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

Abstract

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.

Comparative Transcriptome Analysis Unveils the Molecular Mechanism Underlying Sepal Colour Changes under Acidic pH Substratum in Hydrangea macrophylla

“…The majority of the species in the genus are shrubs; however, there are some arboreal forms, such as, H. japonica , and evergreen climbers, such as H. petiolaris . Because of their characteristic umbellate inflorescences, many of these species are sold as cut flowers [ 10 ]. According to the University of Tennessee, hydrangea was the second most widespread deciduous shrub in all horticulture markets in the United States in 2014 [ 11 ], with sales of more than 10 million plants (USD 91.2 million).…”

Breeding, Genetics, and Genomics of Ornamental Plants

“…More specifically, the objectives of this SI were to report novel genes; their functionality and cross talks with other genes; breeding activities, including the development and characterization of new cultivars; and the development of genomic resources, including high-density linkage map and transcriptome, and their applications in breeding. This SI gathered six research papers [1][2][3][4][5][6] based on a wide array of herbaceous and perennial ornamental crops in the fields of gene identification and interactions, ploidy manipulation, and genomics research.…”

“…Despite high demand and global production, ornamental crops fall behind in the public availability of genomic resources owing to their high level of heterozygosity, varying ploidy level within the same species and wide range of complex genome sizes. Recently, efforts are being made to develop genomic resources in some widely cultivated and economically important ornamental crops, such as hydrangea (Hydrangea macrophylla) [2]. Hydrangea, being a woody ornamental, requires a longer conventional breeding time.…”

“…The development and incorporation of molecular markers can reduce generation interval times and expedite breeding using marker-assisted selection. Wu et al used genome reduction techniques, such as genotyping by sequencing (GBS) and transcriptome sequencing, to identify simple sequence repeat (SSR) and single nucleotide polymorphism (SNP) markers and construct a linkage map in hydrangea [2]. Genome reduction techniques, such as GBS and transcriptome sequencing, can be used to identify SNPs and develop molecular markers to facilitate marker-assisted selection in ornamental crops with highly heterozygous, complex, and relatively large genome sizes.…”

“…When reference genomes or physical maps are not available, linkage maps are used in identifying genomic regions conferring phenotypic traits of interest and developing molecular markers. Wu et al constructed a linkage map consisting of 18 linkage groups incorporating 1621 SNPs and 146 SSRs [2]. These efforts help in realizing the application of marker-assisted and genome-informed selections in ornamental crops in addition to facilitating QTL mapping, association mapping, gene identification and gene cloning.…”