Taraxacum kok-saghyz (rubber dandelion) genomic microsatellite loci reveal modest genetic diversity and cross-amplify broadly to related species

Abstract

Taraxacum kok-saghyz (TKS) carries great potential as alternative natural rubber source. To better inform future breeding efforts with TKS and gain a deeper understanding of its genetic diversity, we utilized de novo sequencing to generate novel genomic simple sequence repeats markers (gSSRs). We utilized 25 gSSRs on a collection of genomic DNA (gDNA) samples from germplasm bank, and two gDNA samples from historical herbarium specimens. PCR coupled with capillary electrophoresis and an array of population genetics tools were employed to analyze the dataset of our study as well as a dataset of the recently published genic SSRs (eSSRs) generated on the same germplasm. Our results using both gSSRs and eSSRs revealed that TKS has low- to- moderate genetic diversity with most of it partitioned to the individuals and individuals within populations, whereas the species lacked population structure. Nineteen of the 25 gSSR markers cross-amplified to other Taraxacum spp. collected from Southeastern United States and identified as T. officinale by ITS sequencing. We used a subset of 14 gSSRs to estimate the genetic diversity of the T. officinale gDNA collection. In contrast to the obligatory outcrossing TKS, T. officinale presented evidence for population structure and clonal reproduction, which agreed with the species biology. We mapped the molecular markers sequences from this study and several others to the well-annotated sunflower genome. Our gSSRs present a functional tool for the biodiversity analyses in Taraxacum, but also in the related genera, as well as in the closely related tribes of the Asteraceae.

Development and Characterization of 15 Novel Genomic SSRs for Viburnum farreri

“…[AT]n was the most (179,546 SSRs) commonly found motif. These results are similar to other gSSR studies developed from NGS data, including [AT]n as the most common di-nucleotide repeat and [GC]n being the least common [45,46]. Primer pairs were developed for 101,174 SSRs including 83,687 di-, 7,996 tri-, and 9,491 tetra-nucleotide repeats.…”

Microsatellite Loci Reveal Genetic Diversity of Asian Callery Pear (Pyrus calleryana) in the Species Native Range and in the North American Cultivars

“…The use of simple sequence repeats (microsatellites; SSRs) in population genetics and phylogenetics provides a more reliable interpretation of genetic diversity than other arbitrary markers such as random amplified polymorphic DNAs (RAPDs) [23,24]. SSRs, highly informative and multi-allele genetic markers, are experimentally reproducible and transferable among closely related species [25]. The presence of multiple alleles at an SSR locus makes SSRs more informative than other molecular markers, including SNPs [26].…”

Natural rubber biosynthesis in plants, the rubber transferase complex, and metabolic engineering progress and prospects

“…The triploid, apomictic T. brevicorniculatum Koroleva (TB), a vigorous dandelion often co‐located with T. kok‐saghyz , has proved useful as an analog for T. kok‐saghyz because it is much less variable and produces some rubber. Both species have been used for rapid genetic analysis and gene function studies in recent years (Collins‐Silva et al ., ; van Deenen et al ., ; Hillebrand et al ., ; Lin et al ., ; Nowicki et al ., ; Post et al ., ; Schmidt et al ., ; Tata et al ., ).…”