus traits revealed by our GWAS highlight the role of transposon variations, particularly MITEs, in shaping floral trait diversity.

High-density genetic map and genome-wide association studies of aesthetic traits in Phalaenopsis orchids

Phalaenopsis spp. represent the most popular orchids worldwide. Both P. equestris and P. aphrodite are the two important breeding parents with the whole genome sequence available. However, marker–trait association is rarely used for floral traits in Phalaenopsis breeding. Here, we analyzed markers associated with aesthetic traits of Phalaenopsis orchids by using genome-wide association study (GWAS) with the F1 population P. Intermedia of 117 progenies derived from the cross between P. aphrodite and P. equestris. A total of 113,517 single nucleotide polymorphisms (SNPs) were identified in P. Intermedia by using genotyping-by-sequencing with the combination of two different restriction enzyme pairs, Hinp1 I/Hae III and Apek I/Hae III. The size-related traits from flowers were negatively related to the color-related traits. The 1191 SNPs from Hinp1 I/ Hae III and 23 simple sequence repeats were used to establish a high-density genetic map of 19 homolog groups for P. equestris. In addition, 10 quantitative trait loci were highly associated with four color-related traits on chromosomes 2, 5 and 9. According to the sequence within the linkage disequilibrium regions, 35 candidate genes were identified and related to anthocyanin biosynthesis. In conclusion, we performed marker-assisted gene identification of aesthetic traits with GWAS in Phalaenopsis orchids.

Identification of Chilling Accumulation-Associated Genes for Litchi Flowering by Transcriptome-Based Genome-Wide Association Studies

Litchi is an important Sapindaceae fruit tree. Flowering in litchi is triggered by low temperatures in autumn and winter. It can be divided into early-, medium-, and late-flowering phenotypes according to the time for floral induction. Early-flowering varieties need low chilling accumulation level for floral induction, whereas the late-flowering varieties require high chilling accumulation level. In the present study, RNA-Seq of 87 accessions was performed and transcriptome-based genome-wide association studies (GWAS) was used to identify candidate genes involved in chilling accumulation underlying the time for floral induction. A total of 98,155 high-quality single-nucleotide polymorphism (SNP) sites were obtained. A total of 1,411 significantly associated SNPs and 1,115 associated genes (AGs) were identified, of which 31 were flowering-related, 23 were hormone synthesis-related, and 27 were hormone signal transduction-related. Association analysis between the gene expression of the AGs and the flowering phenotypic data was carried out, and differentially expressed genes (DEGs) in a temperature-controlled experiment were obtained. As a result, 15 flowering-related candidate AGs (CAGs), 13 hormone synthesis-related CAGs, and 11 hormone signal transduction-related CAGs were further screened. The expression levels of the CAGs in the early-flowering accessions were different from those in the late-flowering ones, and also between the flowering trees and non-flowering trees. In a gradient chilling treatment, flowering rates of the trees and the CAGs expression were affected by the treatment. Our present work for the first time provided candidate genes for genetic regulation of flowering in litchi using transcriptome-based GWAS.

Morphological studies of rose prickles provide new insights

Prickles are common structures in plants that play a key role in defense against herbivores. In the Rosa genus, prickles are widely present with great diversity in terms of form and density. For cut rose production, prickles represent an important issue, as they can damage the flower and injure workers. Our objectives were to precisely describe the types of prickles that exist in roses, their tissues of origin and their development. We performed a detailed histological analysis of prickle initiation and development in a rose F1 population. Based on the prickle investigation of 110 roses, we proposed the first categorization of prickles in the Rosa genus. They are mainly divided into two categories, nonglandular prickles (NGPs) and glandular prickles (GPs), and subcategories were defined based on the presence/absence of hairs and branches. We demonstrated that NGPs and GPs both originate from multiple cells of the ground meristem beneath the protoderm. For GPs, the gland cells originate from the protoderm of the GP at the early developmental stage. Our findings clearly demonstrate that prickles are not modified trichomes (which originate from the protoderm). These conclusions are different from the current mainstream hypothesis. These results provide a foundation for further studies on prickle initiation and development in plants.

