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Dryad

Microsatellite exploration in the climbing hydrangea (Hydrangea petiolaris Siebold & Zucc.) transcriptome: A resource for population genetics and functional genomics

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Jan 22, 2024 version files 66.01 MB

Abstract

Background

Hydrangea petiolaris Siebold & Zucc., also known as climbing hydrangea, is a vine native to the woodlands of Korea, Japan, and Sakhalin Island. It is an economically important ornamental plant with fertile and sterile flowers. Despite the recent increase in Hydrangea breeding and interest in germplasm conservation, relatively little is known about the relationships between Hydrangea species.

Results

We employed Illumina NovaSeq 6000 sequencing technology to generate a total of 39,945,480 reads, which were assembled into 137,715 contigs. A total of 109,092 filtered transcripts were used to identify microsatellites, and 54,587 microsatellite repeat motifs were revealed within 33,556 contigs. Among these, 4,510 transcripts harboring microsatellites had Gene Ontology annotations, and numerous microsatellite-containing transcripts exhibited associations with genes, including those encoding PPR proteins, aldehyde dehydrogenases, and bHLH transcription factors, related to the restorer of fertility (Rf) genes, which play a critical role in restoring fertility in plants with cytoplasmic male sterility. Validation of transcriptomic SSR markers demonstrated high levels of polymorphism, revealing significant genetic diversity within populations. However, null alleles and deviations from Hardy‒Weinberg equilibrium at specific loci suggested caution in genotyping accuracy. Population-level analysis disclosed high genetic differentiation and distinct clustering of populations.

Conclusions

The H. petiolaris transcriptomic SSR markers offer valuable insight for gaining insights into the population genetics, evolutionary background, and practical strategies for conserving this species. Moreover, the microsatellite loci we have identified and their associations with annotated genes hold promise for creating functional markers specifically tailored for H. petiolaris. These markers include valuable resources of transcriptomic SSR markers suitable for population genetic investigations and have a reasonable degree of applicability across different taxa.