Dissecting the genome-wide evolution and function of R2R3-MYB transcription factor family in Rosa chinensis

Rosa chinensis, an important ancestor species of Rosa hybrida, the most popular ornamental plant species worldwide, produces flowers with diverse colors and fragrances. The R2R3-MYB transcription factor family controls a wide variety of plant-specific metabolic processes, especially phenylpropanoid metabolism. Despite their importance for the ornamental value of flowers, the evolution of R2R3-MYB genes in plants has not been comprehensively characterized. In this study, 121 predicted R2R3-MYB gene sequences were identified in the rose genome. Additionally, a phylogenomic synteny network (synnet) was applied for the R2R3-MYB gene families in 35 complete plant genomes. We also analyzed the R2R3-MYB genes regarding their genomic locations, Ka/Ks ratio, encoded conserved motifs, and spatiotemporal expression. Our results indicated that R2R3-MYBs have multiple synteny clusters. The RcMYB114a gene was included in the Rosaceae-specific Cluster 54, with independent evolutionary patterns. On the basis of these results and an analysis of RcMYB114a-overexpressing tobacco leaf samples, we predicted that RcMYB114a functions in the phenylpropanoid pathway. We clarified the relationship between R2R3-MYB gene evolution and function from a new perspective. Our study data may be relevant for elucidating the regulation of floral metabolism in roses at the transcript level

Genome-wide DNA polymorphisms in two cultivars of mei (Prunus mume sieb. et zucc.)

BACKGROUND: Mei (Prunus mume Sieb. et Zucc.) is a famous ornamental plant and fruit crop grown in East Asian countries. Limited genetic resources, especially molecular markers, have hindered the progress of mei breeding projects. Here, we performed low-depth whole-genome sequencing of Prunus mume ‘Fenban’ and Prunus mume ‘Kouzi Yudie’ to identify high-quality polymorphic markers between the two cultivars on a large scale. RESULTS: A total of 1464.1 Mb and 1422.1 Mb of ‘Fenban’ and ‘Kouzi Yudie’ sequencing data were uniquely mapped to the mei reference genome with about 6-fold coverage, respectively. We detected a large number of putative polymorphic markers from the 196.9 Mb of sequencing data shared by the two cultivars, which together contained 200,627 SNPs, 4,900 InDels, and 7,063 SSRs. Among these markers, 38,773 SNPs, 174 InDels, and 418 SSRs were distributed in the 22.4 Mb CDS region, and 63.0% of these marker-containing CDS sequences were assigned to GO terms. Subsequently, 670 selected SNPs were validated using an Agilent’s SureSelect solution phase hybridization assay. A subset of 599 SNPs was used to assess the genetic similarity of a panel of mei germplasm samples and a plum (P. salicina) cultivar, producing a set of informative diversity data. We also analyzed the frequency and distribution of detected InDels and SSRs in mei genome and validated their usefulness as DNA markers. These markers were successfully amplified in the cultivars and in their segregating progeny. CONCLUSIONS: A large set of high-quality polymorphic SNPs, InDels, and SSRs were identified in parallel between ‘Fenban’ and ‘Kouzi Yudie’ using low-depth whole-genome sequencing. The study presents extensive data on these polymorphic markers, which can be useful for constructing high-resolution genetic maps, performing genome-wide association studies, and designing genomic selection strategies in mei

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

A cytosolic class II small heat shock protein, PfHSP17.2, confers resistance to heat, cold, and salt stresses in transgenic Arabidopsis

Abstract We cloned and characterized the full-length coding sequence of a small heat shock (sHSP) gene, PfHSP17.2, from Primula forrestii leaves following heat stress treatment. Homology and phylogenetic analysis suggested that PfHSP17.2 is a cytosolic class II sHSP, which was further supported by the cytosolic localization of transient expression of PfHSP17.2 fused with green fluorescent protein reporter. Expression analysis showed that PfHSP17.2 was highly inducible by heat stress in almost all the vegetative and generative tissues and was expressed under salt, cold, and oxidative stress conditions as well. Moreover, the expression of PfHSP17.2 in P. forrestii was detected in certain developmental growth stages. Transgenic Arabidopsis thaliana constitutively expressing PfHSP17.2 displayed increased thermotolerance and higher resistance to salt and cold compared with wild type plants. It is suggested that PfHSP17.2 plays a key role in heat and other abiotic stresses

