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Main Conclusion: Hand-held Raman spectroscopy is a potential tool for a confirmatory, non-invasive, and non-destructive detection and identification of rose rosette disease. Using this spectroscopic approach, structural changes in roses that are associated with this viral infection can be revealed. The commercial rose shrub industry in the United States is one of the largest of its kind. All commercial rose varieties are susceptible to rose rosette disease (RRD), a deadly viral disease vectored by eriophyid mites. This disease is typically diagnosed visually and/or by PCR-based detection assays. The present work demonstrates that Raman spectroscopy can detect RRD in intact leaf tissue. It is shown that chemometric analysis can distinguish between spectra collected from symptomatic and asymptomatic tissue, as well as between healthy and asymptomatic tissue. This method will be useful as an initial screen for RRD prior to PCR analysis to help conserve reagents and save time.

The cultivated rose is a multispecies complex for which a high level of disease protection is needed due to the low tolerance of blemishes in ornamental plants. The most important fungal diseases are black spot, powdery mildew, botrytis and downy mildew. Rose rosette, a lethal viral pathogen, is emerging as a devastating disease in North America. Currently rose breeders use a recurrent phenotypic selection approach and perform selection for disease resistance for most pathogen issues in a 2-3 year field trial. Marker assisted selection could accelerate this breeding process. Thus far markers have been identified for resistance to black spot (Rdrs) and powdery mildew and with the ability of genotyping by sequencing to generate 1000s of markers our ability to identify markers useful in plant improvement should increase exponentially. Transgenic rose lines with various fungal resistance genes inserted have shown limited success and RNAi technology has potential to provide virus resistance. Roses, as do other plants, have sequences homologous to characterized R-genes in their genomes, some which have been related to specific disease resistance. With improving next generation sequencing technology, our ability to do genomic and transcriptomic studies of the resistance related genes in both the rose and the pathogens to reveal novel gene targets to develop resistant roses will accelerate. Finally, the development of designer nucleases opens up a potentially non-GMO approach to directly modify a rose's DNA to create a disease resistant rose. Although there is much potential, at present rose breeders are not using marker assisted breeding primarily because a good suite of marker/trait associations (MTA) that would ensure a path to stable disease resistance is not available. As our genomic analytical tools improve, so will our ability to identify useful genes and linked markers. Once these MTAs are available, it will be the cost savings, both in time and money, that will convince the breeders to use the technology., (Copyright © 2014 Elsevier Ireland Ltd. All rights reserved.)

We have constructed the first integrated consensus map (ICM) for rose, based on the information of four diploid populations and more than 1,000 initial markers. The single population maps are linked via 59 bridge markers, on average 8.4 per linkage group (LG). The integrated map comprises 597 markers, 206 of which are sequence-based, distributed over a length of 530 cM on seven LGs. By using a larger effective population size and therefore higher marker density, the marker order in the ICM is more reliable than in the single population maps. This is supported by a more even marker distribution and a decrease in gap sizes in the consensus map as compared to the single population maps. This unified map establishes a standard nomenclature for rose LGs, and presents the location of important ornamental traits, such as self-incompatibility, black spot resistance (Rdr1), scent production and recurrent blooming. In total, the consensus map includes locations for 10 phenotypic single loci, QTLs for 7 different traits and 51 ESTs or gene-based molecular markers. This consensus map combines for the first time the information for traits with high relevance for rose variety development. It will serve as a tool for selective breeding and marker assisted selection. It will benefit future efforts of the rose community to sequence the whole rose genome and will be useful for synteny studies in the Rosaceae family and especially in the section Rosoideae.