Drying Operation Effects on the Pigments and Phytochemical Properties of Rose Cultivars

BACKGROUND

Roses are flowers which contain various phytochemicals and have been used for food and medicinal purposes in many countries. Materials, including flowers, are available for limited periods when plants can be cultivated.

OBJECTIVE

To evaluate the quality of rose petals on the basis of cultivars and drying methods, chromaticity, phytochemical contents, and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical scavenging activity.

METHOD

Petals of three rose cultivars were dried by hot air drying (HD) and freeze drying (FD). Subsequently, the chromaticity and the contents of pigment, total flavonoids, and ascorbic acid, and DPPH radical scavenging activity were analyzed.

RESULTS

The total color difference (△E)values of rose red (RR, Calypso) and rose orange (RO, Lambada) were low in FD. In contrast, in rose yellow (RY, Ileos), there was no significant difference in chromaticity regulation regardless of the drying methods. The pigment contents were generally increased by drying. The carotenoid content in the RR and anthocyanin and carotenoid contents in RO were higher in FD than in HD. The drying operations increased the flavonoid and ascorbic acid content and antioxidant activity in roses, but the difference between the drying methods was not significant. Correlation coefficient analysis revealed ascorbic acid and anthocyanin to have a high positive correlation (r = 0.843), followed by flavonoid and DPPH radical scavenging activity.

CONCLUSIONS

This study showed that the drying operations increased the flavonoid and ascorbic acid contents, and the chromaticity and pigment content of some cultivars was higher in FD.

HIGHLIGHTS

Comparison of the color change, phytochemical content, and antioxidant activity by the drying methods (FD and HD treatment) in the three rose cultivars with red, orange, and yellow petals showed the increased phytochemical contents and antioxidant activity after drying, and chromaticity and pigment content were more stable and higher in FD.

Identification and QTL Analysis of Flavonoids and Carotenoids in Tetraploid Roses Based on an Ultra-High-Density Genetic Map

Roses are highly valuable within the flower industry. The metabolites of anthocyanins, flavonols, and carotenoids in rose petals are not only responsible for the various visible petal colors but also important bioactive compounds that are important for human health. In this study, we performed a QTL analysis on pigment contents to locate major loci that determine the flower color traits. An F1 population of tetraploid roses segregating for flower color was used to construct an ultra-high-density genetic linkage map using whole-genome resequencing technology to detect genome-wide SNPs. Previously developed SSR and SNP markers were also utilized to increase the marker density. Thus, a total of 9,259 markers were mapped onto seven linkage groups (LGs). The final length of the integrated map was 1285.11 cM, with an average distance of 0.14 cM between adjacent markers. The contents of anthocyanins, flavonols and carotenoids of the population were assayed to enable QTL analysis. Across the 33 components, 46 QTLs were detected, explaining 11.85-47.72% of the phenotypic variation. The mapped QTLs were physically clustered and primarily distributed on four linkage groups, namely LG2, LG4, LG6, and LG7. These results improve the basis for flower color marker-assisted breeding of tetraploid roses and guide the development of rose products.

Detection of Reproducible Major Effect QTL for Petal Traits in Garden Roses

The detection of QTL by association genetics depends on the genetic architecture of the trait under study, the size and structure of the investigated population and the availability of phenotypic and marker data of sufficient quality and quantity. In roses, we previously demonstrated that major QTL could already be detected in small association panels. In this study, we analyzed petal number, petal size and fragrance in a small panel of 95 mostly tetraploid garden rose genotypes. After genotyping the panel with the 68 K Axiom WagRhSNP chip we detected major QTL for all three traits. Each trait was significantly influenced by several genomic regions. Some of the QTL span genomic regions that comprise several candidate genes. Selected markers from some of these regions were converted into KASP markers and were validated in independent populations of up to 282 garden rose genotypes. These markers demonstrate the robustness of the detected effects independent of the set of genotypes analyzed. Furthermore, the markers can serve as tools for marker-assisted breeding in garden roses. Over an extended timeframe, they may be used as a starting point for the isolation of the genes underlying the QTL.

