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Simple Sequence Repeat Marker Analysis of Genetic Relationships within Hydrangea macrophylla
Abstract and Figures
Genetic diversity studies using 39 simple-sequence repeat (SSR) markers were carried out with 114 taxa of Hydrangea macrophylla (Thunb.) Ser., including 87 H. macrophylla ssp. macrophylla cultivars and 20 members of H. macrophylla ssp. serrata (Thunb.) Makino. The SSR loci were highly variable among the taxa, producing a mean of 8.26 alleles per locus. Overall allelic richness was relatively high at 5.12 alleles per locus. H. macrophylla ssp. serrata contained nearly twice the allelic diversity of H. macrophylla ssp. macrophylla. The majority of genetic diversity was found to reside within the subspecies, with only 12% of the total genetic diversity observed occurring between subspecies. Although the elevation of H. macrophylla ssp. serrata to species level has recently been recommended by several hydrangea authorities, these data support the subspecies designation. Four cultivars (Preziosa, Pink Beauty, Tokyo Delight, and Blue Deckle) appeared to be hybrids between the two subspecies. Genetic similarities were found among five remontant cultivars (Bailmer, Oak Hill, David Ramsey, Decatur Blue, and Penny Mac) and several nonremontant cultivars, including General Vicomtesse de Vibraye, Nikko Blue, All Summer Beauty, and La France. No close genetic relationship was found between the remontant cultivar Early Sensation and other remontant cultivars. Genetic similarities were found among variegated and double-flower cultivars. Within H. macrophylla ssp. macrophylla, cultivars with mophead inflorescences clustered separately from most lacecap cultivars. This indicates the cultivars with lacecap inflorescences that were among some of the earliest introductions to Europe were not widely used in the breeding of mophead forms. Some presumed synonyms were found to be valid ('Preziosa' and 'Pink Beauty', 'Rosalba' and 'Benigaku', 'Geoffrey Chadbund' and 'Mowe'), whereas others were not ('Harlequin' and 'Monrey', 'Nigra' and 'Mandschurica'). This study identified potentially unexploited sources of germplasm within H. macrophylla and relationships between existing cultivars of this popular shrub. This information should be of value when selecting parents for breeding programs.
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... So far, simple sequence repeat (SSR) markers and single-nucleotide polymorphisms (SNPs) have been used to assess the genetic diversity and relationships of Hydrangea species. With these SSR markers, closely related H. macrophylla clones could be distinguished (Reed and Rinehart, 2007;Wu et al., 2021). Additionally, the double flower loci of H. macrophylla could be linked to SNPs (Nashima et al., 2021). ...
Background and Aims
Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. (Hydrangeaceae), and are valued in gardens, households and landscapes across the globe. The phenotypic diversity of hortensia cultivars, hybrids and wild relatives is mirrored by their genomic variation, with differences in genome size, base chromosome numbers and ploidy level. We aim to understand the genomic and chromosomal basis of hortensia genome variation. Therefore, we analysed six hortensias with different origins and chromosomal setups for repeatome divergence, the genome fraction with the highest sequence turnover. This holds information from the hortensias’ evolutionary paths and can guide breeding initiatives.
Methods
We compiled a hortensia genotype panel representing members of the sections Macrophyllae, Hydrangea, Asperae and Heteromallae and reconstructed a plastome-based phylogenetic hypothesis as the evolutionary basis for all our analyses. We comprehensively characterized the repeatomes by whole-genome sequencing and comparative repeat clustering. Major tandem repeats were localized by multicolour FISH.
Key Results
The Hydrangea species show differing repeat profiles reflecting their separation into the two major Hydrangea clades: diploid Hydrangea species from Japan show a conserved repeat profile, distinguishing them from Japanese polyploids as well as Chinese and American hortensias. These results are in line with plastome-based phylogenies. The presence of specific repeats indicates that H. paniculata was not polyploidized directly from the common ancestor of Japanese Hydrangea species, but evolved from a distinct progenitor. Major satellite DNAs were detected over all H. macrophylla chromosomes.
Conclusions
Repeat composition among the Hydrangea species varies in congruence with their origins and phylogeny. Identified species-specific satDNAs may be used as cytogenetic markers to identify Hydrangea species and cultivars, and to infer parental species of old Hydrangea varieties. This repeatome and cytogenetics information helps to expand the genetic toolbox for tracing hortensia evolution and guiding future hortensia breeding.