Polyploidy is a pivotal process in plant evolution as it increase gene redundancy and morphological intricacy but due to the complexity of polysomic inheritance we have only few genetic maps of autopolyploid organisms. A robust mapping framework is particularly important in polyploid crop species, rose included (2n = 4x = 28), where the objective is to study multiallelic interactions that control traits of value for plant breeding. From a cross between the garden, peach red and fragrant cultivar Fragrant Cloud (FC) and a cut-rose yellow cultivar Golden Gate (GG), we generated an autotetraploid GGFC mapping population consisting of 132 individuals. For the map we used 128 sequence-based markers, 141 AFLP, 86 SSR and three morphological markers. Seven linkage groups were resolved for FC (Total 632 cM) and GG (616 cM) which were validated by markers that segregated in both parents as well as the diploid integrated consensus map.The release of the Fragaria vesca genome, which also belongs to the Rosoideae, allowed us to place 70 rose sequenced markers on the seven strawberry pseudo-chromosomes. Synteny between Rosa and Fragaria was high with an estimated four major translocations and six inversions required to place the 17 non-collinear markers in the same order. Based on a verified linear order of the rose markers, we could further partition each of the parents into its four homologous groups, thus providing an essential framework to aid the sequencing of an autotetraploid genome.

Introduction: Prickles are often deemed undesirable traits in many crops, including roses (Rosa sp.), and there is demand for rose cultivars with no or very few prickles. This study aims to identify new and/or validate reported quantitative trait loci (QTLs) associated with stem and leaf rachis prickle density, characterize the effects of functional haplotypes for major QTLs, and identify the sources of QTL-alleles associated with increased/decreased prickle density in roses. Methods: QTL mapping using pedigree-based analysis (PBA), and haplotype analysis were conducted on two multi-parental diploid rose populations (TX2WOB and TX2WSE). Results and discussion: Twelve QTLs were identified on linkage groups (LGs) 2, 3, 4, and 6. The major QTLs for the stem prickle density were located between 42.25 and 45.66 Mbp on chromosome 3 of the Rosa chinensis genome assembly, with individual QTLs explaining 18 to 49% of phenotypic variance (PVE). The remaining mapped QTLs were minor. As for the rachis prickle density, several QTLs were detected on LG3, 4, and 6 with PVE 8 to 17%. Also, this study identified that ancestors R. wichurana 'Basye's Thornless', 'Old Blush', and the pollen parent of M4-4 were common sources of favorable alleles (q) associated with decreased prickle density, whereas 'Little Chief' and 'Srche Europy' were the source of unfavorable alleles (Q) in the TX2WOB and TX2WSE populations, respectively. The outcomes of this work complement other studies to locate factors that affect prickle density. These results can also be utilized to develop high-throughput DNA tests and apply parental selection to develop prickle-free rose cultivars. [ABSTRACT FROM AUTHOR]

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. [ABSTRACT FROM AUTHOR]

Garden roses are an economically important horticultural crop worldwide, and two major fungal pathogens, black spot (Diplocarpon rosae F.A. Wolf) and cercospora leaf spot of rose (Rosisphaerella rosicola Pass.), affect both the health and ornamental value of the plant. Most studies on black spot disease resistance have focused on diploid germplasm, and little work has been performed on cercospora leaf spot resistance. With the use of newly developed software tools for autopolyploid genetics, two interconnected tetraploid garden rose F1 populations (phenotyped over the course of 3 years) were used for quantitative trait locus (QTL) analysis of black spot and cercospora leaf spot resistance as well as plant defoliation. QTLs for black spot resistance were mapped to linkage groups (LGs) 1–6. QTLs for cercospora resistance and susceptibility were found in LGs 1, 4, and 5 and for defoliation in LGs 1, 3, and 5. The major locus on LG 5 for black spot resistance coincides with the previously discovered Rdr4 locus inherited from Rosa L. ‘Radbrite’ (Brite Eyes™), the common parent used in these mapping populations. This work is the first report of any QTL for cercospora resistance/susceptibility in tetraploid rose germplasm and the first report of defoliation QTL in roses. A major QTL for cercospora susceptibility coincides with the black spot resistance QTL on LG 5 (Rdr4). A major cercospora resistance QTL was found on LG 1. These populations provide a genetic resource that will further the knowledge base of rose genetics as more traits are studied. Studying more traits from these populations will allow for the stacking of various QTLs for desirable traits. [ABSTRACT FROM AUTHOR]

