Brian J. Iaffaldano

Genome size variation among common dandelion accessions informs their mode of reproduction and suggests the absence of sexual diploids in North America

Apomixis is the ability of plants to produce asexual seeds, which are clones of the mother plant. The phenomenon of apomixis is tightly linked to ploidy, where diploids lack apomixis and reproduce sexually, while higher ploidy levels can exhibit apomixis. Taraxacum F.H.Wigg. species (dandelions) commonly exhibit apomixis; however, only limited studies have evaluated genome size variation of the iconic weedy dandelion, Taraxacum officinale F.H.Wigg. (common dandelion), particularly in North America. To evaluate the ploidy and reproductive biology of common dandelion, we created a global collection, with an emphasis on North America and determined genome size by evaluating seeds with flow cytometry. A total of 635 accessions were screened, and with the exception of two accessions from Germany and Austria, all were found to exclusively contain polyploid seed. The mode of reproduction of a sample of 96 of these accessions was observed by conducting emasculations. Our results indicate that the diploid, sexual cytotype of common dandelion may be absent in North America, while diploids were found in previously described areas of Central Europe. This suggests that the clonal lineages of common dandelion in North America may largely be derivative from apomictic plants introduced from abroad. Furthermore, if all North American common dandelion is apomictic, it may be unreceptive to pollen, which may isolate it from other dandelion species and inform the potential for gene flow.

Analysis of the first Taraxacum kok-saghyz transcriptome reveals potential rubber yield related SNPs

Taraxacum kok-saghyz (TK) is a potential alternative crop for natural rubber (NR) production, due to its high molecular weight rubber, short breeding cycle, and diverse environmental adaptation. However, improvements in rubber yield and agronomically relevant traits are still required before it can become a commercially-viable crop. An RNA-Seq based transcriptome was developed from a pool of roots from genotypes with high and low rubber yield. A total of 55,532 transcripts with lengths over 200 bp were de novo assembled. As many as 472 transcripts were significantly homologous to 49 out of 50 known plant putative rubber biosynthesis related genes. 158 transcripts were significantly differentially expressed between high rubber and low rubber genotypes. 21,036 SNPs were different in high and low rubber TK genotypes. Among these, 50 SNPs were found within 39 transcripts highly homologous to 49 publically-searched rubber biosynthesis related genes. 117 SNPs were located within 36 of the differentially expressed gene sequences. This comprehensive TK transcriptomic reference, and large set of SNPs including putative exonic markers associated with rubber related gene homologues and differentially expressed genes, provides a solid foundation for further genetic dissection of rubber related traits, comparative genomics and marker-assisted selection for the breeding of TK.

Variance, Inter-Trait Correlation, Heritability, and Marker-Trait Association of Rubber Yield-Related Characteristics in Taraxacum kok-saghyz

Rubber dandelion (Taraxacum kok-saghyz or TK) is a potential industrial crop species that can produce high-quality natural rubber in its roots. The present study estimated trait variance, inter-trait correlation, and entry-mean heritability for rubber yield-related traits and analyzed associations between these traits and 42 single-nucleotide polymorphism (SNP) markers. A trial was conducted at three environments to assess a biparental progeny of 66 F1 full-sibs, in a randomized complete block design (RCBD) with two replicates. Significant correlations, broad ranges of variation, and significant genotypic variance components were identified for five measured phenotypic traits. Moderate broad-sense heritability on an entry-mean heritability estimates (0.51–0.61) were obtained for five rubber yield-related traits based on a 1-year trial. However, the broad-sense heritability in general sense ranged from 0.09 to 0.15 depending on the trait. Two linkage groups were identified. Association analysis identified seven significant marker-trait gene associations, and only one marker was related to two traits. The implications of trait correlations and heritability for selection and improvement are discussed.

Molecular Identification and Characterization of Two Rubber Dandelion Amalgaviruses

The Amalgaviridae family is composed of persistent viruses that share the genome architecture of Totiviridae and gene evolutionary resemblance to Partitiviridae. A single Amalgavirus genus has been assigned to this family, presenting only four recognized species, corresponding to plant infecting viruses with dsRNA monopartite genomes of ca. 3.4 kb. Here, we present the genomic identification and characterization of two novel viruses detected in rubber dandelion (Taraxacum kok-saghyz). The sequenced isolates presented genomes of 3,409 and 3,413 nt long, including two partially overlapping ORFs encoding a putative coat protein and an RNA-dependent RNA polymerase (RdRP). Phylogenetic insights based on the detected virus sequences suggest them to be members of two new species within the Amalgavirus genus. Multiple independent RNAseq data suggest that the identified viruses have a dynamic distribution and low relative RNA levels in infected plants. Virus presence was not associated with any apparent symptoms on the plant hosts. We propose the names rubber dandelion latent virus 1 & 2 to the detected amalgaviruses; the first viruses to be associated to this emergent and sustainable natural rubber crop.