... The history of taxonomic debates between H. macrophylla and H. serrata has endured for a long time, and studies using molecular techniques have been conducted to resolve them (Wilson 1923;Hara 1955;McClintock 1957;Reed and Rinehart 2007). In this study, H. macrophylla and H. serrata were grouped into one cluster in the dendrogram, and high cross compatibility between the two species was also confirmed. ...
Hydrangeas with large inflorescences are widely used as cut flowers and in floral arrangements. However, the genetic diversity of commercially grown hydrangeas has been limited owing to the breeding focus on popular species. Therefore, this study was conducted to suggest interspecific breeding strategies for expanding the genetic diversity in Hydrangea L . by evaluating genetic diversity in the seven main species collected in Korea and analyzing cross compatibility via intra- and interspecific hybridization. Interspecific diversity evaluation using simple sequence repeat markers resulted in the segregation of 35 varieties accounting for seven species into five groups as follows: (1) Hydrangea paniculate group, (2) Hydrangea arborescnes group, (3) Hydrangea anomala and Hydrangea aspera group, (4) Hydrangea quercifolia group, and (5) Hydrangea macrophylla and Hydrangea serrata group. Cross compatibility was confirmed via intra- and interspecific crossing, and hybrids were obtained in 18 crossing combinations. Intraspecific hybrids tend to be easy to obtain, but interspecific hybrids are difficult to obtain due to a variety of factors. While most of the interspecific hybrids were obtained using ovule culture, the crossing between H. macrophylla and H. serrata created hybrids from seed sowing, indicating that H. serrata is a subspecies of H. macrophylla . Bilateral and unilateral incompatibilities were observed across the obtained hybrids. Particularly, weak bilateral compatibility was observed between H. serrata and H.paniculata . Accordingly, it was proposed that hybrids between H. macrophylla and H. serrata can be successfully used as parental materials in crossing with H. paniculata to improve cold tolerance. In addition, cross compatibility was improved in interspecific crossing using H. macrophylla and H. arborescens as maternal plants. It is anticipated that these finding will help improve the genetic diversity in commercial hydrangeas.
... nucleotide polymorphisms (SNPs) have been effectively used in the study of Hydrangea species to assess their genetic diversity and relationships. The application of these markers in H. macrophylla has highlighted their utility in distinguishing closely related clones. Genetic diversity in 114 taxa of H. macrophylla were analyzed using SSR markers (Reed and Rinehart. 2007). Wu et al. (2021) conducted a transcriptomic study on the cultivars to discover SSR markers in H. macrophylla. Nashima et al. (2021) identified specific genetic markers using SNPs linked to the double flower loci of H. macrophylla. These studies utilized genome sequence data to identify DNA markers, demonstrating their valuable roles i ...
Background and Aims
Ornamental hortensias are bred from a reservoir of over 200 species in the genus Hydrangea s.l. and are valued in gardens, households and landscapes across the globe. The phenotypic diversity of hortensia cultivars, hybrids and wild relatives is mirrored by their genomic variation, with differences in genome size, base chromosome numbers and ploidy level. We aim to understand the genomic and chromosomal basis of hortensia genome variation. Therefore, we analyze six hortensias with different origins and chromosomal setups for repeatome divergence, the genome fraction with the highest sequence turnover. This holds information from the hortensia's evolutionary paths and can inform breeding initiatives.
Methods
We compiled a hortensia genotype panel representing members of the sections Macrophyllae, Hydrangea, Asperae, and Heteromallae and reconstructed a plastome-based phylogenetic hypothesis as evolutionary basis for all our analyses. We comprehensively characterized the repeatomes by whole genome sequencing and comparative repeat clustering. Major tandem repeats were localized by multi-color FISH.
Key Results
The Hydrangea species show differing repeat profiles reflecting their separation into the two major Hydrangea clades: Diploid Hydrangea species from Japan show a conserved repeat profile, distinguishing them from Japanese polyploids as well as Chinese and American hortensias. These results are in line with plastome-based phylogenies. The presence of specific repeats indicates that H. paniculata was not polyploidized directly from the common ancestor of Japanese Hydrangea species, but evolved from a distinct progenitor. Major satellite DNAs were detected over all H. macrophylla chromosomes.
Conclusions
Repeat composition among the Hydrangea species varies in congruence with their origins and phylogeny. Identified species-specific satDNAs may be used as cytogenetic markers to identify Hydrangea species and cultivars, and to infer parental species of old Hydrangea varieties. This repeatome and cytogenetics information helps to expand the genetic toolbox for tracing hortensia evolution and informing future hortensia breeding.
... Tools for marker-assisted selection and genome-enabled breeding strategies in bigleaf hydrangea include a full-length, annotated genome for cultivars Endless Summer and Veitchii [99], a high-density genetic linkage map [97], and genetic markers for inflorescence shape [98,100] and double flowering [99,101]. High-quality SSR and SNP markers have been developed and used in diversity analysis and genetic mapping [98,100,[102][103][104][105]. Tran-scriptomic analyses have been used to identify genes involved in aluminum tolerance and accumulation [106][107][108], flower development [109], leaf color [110,111], and stress response [112]. ...
Hydrangea macrophylla, commonly known as bigleaf, garden, French, or florist hydrangea, is the most economically important member of the Hydrangea genus, with a breeding history spanning hundreds of years. Bigleaf hydrangea breeding improvement has largely focused on aesthetic traits and there are few varieties tolerant or resistant to major diseases such as powdery mildew. Powdery mildew is an obligate biotrophic Ascomycete in the order Erysiphales represented by approximately 900 species worldwide. The disease-causing agent in hydrangeas is Golovinomyces orontii (formerly Erysiphe polygoni DC), which tarnishes the beauty, growth, and salability of bigleaf hydrangea plants, especially those packed closely in production environments. Chemical or biological control is commonly used in production. A recently published haplotype-resolved genome of bigleaf hydrangea enables targeted analyses and breeding techniques for powdery mildew resistance. Analyzing transcriptomes of tolerant and susceptible hydrangeas through RNA sequencing will lead to the identification of differentially expressed genes and/or pathways. Concurrent application of marker-assisted selection, genetic transformation, and gene editing will contribute to the development of powdery-mildew-resistant varieties of bigleaf hydrangea. The aim of this review is to give a general overview of powdery mildew, its impact on bigleaf hydrangea, current control methods, molecular mechanisms, and breeding prospects for powdery mildew resistance in bigleaf hydrangea.
... Out of these, H. macrophylla is the economically most important species (De Smet et al., 2015). H. macrophylla is a perennial shrub, which is native to eastern Asia (Reed and Rinehart, 2007). It has great economic importance as ornamental crop plant due to its attractive foliage and its large, showy and colourful inflorescences, which are white, red, pink or blue. ...
... Twelve primer pairs producing SSR fragments were tested for DNA amplification [32]. Only three SSR markers (STAB 305_306, STAB 317_318, and STAB 321_322) showed different profiles in the parental lines and were chosen for further analysis, while nine did not produce any polymorphic band to infer any parentage or paternity ( Table 7). ...
In flowering plants, such as Hydrangea macrophylla, the main breeding objective is to increase genetic variability in ornamental traits. This study investigates in vitro techniques, through ovule culture, to overcome the hybridization barriers and increase the efficiency of crossing in Hydrangea macrophylla in which breeding has been hampered by a fairly long breeding cycle and lack of information about its genetic resources. Two different types of media were compared, Gamborg B5 and Murashige and Skoog basal salts, to verify the germination rate of immature ovules in different intraspecific crosses. The germination rate and viability of the seedlings were influenced by the parental genotypes in the different combinations of crossing, highlighting, in some cases, the poor compatibility between some of them. The crossing combination “Parental A × Parental B”, showed the highest germinated ovules percentage (78.3%). The media used seem to less affect the ovule germination while mainly influencing the development and growth of the young seedlings and in particular the number of leaves, the branching attitude, and root length, with the Gamborg medium determining up to a 30% increase, compared to MS medium. In addition, we tested the effectiveness of using SSR markers to assess the parentage of the putative hybrids even though only three out of twelve SSR markers showed allelism. Although the number of SSR markers was low, they were allowed to profile the parentage according to Mendelian laws.