Rose rosette disease (RRD), caused by the rose rosette emaravirus (RRV), is a major viral disease in roses (Rosa sp.) that threatens the rose industry. Recent studies have revealed quantitative trait loci (QTL) for reduced susceptibility to RRD in the linkage groups (LGs) 1, 5, 6, and 7 in tetraploid populations and the LGs 1, 3, 5, and 6 in diploid populations. In this study, we seek to better localize and understand the relationship between QTL identified in both diploid and tetraploid populations. We do so by remapping the populations found in these studies and performing a meta-analysis. This analysis reveals that the peaks and intervals for QTL using diploid and tetraploid populations co-localized on LG 1, suggesting that these are the same QTL. The same was seen on LG 3. Three meta-QTL were identified on LG 5, and two were discovered on LG 6. The meta-QTL on LG 1, MetaRRD1.1, had a confidence interval (CI) of 10.53 cM. On LG 3, MetaRRD3.1 had a CI of 5.94 cM. MetaRRD5.1 had a CI of 17.37 cM, MetaRRD5.2 had a CI of 4.33 cM, and MetaRRD5.3 had a CI of 21.95 cM. For LG 6, MetaRRD6.1 and MetaRRD6.2 had CIs of 9.81 and 8.81 cM, respectively. The analysis also led to the identification of potential disease resistance genes, with a primary interest in genes localized in meta-QTL intervals on LG 5 as this LG was found to explain the greatest proportion of phenotypic variance for RRD resistance. The results from this study may be used in the design of more robust marker-based selection tools to track and use a given QTL in a plant breeding context. [ABSTRACT FROM AUTHOR]

Rose rosette disease (RRD) caused by the rose rosette emaravirus (RRV) and transmitted by the eriophyid mite Phyllocoptes fructiphilus (Pf), both native to North America, has caused significant damage to roses over the last several decades. As cultural and chemical control of this disease is difficult and expensive, a field trial was established to systematically screen rose germplasm for potential sources of resistance. One hundred and eight rose accessions representing the diversity of rose germplasm were planted in Tennessee and Delaware, managed to encourage disease development, and evaluated for symptom development and viral presence for three years. All major commercial rose cultivars were susceptible to this viral disease to varying levels. The rose accessions with no or few symptoms were species accessions from the sections Cinnamomeae, Carolinae, Bracteatae, and Systylae or hybrids with these. Among these, some were asymptomatic; they displayed no symptoms but were infected by the virus. Their potential depends on their ability to serve as a source of viruses. The next step is to understand the mechanism of resistance and genetic control of the various sources of resistance identified. [ABSTRACT FROM AUTHOR]

Cercospora leaf spot (CLS) (Cercospora rosicola) is a major fungal disease of roses (Rosa sp.) in the southeastern U.S. Developing CLS-resistant cultivars offers a potential solution to reduce pesticide use. Yet, no work has been performed on CLS resistance. This study aimed to identify QTLs and to characterize alleles for resistance to CLS. The study used pedigree-based QTL analysis to dissect the genetic basis of CLS resistance using two multiparental diploid rose populations (TX2WOB and TX2WSE) evaluated across five years in two Texas locations. A total 38 QTLs were identified across both populations and distributed over all linkage groups. Three QTLs on LG3, LG4, and LG6 were consistently mapped over multiple environments. The LG3 QTL was mapped in a region between 18.9 and 27.8 Mbp on the Rosa chinensis genome assembly. This QTL explained 13 to 25% of phenotypic variance. The LG4 QTL detected in the TX2WOB population spanned a 35.2 to 39.7 Mbp region with phenotypic variance explained (PVE) up to 48%. The LG6 QTL detected in the TX2WSE population was localized to 17.9 to 33.6 Mbp interval with PVE up to 36%. Also, this study found multiple degrees of favorable allele effects (q-allele) associated with decreasing CLS at major loci. Ancestors 'OB', 'Violette', and PP-M4-4 were sources of resistance q-alleles. These results will aid breeders in parental selection to develop CLS-resistant rose cultivars. Ultimately, high throughput DNA tests that target major loci for CLS could be developed for routine use in a DNA-informed breeding program. [ABSTRACT FROM AUTHOR]

