Natural rubber is a biopolymer with irreplaceable properties and is essential in tire manufacturing, many medical devices and numerous other applications. Nearly all natural rubber production comes from a single species, Hevea brasiliensis.
However, production of natural rubber from Hevea is faced with many challenges, including a long regeneration cycle, epidemic diseases, and unstable production costs. This has led to the exploration of alternative sources of rubber with similar quality to Hevea’s. One species that meets this criterion is Taraxacum kok-saghyz (TK), a perennial species of dandelion that can adapt to a wide geographical area and could be cultivated as an annual crop. However, TK does have several shortcomings which include reduced ability to compete with many weed species, poor stand establishment and lower yields in field production systems. In order to address these shortcomings, plant breeding may be used to select desirable traits such as larger root biomass, higher rubber concentration and yields. Other domestication traits, including apomixis, self-compatibility, large seeds, reduced seed shattering, delayed flowering, and herbicide resistance, may also be targeted.
Since the development of molecular markers in the 1980s, scientists have started to integrate molecular biotechnologies with conventional breeding, resulting in reduced breeding time and improved breeding efficiency. In order to accelerate breeding and domestication procedures in TK, an evaluation of heritability and genetic variance of each
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trait of interest is needed. In addition, a lack of current genomic resources in TK makes it imperative to develop and enrich the genetic and genomic resources, to lay a solid foundation for future marker-assisted selection and molecular breeding. Therefore, we conducted a one-year, multi-environment trial to preliminarily estimate the heritability of each rubber-related trait. Traits that were measured at each environment were plant weight, fresh root weight, dry root weight, rubber concentration, and rubber yield, with each one had a moderate level of heritability ranging from 0.51 to 0.61, indicating that there is at least some genetic regulation of each trait and that it should be possible to obtain genetic gain with selection for these traits. This is the first time in TK when the heritability of rubber-related traits was estimated in a well-designed experiment context. However, the limitations of poor growth of plants in the field and planting box resulted in small population size as well as many missing data. Moreover, one-year field trial may confound genetic effects with genotype by year effects and non-significant genetic effects were weighted positively as a proportion of total phenotypic variance. Therefore, the heritability in this dissertation may be overestimated. An inter-trait correlation identified that root biomass is more important when determining final rubber yield when compared to rubber concentration. Additionally, we developed the first TK transcriptome and identified homologues genes for 98% of previously characterized rubber-related genes in other rubber-producing species or Asteracae species. A total of 158 differentially expressed genes were identified between high rubber and low rubber plants. Over 21,000 single nucleotide polymorphisms (SNPs) were detected that differentiated between high and low rubber groups, from which the SNPs assigned on differentially expressed genes and rubber- related homologues genes were filtered.
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Forty-two SNPs assigned on the metabolism pathways related to rubber biosynthesis were developed as KASP markers, which were then used to screen an F1 progeny population derived from a high rubber and a low rubber plant. Combined with the one-year phenotypic data from the multi-environment field trial, the genotypic scores were used for a single marker-trait association analysis, where 7 out of 42 SNP markers were finally found to be significantly related to 3 out of 5 traits of interest. However, due to the small population size, skewing distribution of progeny genotypes occurred, which may result in somewhat statistical bias. Therefore, a larger population or a validation population are needed in future TK breeding efforts to accurately represent linkage between markers and the traits of interest. The environment of these identified SNP markers was tracked and can be further validated in future marker-assisted selection (MAS). