Genotyping-by-sequencing application on diploid rose and a resulting high-density SNP-based consensus map

The CALCINEURIN B-LIKE 4/CBL-INTERACTING PROTEIN 3 module degrades repressor JAZ5 during rose petal senescence

Flower senescence is genetically regulated and developmentally controlled. The phytohormone ethylene induces flower senescence in rose (Rosa hybrida), but the underlying signaling network is not well understood. Given that calcium regulates senescence in animals and plants, we explored the role of calcium in petal senescence. Here, we report that the expression of calcineurin B-like protein 4 (RhCBL4), which encodes a calcium receptor, is induced by senescence and ethylene signaling in rose petals. RhCBL4 interacts with CBL-interacting protein kinase 3 (RhCIPK3), and both positively regulate petal senescence. Furthermore, we determined that RhCIPK3 interacts with the jasmonic acid response repressor jasmonate ZIM-domain 5 (RhJAZ5). RhCIPK3 phosphorylates RhJAZ5 and promotes its degradation in the presence of ethylene. Our results reveal that the RhCBL4-RhCIPK3-RhJAZ5 module mediates ethylene-regulated petal senescence. These findings provide insights into flower senescence, which may facilitate innovations in postharvest technology for extending rose flower longevity.

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.

QTL discovery for resistance to black spot and cercospora leaf spot, and defoliation in two interconnected F1 bi-parental tetraploid garden rose populations

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.

Meta-Analysis of Rose Rosette Disease-Resistant Quantitative Trait Loci and a Search for Candidate Genes

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.

Pedigree-based analysis in multi-parental diploid rose populations reveals QTLs for cercospora leaf spot disease resistance

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 multi-parental 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.

QTL mapping and characterization of black spot disease resistance using two multi-parental diploid rose populations

Black spot disease (BSD) (Diplocarpon rosae) is the most common and damaging fungal disease in garden roses (Rosa sp.). Although qualitative resistance to BSD has been extensively investigated, the research on quantitative resistance lags behind. The goal of this research was to study the genetic basis of BSD resistance in two multi-parental populations (TX2WOB and TX2WSE) through a pedigree-based analysis approach (PBA). Both populations were genotyped and evaluated for BSD incidence over five years in three locations in Texas. A total of 28 QTLs, distributed over all linkage groups (LGs), were detected across both populations. Consistent minor effect QTLs included two on LG1 and LG3 (TX2WOB and TX2WSE), two on LG4 and LG5 (TX2WSE), and one QTL on LG7 (TX2WOB). In addition, one major QTL detected in both populations was consistently mapped on LG3. This QTL was localized to an interval ranging from 18.9 to 27.8 Mbp on the Rosa chinensis genome and explained 20 and 33% of the phenotypic variation. Furthermore, haplotype analysis showed that this QTL had three distinct functional alleles. The parent PP-J14-3 was the common source of the LG3 BSD resistance in both populations. Taken together, this research presents the characterization of new SNP-tagged genetic determinants of BSD resistance, the discovery of marker-trait associations to enable parental choice based on their BSD resistance QTL haplotypes, and substrates for the development of trait-predictive DNA tests for routine use in marker-assisted breeding for BSD resistance.

Rose Rosette Disease Resistance Loci Detected in Two Interconnected Tetraploid Garden Rose Populations

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.

Identification of QTLs for Reduced Susceptibility to Rose Rosette Disease in Diploid Roses

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.