Recent Large-Scale Genotyping and Phenotyping of Plant Genetic Resources of Vegetatively Propagated Crops

Several recent national and international projects have focused on large-scale genotyping of plant genetic resources in vegetatively propagated crops like fruit and berries, potatoes and woody ornamentals. The primary goal is usually to identify true-to-type plant material, detect possible synonyms, and investigate genetic diversity and relatedness among accessions. A secondary goal may be to create sustainable databases that can be utilized in research and breeding for several years ahead. Commonly applied DNA markers (like microsatellite DNA and SNPs) and next-generation sequencing each have their pros and cons for these purposes. Methods for large-scale phenotyping have lagged behind, which is unfortunate since many commercially important traits (yield, growth habit, storability, and disease resistance) are difficult to score. Nevertheless, the analysis of gene action and development of robust DNA markers depends on environmentally controlled screening of very large sets of plant material. Although more time-consuming, co-operative projects with broad-scale data collection are likely to produce more reliable results. In this review, we will describe some of the approaches taken in genotyping and/or phenotyping projects concerning a wide variety of vegetatively propagated crops.

Benefiting others and self: Production of vitamins in plants

Vitamins maintain growth and development in humans, animals, and plants. Because plants serve as essential producers of vitamins, increasing the vitamin contents in plants has become a goal of crop breeding worldwide. Here, we begin with a summary of the functions of vitamins. We then review the achievements to date in elucidating the molecular mechanisms underlying how vitamins are synthesized, transported, and regulated in plants. We also stress the exploration of variation in vitamins by the use of forward genetic approaches, such as quantitative trait locus mapping and genome-wide association studies. Overall, we conclude that exploring the diversity of vitamins could provide new insights into plant metabolism and crop breeding.

A genome-wide association study uncovers a critical role of the RsPAP2 gene in red-skinned Raphanus sativus L

Radish (Raphanus sativus L.) taproot contains high concentrations of flavonoids, including anthocyanins (ATCs), in red-skinned genotypes. However, little information on the genetic regulation of ATC biosynthesis in radish is available. A genome-wide association study of radish red skin color was conducted using whole-genome sequencing data derived from 179 radish genotypes. The R2R3-MYB transcription factor production of anthocyanin pigment 2 (PAP2) gene was found in the region associated with a leading SNP located on chromosome 2. The amino acid sequence encoded by the RsPAP2 gene was different from those of the other published RsMYB genes responsible for the red skin color of radish. The overexpression of the RsPAP2 gene resulted in ATC accumulation in Arabidopsis and radish, which was accompanied by the upregulation of several ATC-related structural genes. RsPAP2 was found to bind the RsUFGT and RsTT8 promoters, as shown by a dual-luciferase reporter system and a yeast one-hybrid assay. The promoter activities of the RsANS, RsCHI, RsPAL, and RsUFGT genes could be strongly activated by coinfiltration with RsPAP2 and RsTT8. These findings showed the effectiveness of GWAS in identifying candidate genes in radish and demonstrated that RsPAP2 could (either directly or together with its cofactor RsTT8) regulate the transcript levels of ATC-related genes to promote ATC biosynthesis, facilitating the genetic enhancement of ATC contents and other related traits in radish.

Identification of QTLs for high grain yield and component traits in new plant types of rice