Analysis of Spatial-Temporal Variation in Floral Volatiles Emitted from <i>Lagerstroemia caudata</i> by Headspace Solid-Phase Microextraction and GC–MS

Lagerstroemia caudata is a rare aromatic species native to southeastern China, but its floral scent properties and release dynamics remain unclear. This study is the first systematic analysis of spatial-temporal variation in volatile organic compounds (VOCs) emitted from L. caudata by headspace solid-phase microextraction (HS-SPME) with gas chromatography–mass spectrometry (GC-MS). Thirty-two VOCs were identified, 20 of which were detected for the first time. Aldehydes, alcohols, and monoterpenoids were the main VOC categories, each with different releasing rhythms. Total emission of VOCs was much higher in the full-blooming stage (140.90 ng g−1min−1) than in the pre-blooming (36.54 ng g−1min−1) or over-blooming (24.92 ng g−1min−1). Monoterpenoids, especially nerol, geraniol, and linalool, were the characteristic VOCs for full-blooming flowers. Daily emissions of nine compounds (nerol, geraniol, linalool, citronellol, β-citral, (E)-citral, phenylethyl alcohol, 2-heptanol, 2-nonanol) correlated closely with the opening of L. caudata, presenting an apparent diurnal pattern of scent emission. Tissue-specific emission was found in most isolated floral parts. Stamen was the most significant source of floral VOCs, considering its high emission levels of total VOC (627.96 ng g−1min−1). Our results extend the information on floral VOCs of Lagerstroemia and provide a theoretical basis for breeding new cultivars with desirable floral scents

Transcriptomics Investigation into the Mechanisms of Self-Incompatibility between Pin and Thrum Morphs of Primula maximowiczii

Heteromorphic self-incompatibility (SI) is an important system for preventing inbreeding in the genus Primula. However, investigations into the molecular mechanisms of Primula SI are lacking. To explore the mechanisms of SI in Primula maximowiczii, the pollen germination and fruiting rates of self- and cross-pollinations between pin and thrum morphs were investigated, and transcriptomics analyses of the pistils after pollination were performed to assess gene expression patterns in pin and thrum SI. The results indicated that P. maximowiczii exhibits strong SI and that the mechanisms of pollen tube inhibition differ between pin and thrum morphs. While self-pollen tubes of the pin morph were able to occasionally, though rarely, enter the style, those of the thrum morph were never observed to enter the style. The transcriptomics analysis of the pistils revealed 1311 and 1048 differentially expressed genes (DEGs) that were identified by comparing pin self-pollination (PS) vs. pin cross-pollination (PT) and thrum self-pollination (TS) vs. thrum cross-pollination (TP). Notably, about 90% of these DEGs exhibited different expression patterns in the two comparisons. Moreover, pin and thrum DEGs were associated with different Gene Ontology (GO) categories and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathways following enrichment analyses. Based on our results, the molecular mechanisms underlying the pin and thrum SI in P. maximowiczii appear to be distinct. Furthermore, the genes involved in the SI processes are commonly associated with carbohydrate metabolism and environmental adaptation. These results provide new insight into the molecular mechanisms of Primula SI

Epigenetic Variance, Performing Cooperative Structure with Genetics, Is Associated with Leaf Shape Traits in Widely Distributed Populations of Ornamental Tree Prunus mume

Increasing evidence shows that epigenetics plays an important role in phenotypic variance. However, little is known about epigenetic variation in the important ornamental tree Prunus mume. We used amplified fragment length polymorphism (AFLP) and methylation-sensitive amplified polymorphism (MSAP) techniques, and association analysis and sequencing to investigate epigenetic variation and its relationships with genetic variance, environment factors, and traits. By performing leaf sampling, the relative total methylation level (29.80%) was detected in 96 accessions of P. mume. And the relative hemi-methylation level (15.77%) was higher than the relative full methylation level (14.03%). The epigenetic diversity (I∗ = 0.575, h∗ = 0.393) was higher than the genetic diversity (I = 0.484, h = 0.319). The cultivated population displayed greater epigenetic diversity than the wild populations in both southwest and southeast China. We found that epigenetic variance and genetic variance, and environmental factors performed cooperative structures, respectively. In particular, leaf length, width and area were positively correlated with relative full methylation level and total methylation level, indicating that the DNA methylation level played a role in trait variation. In total, 203 AFLP and 423 MSAP associated markers were detected and 68 of them were sequenced. Homologous analysis and functional prediction suggested that the candidate marker-linked genes were essential for leaf morphology development and metabolism, implying that these markers play critical roles in the establishment of leaf length, width, area, and ratio of length to width

