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

Marcin Nowicki,Margaret E Staton,Denita Hadziabdic,Sarah L Boggess,Helge Fluess,Yichen Zhao,Logan C Houston,Robert N Trigiano,Miriam Payá-Milans

doi:10.1038/s41598-019-38532-8

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.

Highlights

The growing human population has generated an increased demand for resources, including rubber, a substrate used for over 40,000 commercial products[1] (Supplementary Fig. S1)
Taraxacum kok-saghyz (TKS): Population genetics analyses. genomic simple sequence repeats markers (gSSRs): Analysis of TKS spatial fixation genetics indices, Multi-locus genotype (MLG) networks, and population structure: Our results suggest no significant deviations from the Hardy-Weinberg equilibrium (HWE) across the 25 gSSR markers used to analyze the TKS populations (Supplementary Fig. S2) despite low sampling
We developed a set of genomic SSRs based on our de novo sequencing of TKS and utilized them for evaluating the genetic diversity of TKS germplasm

Summary

Introduction

The growing human population has generated an increased demand for resources, including rubber, a substrate used for over 40,000 commercial products[1] (Supplementary Fig. S1). The TKS rubber is of particular interest to the tire industry due to its high molecular weight (polymer index) and fast generation time (six months in TKS vs seven years in Hevea), albeit with a comparatively higher content of allergenic proteins[1,2,3] Each of these species could be grown in areas complementary to the Hevea palm (24°S through 23°N7) with latitudes reaching as high as temperate zones (P. argentatum: 21°N through 37°N; F. elastica: 10°S through 35°N; TKS: 35°N through at least 45°N). The tire industry reported in their very first uses of TKS rubber that the tires “differed but little, according to their mechanical characteristics, from those made from imported natural rubber9” (citing[10]) It offers an accessory gain of inulin used in the manufacturing of numerous commercial products[11,12,13,14].

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