A panel of 60 genotypes comprising New Plant Types (NPTs) along with indica, tropical and temperate japonica genotypes was phenotypically evaluated for four seasons in irrigated situation for grain yield per se and component traits. Twenty NPT genotypes were found promising with an average grain yield varying from 5.45 to 8.8 t/ha. A total of 85 SSR markers were used in the study to identify QTLs associated with grain yield per se and related traits. Sixty-six (77.65%) markers were found to be polymorphic. The PIC values varied from 0.516 to 0.92 with an average of 0.704. A moderate level of genetic diversity (0.39) was detected among genotypes. Variation to the tune of 8% within genotypes, 68% among the genotypes within the population and 24% among the populations were observed (AMOVA). This information may help in identification of potential parents for development of transgressive segregants with very high yield. The association analysis using GLM and MLM models led to the identification of 30 and 10 SSR markers associated with 70 and 16 QTLs, respectively. Thirty novel QTLs linked with 16 SSRs were identified to be associated with eleven traits, namely tiller number (qTL-6.1, qTL-11.1, qTL-4.1), panicle length (qPL-1.1, qPL-5.1, qPL-7.1, qPL-8.1), flag leaf length (qFLL-8.1, qFLL-9.1), flag leaf width (qFLW-6.2, qFLW-5.1, qFLW-8.1, qFLW-7.1), total no. of grains (qTG-2.2, qTG-a7.1), thousand-grain weight (qTGW-a1.1, qTGW-a9.2, qTGW-5.1, qTGW-8.1), fertile grains (qFG-7.1), seed length-breadth ratio (qSlb-3.1), plant height (qPHT-6.1, qPHT-9.1), days to 50% flowering (qFD-1.1) and grain yield per se (qYLD-5.1, qYLD-6.1a, qYLD-11.1).Some of the SSRs were co-localized with more than two traits. The highest co-localization was identified with RM5709 linked to nine traits, followed by RM297 with five traits. Similarly, RM5575, RM204, RM168, RM112, RM26499 and RM22899 were also recorded to be co-localized with more than one trait and could be rated as important for marker-assisted backcross breeding programs, for pyramiding of these QTLs for important yield traits, to produce new-generation rice for prospective increment in yield potentiality and breaking yield ceiling.

Genome-wide association studies for inflorescence type and remontancy in Hydrangea macrophylla

Inflorescence type and remontancy are two valuable traits in bigleaf hydrangea (Hydrangea macrophylla L.) and both are recessively inherited. Molecular marker-assisted selection (MAS) can greatly reduce the time necessary to breed cultivars with desired traits. In this study, a genome-wide association study (GWAS) using 5803 single-nucleotide polymorphisms (SNPs) was performed using a panel of 82 bigleaf hydrangea cultivars. One SNP locus (Hy_CAPS_Inflo) associated with inflorescence type was identified with general linear model (GLM) and mixed linear model (MLM) methods that explained 65.5% and 36.1% of the phenotypic variations, respectively. Twenty-three SNPs associated with remontancy were detected in GLM whereas no SNP was detected in MLM. The SNP locus (Hy_CAPS_Inflo) was converted to a cleaved amplified polymorphic sequence (CAPS) marker that showed absolute identification accuracy (100%) of inflorescence type in a validation panel consisting of eighteen H. macrophylla cultivars. The SNP was investigated in 341 F1 progenies using genotyping by sequencing (GBS) and co-segregated with inflorescence type (χ 2 = 0.12; P = 0.73). The SNP was subsequently used for breeding selection using kompetitive allele specific PCR (KASP) technology. Future directions for the use of genomics and MAS in hydrangea breeding improvement are discussed. The results presented in this study provide insights for further research on understanding genetic mechanisms behind inflorescence type and remontancy in H. macrophylla. The CAPS and KASP markers developed here will be immediately useful for applying MAS to accelerate breeding improvement in hydrangea.

Advancing provitamin A biofortification in sorghum: Genome-wide association studies of grain carotenoids in global germplasm

Vitamin A deficiency is one of the most prevalent nutritional deficiencies worldwide. Sorghum [Sorghum bicolor L. (Moench)] is a major cereal crop consumed by millions of people in regions with high vitamin A deficiency. We quantified carotenoid concentrations in a diverse sorghum panel using high-performance liquid chromatography and conducted a genome-wide association study (GWAS) of grain carotenoids to identify genes underlying carotenoid variation. There was moderate variation for β-carotene (00.8 μg g^-1 ), lutein (0.3-9.4 μg g^-1 ), and zeaxanthin (0.2-9.1 μg g^-1 ), but β-cryptoxanthin and α-carotene were nearly undetectable. Genotype had the largest effect size, at 81% for zeaxanthin, 62% for β-carotene, and 53% for lutein. Using multiple models, GWAS identified several significant associations between carotenoids and single nucleotide polymorphisms (SNPs), some of which colocalized with known carotenoid genes that have not been previously implicated in carotenoid variation. Several of the candidate genes identified have also been identified in maize (Zea mays L.) and Arabidopsis (Arabidopsis thaliana) carotenoid GWAS studies. Notably, an SNP inside the putative ortholog of maize zeaxanthin epoxidase (ZEP) had the most significant association with zeaxanthin and with the ratio between lutein and zeaxanthin, suggesting that ZEP is a major gene controlling sorghum carotenoid variation. Overall findings suggest there is oligogenic inheritance for sorghum carotenoids and suitable variation for marker-assisted selection. The high carotenoid germplasm and significant associations identified in this study can be used in biofortification efforts to improve the nutritional quality of sorghum.