Widely Targeted Metabolic Profiling Reveals Differences in Polyphenolic Metabolites during <i>Rosa xanthina</i> f. <i>spontanea</i> Fruit Development and Ripening

Rose hips are rich in various nutrients and have long been used for food and medicinal purposes. Owing to the high phenolic content, rose hips can be used as natural antioxidants. In this study, ultra-performance liquid chromatography-tandem mass spectrometry (UPLC-MS/MS) was used to conduct a widely targeted metabolomics analysis on the polyphenolic components of Rosa xanthina f. spontanea in three ripening stages: unripe, half-ripe and fully ripe fruit. A total of 531 polyphenol metabolites were detected, including 220 phenolic acids, 219 flavonoids, 50 tannins and 42 lignans and coumarins. There were 160 differential metabolites between unripe and half-ripe rose hips (61 downregulated and 99 upregulated) and 157 differential metabolites between half-ripe and fully ripe rose hips (107 downregulated and 50 upregulated). The results of our study not only greatly enrich the chemical composition database of rose hips but also provide metabolomics information on the changes in polyphenolic metabolism during fruit development for the first time, which will help select the optimal harvest time of rose hips to achieve better quality

Molecular Evidence for Hybrid Origin and Phenotypic Variation of Rosa Section Chinenses

Rosa sect. Chinenses (Rosaceae) is an important parent of modern rose that is widely distributed throughout China and plays an important role in breeding and molecular biological research. R. sect. Chinenses has variable morphological traits and mixed germplasm. However, the taxonomic status and genetic background of sect. Chinenses varieties remain unclear. In this study, we collected germplasm resources from sect. Chinenses varieties with different morphological traits. Simple sequence repeat (SSR) markers, chloroplast markers, and single copy nuclear markers were used to explore the genetic background of these germplasm resources. We described the origin of hybridization of rose germplasm resources by combining different molecular markers. The results showed that the flower and hip traits of different species in R. sect. Chinenses were significantly different. The SSR analysis showed that the two wild type varieties have different genetic backgrounds. The double petal varieties of R. sect. Chinenses could be hybrids of two wild type varieties. A phylogenetic analysis showed that the maternal inheritance of sect. Chinenses varieties had two different origins. To some extent, variation in the morphological traits of double petal species of R. sect. Chinenses reflects the influence of cultivation process. This study emphasizes that different genetic markers vary in their characteristics. Therefore, analyzing different genetic markers in could provide an insight into highly heterozygous species

Establishment and Verification of An Efficient Virus-induced Gene Silencing System in Forsythia

To understand the functional identification of large-scale genomic sequences in Forsythia, tobacco rattle virus (TRV)-mediated virus-induced gene silencing (VIGS), suitable for the plant, was explored in this study. The results showed that the TRV-mediated VIGS system could be successfully used in Forsythia for silencing the reporter gene FsPDS (Forsythia phytoene desaturase) using stem infiltration and leaf infiltration methods. All the treated plants were pruned below the injection site after 7–15 d infection; the FsPDS was silenced and typical photobleaching symptoms were observed in newly sprouted leaves at the whole-plant level. Meanwhile, this system has been successfully tested and verified through virus detection and qRT-PCR analysis. After the optimization, Forsythia magnesium chelatase subunit H (FsChlH) was silenced successfully in Forsythia using this system, resulting in yellow leaves with decreased chlorophyll content. The system was stable, highly efficient and had greater rapidity and convenience, which made it suitable to study the function of genes related to physiological pathways such as growth and development, and metabolic regulation in Forsythia