Analysis of allelic variants of RhMLO genes in rose and functional studies on susceptibility to powdery mildew related to clade V homologs

Rose has 19 MLO genes. Of these, RhMLO1 and RhMLO2 were shown to be required for powdery mildew infection, which suggests their potential as susceptibility targets towards disease resistance. Powdery mildew, caused by Podosphaera pannosa, is one of the most serious and widespread fungal diseases for roses, especially in greenhouse-grown cut roses. It has been shown that certain MLO genes are involved in powdery mildew susceptibility and that loss of function in these genes in various crops leads to broad-spectrum, long-lasting resistance against this fungal disease. For this reason, these MLO genes are called susceptibility genes. We carried out a genome-wide identification of the MLO gene family in the Rosa chinensis genome, and screened for allelic variants among 22 accessions from seven different Rosa species using re-sequencing and transcriptome data. We identified 19 MLO genes in rose, of which four are candidate genes for functional homologs in clade V, which is the clade containing all dicot MLO susceptibility genes. We detected a total of 198 different allelic variants in the set of Rosa species and accessions, corresponding to 5-15 different alleles for each of the genes. Some diploid Rosa species shared alleles with tetraploid rose cultivars, consistent with the notion that diploid species have contributed to the formation of tetraploid roses. Among the four RhMLO genes in clade V, we demonstrated using expression study, virus-induced gene silencing as well as transient RNAi silencing that two of them, RhMLO1 and RhMLO2, are required for infection by P. pannosa and suggest their potential as susceptibility targets for powdery mildew resistance breeding in rose.

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.

Comprehensive analysis of SSRs and database construction using all complete gene-coding sequences in major horticultural and representative plants

Simple sequence repeats (SSRs) are one of the most important genetic markers and widely exist in most species. Here, we identified 249,822 SSRs from 3,951,919 genes in 112 plants. Then, we conducted a comprehensive analysis of these SSRs and constructed a plant SSR database (PSSRD). Interestingly, more SSRs were found in lower plants than in higher plants, showing that lower plants needed to adapt to early extreme environments. Four specific enriched functional terms in the lower plant Chlamydomonas reinhardtii were detected when it was compared with seven other higher plants. In addition, Guanylate_cyc existed in more genes of lower plants than of higher plants. In our PSSRD, we constructed an interactive plotting function in the chart interface, and users can easily view the detailed information of SSRs. All SSR information, including sequences, primers, and annotations, can be downloaded from our database. Moreover, we developed Web SSR Finder and Batch SSR Finder tools, which can be easily used for identifying SSRs. Our database was developed using PHP, HTML, JavaScript, and MySQL, which are freely available at http://www.pssrd.info/ . We conducted an analysis of the Myb gene families and flowering genes as two applications of the PSSRD. Further analysis indicated that whole-genome duplication and whole-genome triplication played a major role in the expansion of the Myb gene families. These SSR markers in our database will greatly facilitate comparative genomics and functional genomics studies in the future.

Genomic Resource Development for Hydrangea (Hydrangea macrophylla (Thunb.) Ser.)—A Transcriptome Assembly and a High-Density Genetic Linkage Map

Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite the economic importance, genetic studies for hydrangea have been limited by the lack of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. A transcriptomic study was performed on two important cultivars, Veitchii and Endless Summer, to discover simple sequence repeat (SSR) markers and an F1 population based on the cross ‘Veitchii’ × ‘Endless Summer’ was established for genetic linkage map construction. Genotyping by sequencing (GBS) was performed on the mapping population along with SSR genotyping. From an analysis of 42,682 putative transcripts, 8780 SSRs were identified and 1535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4190 markers that were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1767 positioned markers (146 SSRs and 1621 SNPs), spanned 1383.4 centiMorgans (cM), and was comprised of 18 linkage groups, with an average mapping interval of 0.8 cM. The transcriptome information and large-scale marker development in this study greatly expanded the genetic resources that are available for hydrangea. The high-density genetic linkage maps presented here will serve as an important foundation for quantitative trait loci mapping, map-based gene cloning, and marker-assisted selection of H. macrophylla.