Hybrid-Transcriptome Sequencing and Associated Metabolite Analysis Reveal Putative Genes Involved in Flower Color Difference in Rose Mutants

Gene mutation is a common phenomenon in nature that often leads to phenotype differences, such as the variations in flower color that frequently occur in roses. With the aim of revealing the genomic information and inner mechanisms, the differences in the levels of both transcription and secondary metabolism between a pair of natural rose mutants were investigated by using hybrid RNA-sequencing and metabolite analysis. Metabolite analysis showed that glycosylated derivatives of pelargonidin, e.g., pelargonidin 3,5 diglucoside and pelargonidin 3-glucoside, which were not detected in white flowers (Rosa 'Whilte Mrago Koster'), constituted the major pigments in pink flowers. Conversely, the flavonol contents of petal, such as kaempferol-3-glucoside, quercetin 3-glucoside, and rutin, were higher in white flowers. Hybrid RNA-sequencing obtained a total of 107,280 full-length transcripts in rose petal which were annotated in major databases. Differentially expressed gene (DEG) analysis showed that the expression of genes involved in the flavonoid biosynthesis pathway was significantly different, e.g., CHS, FLS, DFR, LDOX, which was verified by qRT-PCR during flowering. Additionally, two MYB transcription factors were found and named RmMYBAN2 and RmMYBPA1, and their expression patterns during flowering were also analyzed. These findings indicate that these genes may be involved in the flower color difference in the rose mutants, and competition between anthocyanin and flavonol biosynthesis is a primary cause of flower color variation, with its regulation reflected by transcriptional and secondary metabolite levels.

Changing Form and Function through Carotenoids and Synthetic Biology

The diverse structures and multifaceted roles of carotenoids make these colorful pigments attractive targets for synthetic biology.

Biosynthesis of 2-Phenylethanol in Rose Petals Is Linked to the Expression of One Allele of RhPAAS

Floral scent is one of the most important characters in horticultural plants. Roses (Rosa spp.) have been cultivated for their scent since antiquity. However, probably by selecting for cultivars with long vase life, breeders have lost the fragrant character in many modern roses, especially the ones bred for the cut flower market. The genetic inheritance of scent characters has remained elusive so far. In-depth knowledge of this quantitative trait is thus very much needed to breed more fragrant commercial cultivars. Furthermore, rose hybrids harbor a composite genomic structure, which complexifies quantitative trait studies. To understand rose scent inheritance, we characterized a segregating population from two diploid cultivars, Rosa × hybrida cv H190 and Rosa wichurana, which have contrasting scent profiles. Several quantitative trait loci for the major volatile compounds in this progeny were identified. One among these loci contributing to the production of 2-phenylethanol, responsible for the characteristic odor of rose, was found to be colocalized with a candidate gene belonging to the 2-phenylethanol biosynthesis pathway: the PHENYLACETALDEHYDE SYNTHASE gene RhPAAS An in-depth allele-specific expression analysis in the progeny demonstrated that only one allele was highly expressed and was responsible for the production of 2-phenylethanol. Unexpectedly, its expression was found to start early during flower development, before the production of the volatile 2-phenylethanol, leading to the accumulation of glycosylated compounds in petals.

In the name of the rose: a roadmap for rose research in the genome era

The recent completion of the rose genome sequence is not the end of a process, but rather a starting point that opens up a whole set of new and exciting activities. Next to a high-quality genome sequence other genomic tools have also become available for rose, including transcriptomics data, a high-density single-nucleotide polymorphism array and software to perform linkage and quantitative trait locus mapping in polyploids. Rose cultivars are highly heterogeneous and diverse. This vast diversity in cultivated roses can be explained through the genetic potential of the genus, introgressions from wild species into commercial tetraploid germplasm and the inimitable efforts of historical breeders. We can now investigate how this diversity can best be exploited and refined in future breeding work, given the rich molecular toolbox now available to the rose breeding community. This paper presents possible lines of research now that rose has entered the genomics era, and attempts to partially answer the question that arises after the completion of any draft genome sequence: 'Now that we have "the" genome, what's next?'. Having access to a genome sequence will allow both (fundamental) scientific and (applied) breeding-orientated questions to be addressed. We outline possible approaches for a number of these questions.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r ² = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.

