Genomic resource development for hydrangea (Hydrangea macrophylla (Thunb.) Ser.) – A transcriptome assembly and a high-density genetic linkage map

Authors: WU, XINGBO - North Carolina State University; Hulse-Kemp, Amanda; Wadl, Phillip; SMITH, ZACH - Beckman Coulter, Inc; MOCKAITIS, KEITHANNE - Corteva Agriscience; STATON, MARGARET - University Of Kentucky; Rinehart, Timothy - Tim; Alexander, Lisa

Submitted to: Horticulturae
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/2/2021
Publication Date: 2/5/2021
Citation: Wu, X., Hulse-Kemp, A.M., Wadl, P.A., Smith, Z., Mockaitis, K., Staton, M.E., Rinehart, T.A., Alexander, L.W. 2021. Genomic resource development for hydrangea (Hydrangea macrophylla (Thunb.) Ser.) – A transcriptome assembly and a high-density genetic linkage map. Horticulturae. https://doi.org/10.3390/horticulturae7020025.
DOI: https://doi.org/10.3390/horticulturae7020025

Interpretive Summary: Hydrangea (Hydrangea macrophylla) is an important ornamental crop that has been cultivated for more than 300 years. Despite its economic importance, advanced breeding methods for hydrangea have been limited by the lack of genetic resources for this species. Development of molecular markers and high-density genetic linkage maps are needed for genetic improvement of important traits in hydrangea such as flower form, continuous blooming, and disease resistance. To that end, USDA scientists in McMinnville, TN, Poplarville, MS, and Raleigh, NC, along with university partners, have developed the largest and most saturated genetic linkage map for hydrangea to date. The linkage map is comprised of a unique set of 1,767 markers distributed in 18 linkage groups, which is equal to the number of chromosomes in hydrangea. The molecular markers developed in this study greatly expand the current set of genetic resources in H. macrophylla and can be immediately used for both breeding improvement and genomic research. The linkage map developed here will be useful to further study traits of interest and provide a long-term base for genetic improvement of hydrangea to support continued profitability of the nursery and floriculture industries.

Technical 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 availability of genetic resources. Genetic linkage maps and subsequent trait mapping are essential tools to identify and make markers available for marker-assisted breeding. To expand the genetic resources of hydrangea, 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 for linkage mapping. From an analysis of 42,682 putative transcripts, 8,780 SSRs were identified and 1,535 were validated in the mapping parents. A total of 267 polymorphic SSRs were selected for linkage map construction. The GBS yielded 3,923 high quality single nucleotide polymorphisms (SNPs) in the mapping population, resulting in a total of 4,190 markers which were used to generate maps for each parent and a consensus map. The consensus linkage map contained 1,767 uniquely positioned markers (146 SSRs and 1,621 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-scare 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.