Molecular markers from the chloroplast genome of rose provide a complementary tool for variety discrimination and profiling

The rose is one of the most important ornamental woody plants because of its extensive use and high economic value. Herein, we sequenced a complete chloroplast genome of the miniature rose variety Rosa 'Margo Koster' and performed comparative analyses with sequences previously published for other species in the Rosaceae family. The chloroplast genome of Rosa 'Margo Koster', with a size of 157,395 bp, has a circular quadripartite structure typical of angiosperm chloroplast genomes and contains a total of 81 protein-coding genes, 30 tRNA genes and 4 rRNA genes. Conjunction regions in the chloroplast genome of Rosa 'Margo Koster' were verified and manually corrected by Sanger sequencing. Comparative genome analysis showed that the IR contraction and expansion events resulted in rps19 and ycf1 pseudogenes. The phylogenetic analysis within the Rosa genus showed that Rosa 'Margo Koster' is closer to Rosa odorata than to other Rosa species. Additionally, we identified and screened highly divergent sequences and cpSSRs and compared their power to discriminate rose varieties by Sanger sequencing and capillary electrophoresis. The results showed that 15 cpSSRs are polymorphic, but their discriminating power is only moderate among a set of rose varieties. However, more than 150 single nucleotide variations (SNVs) were discovered in the flanking region of cpSSRs, and the results indicated that these SNVs have a higher divergence and stronger power for profiling rose varieties. These findings suggest that nucleotide mutations in the chloroplast genome may be an effective and powerful tool for rose variety discrimination and DNA profiling. These molecular markers in the chloroplast genome sequence of Rosa spp. will facilitate population and phylogenetic studies and other related studies of this species.

The development of a high-density genetic map significantly improves the quality of reference genome assemblies for rose

Roses are important woody plants featuring a set of important traits that cannot be investigated in traditional model plants. Here, we used the restriction-site associated DNA sequencing (RAD-seq) technology to develop a high-density linkage map of the backcross progeny (BC1F1) between Rosa chinensis 'Old Blush' (OB) and R. wichuraiana 'Basyes' Thornless' (BT). We obtained 643.63 million pair-end reads and identified 139,834 polymorphic tags that were distributed uniformly in the rose genome. 2,213 reliable markers were assigned to seven linkage groups (LGs). The length of the genetic map was 1,027.425 cM in total with a mean distance of 0.96 cM per marker locus. This new linkage map allowed anchoring an extra of 1.21/23.14 Mb (12.18/44.52%) of the unassembled OB scaffolds to the seven reference pseudo-chromosomes, thus significantly improved the quality of assembly of OB reference genome. We demonstrate that, while this new linkage map shares high collinearity level with strawberry genome, it also features two chromosomal rearrangements, indicating its usefulness as a resource for understanding the evolutionary scenario among Rosaceae genomes. Together with the newly released genome sequences for OB, this linkage map will facilitate the identification of genetic components underpinning key agricultural and biological traits, hence should greatly advance the studies and breeding efforts of rose.

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.

Cgr1, a ripe rot resistance QTL in Vitis amurensis 'Shuang Hong' grapevine

Ripe rot is a serious grapevine disease in Vitis L. and Muscadinia (Planch.) Small. However, resistance to this disease has been reported in some oriental Vitis species. To identify resistance-related Quantitative Trait Loci (QTLs) from the Chinese grape species V. amurensis, an F₁ population of V. vinifera 'Cabernet Sauvignon' × V. amurensis 'Shuang Hong' was used to map the ripe rot resistance loci expected in 'Shuang Hong' grape. A total of 7598 single nucleotide polymorphisms (SNPs) between the parents were identified in our previous study, and 934 SNPs were selected for genetic map construction. These SNPs are distributed across the 19 chromosomes covering a total of 1665.31 cM in length, with an average of 1.81 cM between markers. Ripe rot resistance phenotypes among the hybrids were evaluated in vitro using excised leaves for three consecutive years from 2016 to 2018; a continuous variation was found among the F₁ hybrids, and the Pearson correlation coefficients of the phenotypes scored in all three years were significant at the 0.01 level. Notably, the first QTL reported for resistance to grape ripe rot disease, named Cgr1, was identified on chromosome 14 of 'Shuang Hong' grapevine. Cgr1 could explain up to 19.90% of the phenotypic variance. In addition, a SNP named 'np19345' was identified as a molecular marker closely linked to the peak of Cgr1 and has the potential to be developed as a marker for the Cgr1 resistance haplotype.