Genome-wide association study identifies favorable SNP alleles and candidate genes for waterlogging tolerance in chrysanthemums

Chrysanthemums are sensitive to waterlogging stress, and the development of screening methods for tolerant germplasms or genes and the breeding of tolerant new varieties are of great importance in chrysanthemum breeding. To understand the genetic basis of waterlogging tolerance (WT) in chrysanthemums, we performed a genome-wide association study (GWAS) using 92,811 single nucleotide polymorphisms (SNPs) in a panel of 88 chrysanthemum accessions, including 64 spray cut and 24 disbud chrysanthemums. The results showed that the average MFVW (membership function value of waterlogging) of the disbud type (0.65) was significantly higher than that of the spray type (0.55) at P < 0.05, and the MFVW of the Asian accessions (0.65) was significantly higher than that of the European accessions (0.48) at P < 0.01. The GWAS performed using the general linear model (GLM) and mixed linear model (MLM) identified 137 and 14 SNP loci related to WT, respectively, and 11 associations were commonly predicted. By calculating the phenotypic effect values for 11 common SNP loci, six highly favorable SNP alleles that explained 12.85-21.85% of the phenotypic variations were identified. Furthermore, the dosage-pyramiding effects of the favorable alleles and the significant linear correlations between the numbers of highly favorable alleles and phenotypic values were identified (r ² = 0.45; P < 0.01). A major SNP locus (Marker6619-75) was converted into a derived cleaved amplified polymorphic sequence (dCAPS) marker that cosegregated with WT with an average efficiency of 78.9%. Finally, four putative candidate genes in the WT were identified via quantitative real-time PCR (qRT-PCR). The results presented in this study provide insights for further research on WT mechanisms and the application of molecular marker-assisted selection (MAS) in chrysanthemum WT breeding programs.

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

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. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It 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.

A high-quality genome sequence of Rosa chinensis to elucidate ornamental traits

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. Roses are outbred and can have various ploidy levels. Our objectives were to develop a high-quality reference genome sequence for the genus Rosa by sequencing a doubled haploid, combining long and short reads, and anchoring to a high-density genetic map, and to study the genome structure and genetic basis of major ornamental traits. We produced a doubled haploid rose line ('HapOB') from Rosa chinensis 'Old Blush' and generated a rose genome assembly anchored to seven pseudo-chromosomes (512 Mb with N50 of 3.4 Mb and 564 contigs). The length of 512 Mb represents 90.1-96.1% of the estimated haploid genome size of rose. Of the assembly, 95% is contained in only 196 contigs. The anchoring was validated using high-density diploid and tetraploid genetic maps. We delineated hallmark chromosomal features, including the pericentromeric regions, through annotation of transposable element families and positioned centromeric repeats using fluorescent in situ hybridization. The rose genome displays extensive synteny with the Fragaria vesca genome, and we delineated only two major rearrangements. Genetic diversity was analysed using resequencing data of seven diploid and one tetraploid Rosa species selected from various sections of the genus. Combining genetic and genomic approaches, we identified potential genetic regulators of key ornamental traits, including prickle density and the number of flower petals. A rose APETALA2/TOE homologue is proposed to be the major regulator of petal number in rose. This reference sequence is an important resource for studying polyploidization, meiosis and developmental processes, as we demonstrated for flower and prickle development. It 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.

Genomic and transcriptomic sequencing of Rosa hybrida provides microsatellite markers for breeding, flower trait improvement and taxonomy studies

BACKGROUND

Rosa hybrida is a valuable ornamental, food and medicinal crop worldwide, but with relatively limited molecular marker resources, especially for flower-specific markers. In this study, we performed genomic and floral transcriptomic sequencing of modern rose. We obtained comprehensive nucleotide information, from which numerous potential simple sequence repeat (SSR) markers were identified but were found to have high rates of amplification failure and PCR product redundancy.