Rose rosette disease (RRD), caused by the Rose rosette emaravirus (RRV), is a major threat to the garden rose industry in the United States. There has been limited work on the genetics of host plant resistance to RRV. Two interconnected tetraploid garden rose F1 biparental mapping populations were created to develop high-quality tetraploid rose linkage maps that allowed the discovery of RRD resistance quantitative trait loci (QTLs) on linkage groups (LGs) 5, 6, and 7. These QTLs individually accounted for around 18-40% of the phenotypic variance. The locus with the greatest effect on partial resistance was found in LG 5. Most individuals with the LG 5 QTL were in the simplex configuration; however, two individuals were duplex (likely due to double reduction). Identification of resistant individuals and regions of interest can help the development of diagnostic markers for marker-assisted selection in a breeding program. [ABSTRACT FROM AUTHOR]

Resistance to rose rosette disease (RRD), a fatal disease of roses (Rosa spp.), is a high priority for rose breeding. As RRD resistance is time-consuming to phenotype, the identification of genetic markers for resistance could expedite breeding efforts. However, little is known about the genetics of RRD resistance. Therefore, we performed a quantitative trait locus (QTL) analysis on a set of inter-related diploid rose populations phenotyped for RRD resistance and identified four QTLs. Two QTLs were found in multiple years. The most consistent QTL is qRRV_TX2WSE_ch5, which explains approximately 20% and 40% of the phenotypic variation in virus quantity and severity of RRD symptoms, respectively. The second, a QTL on chromosome 1, qRRD_TX2WSE_ch1, accounts for approximately 16% of the phenotypic variation for severity. Finally, a third QTL on chromosome 3 was identified only in the multiyear analysis, and a fourth on chromosome 6 was identified in data from one year only. In addition, haplotypes associated with significant changes in virus quantity and severity were identified for qRRV_TX2WSE_ch5 and qRRD_TX2WSE_ch1. This research represents the first report of genetic determinants of resistance to RRD. In addition, marker trait associations discovered here will enable better parental selection when breeding for RRD resistance and pave the way for marker-assisted selection for RRD resistance. [ABSTRACT FROM AUTHOR]

The effect of heat on rose flowers was examined by measuring flower size in 10 diploid rose populations created by crossing the heat-tolerant Texas A&M University (TAMU) breeding lines (M4-4, J06-20-14-3) and sensitive (97/7-2, 'Red Fairy', 'Sweet Chariot', 'Vineyard Song', 'Old Blush', and 'Little Chief') diploid roses. As expected, the populations and individual seedlings differed in flower size. The heat-shock treatment (1 hour at 44 8C) decreased flower diameter (15.7%), petal number (23.3%), and flower dry weight (16.9%). Flower-size traits had moderately low narrow-sense (0.24, 0.12, and 0.34 for flower diameter, petal number, and flower dry weight, respectively) and moderately high broad-sense (0.62, 0.74, and 0.76 for flower diameter, petal number, and flower dry weight, respectively) heritability indicating important nonadditive genetic effects. If rose genotypes vary in floral heat tolerance, a differential response to heat among populations, seedlings, or both detected statistically by a significant interaction effectwould be expected. Both the analysis of variance (ANOVA) and the restricted estimated maximum likelihood (REML) analyses showed a positive population 3 heat stress interaction effect for flower diameter. Although our data indicate differences in floral heat tolerance among the populations and genotypes, the effect was small as compared with the other sources of variation. Thus, using this 1-hour heat-shock approachwould not be an effective strategy to select for floral heat tolerance in rose. [ABSTRACT FROM AUTHOR]