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

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.