RESULTS

We applied a filtering strategy for BLAST analysis with the assembled genomic sequence and identified 124,591 genomic and 2,292 EST markers with unique annealing sites. These markers had much greater reliability than those obtained before filtering. Additional BLAST analysis against the transcriptomic sequences uncovered 5225 genomic SSRs associated with 4100 transcripts, 2138 of which were associated with functional genes that were annotated against the non-redundant database. More than 90% of these newly developed molecular markers were polymorphic, based on PCR using a subset of SSRs to analyze tetraploid modern rose accessions, diploid Rosa species and one strawberry accession. The relationships among Rosa species determined by cluster analysis (based on these results) were in agreement with modern rose breeding history, whereas strawberry was isolated in a separate cluster, as expected.

CONCLUSIONS

Our results provide valuable molecular-genetic tools for rose flower trait improvement, breeding and taxonomy. Importantly, we describe a reproducible organ-specific strategy for molecular marker development and selection in plants, which can be applied to other crops.

Genetic dissection of adventitious shoot regeneration in roses by employing genome-wide association studies

We analysed the capacity to regenerate adventitious shoots in 96 rose genotypes and found 88 SNP markers associated with QTLs, some of which are derived from candidate genes for shoot regeneration. In an association panel of 96 rose genotypes previously analysed for petal colour, we conducted a genome-wide association study on the capacity of leaf petioles for direct shoot regeneration. Shoot regeneration rate and shoot ratio (number of shoots/total number of explants) were used as phenotypic descriptors for regeneration capacity. Two independent experiments were carried out with six replicates of ten explants each. We found significant variation between the genotypes ranging from 0.88 to 88.33% for the regeneration rate and from 0.008 to 1.2 for the shoot ratio, which exceeded the rates reported so far. Furthermore, we found 88 SNP markers associated with either the shoot regeneration rate or the shoot ratio. In this association analysis, we found 12 SNP markers from ESTs (expressed sequence tags) matching known candidate genes that are involved in shoot morphogenesis. The best markers explained more than 51% of the variance in the shoot regeneration rate and more than 0.65 of the variance in the shoot regeneration ratio between the homozygote marker classes. The genes underlying some of the best markers such as a GT-transcription factor or an LRR receptor-like protein kinase are novel candidate genes putatively involved in the observed phenotypic differences. The associated markers were mapped to the closely related genome of Fragaria vesca and revealed many distinct clusters, which also comprised the known candidate genes that functioned in the organogenesis of plant shoots. However, the validation of candidate genes and their functional relationship to shoot regeneration require further analysis in independent rose populations and functional analyses.

Partial preferential chromosome pairing is genotype dependent in tetraploid rose

It has long been recognised that polyploid species do not always neatly fall into the categories of auto- or allopolyploid, leading to the term 'segmental allopolyploid' to describe everything in between. The meiotic behaviour of such intermediate species is not fully understood, nor is there consensus as to how to model their inheritance patterns. In this study we used a tetraploid cut rose (Rosa hybrida) population, genotyped using the 68K WagRhSNP array, to construct an ultra-high-density linkage map of all homologous chromosomes using methods previously developed for autotetraploids. Using the predicted bivalent configurations in this population we quantified differences in pairing behaviour among and along homologous chromosomes, leading us to correct our estimates of recombination frequency to account for this behaviour. This resulted in the re-mapping of 25 695 SNP markers across all homologues of the seven rose chromosomes, tailored to the pairing behaviour of each chromosome in each parent. We confirmed the inferred differences in pairing behaviour among chromosomes by examining repulsion-phase linkage estimates, which also carry information about preferential pairing and recombination. Currently, the closest sequenced relative to rose is Fragaria vesca. Aligning the integrated ultra-dense rose map with the strawberry genome sequence provided a detailed picture of the synteny, confirming overall co-linearity but also revealing new genomic rearrangements. Our results suggest that pairing affinities may vary along chromosome arms, which broadens our current understanding of segmental allopolyploidy.