The hydrangea genus belongs to the Hydrangeaceae family, in the Cornales order of flowering plants which early diverged among the asterids and includes several species that are commonly used ornamental plants. Of them, Hydrangea macrophylla is one of the most valuable in the nursery trade yet few genomic resources are available for this crop or closely related Asterid species. Two high-quality haplotype resolved reference genomes of hydrangea cultivars Veitchii and Endless Summer (highest quality at 2.22Gb, 396 contigs, N50 22.8Mb) were assembled and scaffolded into the expected 18 pseudochromosomes. Utilizing the newly developed high-quality reference genomes along with high-quality genomes of other related flowering plants, nuclear data was found to support a single divergence point in the Asterids clade where both the Cornales and Ericales diverged from the euasterids. Genetic mapping with an F1 hybrid population demonstrated the power of linkage mapping combined with the new genomic resources to identify the gene for inflorescence shape, CYP78A5 located on chromosome 4, and a novel gene, BAM3 located on chromosome 17, for causing double flower. Resources developed in this study will not only help to accelerate hydrangea genetic improvement but also contributes to understanding the largest group of flowering plants, the Asterids.
Hydrangea macrophylla é uma planta exótica, conhecida popularmente por Hortênsia, e cultivada em diversas partes do mundo como planta ornamental. No Rio Grande do Sul [Brasil], as cidades turísticas de Canela, Gramado e São Francisco de Paula, que fazem parte da Região das Hortênsias, ela também está presente. Muitas atividades econômicas e culturais desses municípios são baseadas na atratividade visual dessa planta, que é considerada uma das causas que motivaram o desenvolvimento do turismo da região. Sendo assim, o presente estudo teve por objetivo caracterizar H. macrophylla na Região das Hortênsias, focando as perspectivas cultural, econômica e ecológica. O estudo foi baseado em revisão bibliográfica, visitas a atrativos turísticos e unidades de conservação. Através dos dados coletados pode-se perceber que a planta está entrelaçada a diversos aspectos da cultura e economia da região. No entanto, aspectos ecológicos, tais como os efeitos que a presença dessa planta causa à biodiversidade local, ainda são pouco investigados. ABSTRACT Hydrangea macrophylla is an exotic plant, popularly known as Hydrangea, and cultivated in several parts of the world as an ornamental plant and, in Rio Grande do Sul [Brazil], the tourist cities Canela, Gramado and São Francisco de Paula are part of the Region of Hortensias. Many economic and cultural activities in these municipalities are based on the visual attractiveness of
The application of new molecular technology has greatly increased our understanding of the role of chromosomal change in plant evolution. There is now a broad database on genome size variation within and among species and a wide array of nuclear and cytoplasmic genetic markers. There is a variety of literatures addressing this subject but much of it is scattered. This book created a contemporary synthesis of work in this area and addresses issues such as herogeneity, polyploidy, chromosomal rearrangements within species and phenotypic consequences of chromosome doubling.
Randomly amplified polymorphic DNA (RAPD) markers were used to distinguish five remontant and two cold-hardy Hydrangea macrophylla (Thunb.) Ser. taxa. Eleven primers generated sufficient polymorphisms to separate these seven cultivars into two groups. One group contained ‘Penny Mac’, ‘Dooley’ and ‘Nikko Blue’, while the remaining taxa, ‘David Ramsay’, ‘Endless Summer’, ‘Decatur Blue’ and ‘Oak Hill’ were clustered in the second group. All hydrangea cultivars examined are closely related; the most divergent cultivars exhibited 88% similarity based on RAPD markers.
A new method called the neighbor-joining method is proposed for reconstructing phylogenetic trees from evolutionary distance data. The principle of this method is to find pairs of operational taxonomic units (OTUs [= neighbors]) that minimize the total branch length at each stage of clustering of OTUs starting with a starlike tree. The branch lengths as well as the topology of a parsimonious tree can quickly be obtained by using this method. Using computer simulation, we studied the efficiency of this method in obtaining the correct unrooted tree in comparison with that of five other tree-making methods: the unweighted pair group method of analysis, Farris's method, Sattath and Tversky's method, Li's method, and Tateno et al.'s modified Farris method. The new, neighbor-joining method and Sattath and Tversky's method are shown to be generally better than the other methods.
A method is presented by which the gene diversity (heterozygosity) of a subdivided population can be analyzed into its components, i.e., the gene diversities within and between subpopulations. This method is applicable to any population without regard to the number of alleles per locus, the pattern of evolutionary forces such as mutation, selection, and migration, and the reproductive method of the organism used. Measures of the absolute and relative magnitudes of gene differentiation among subpopulations are also proposed.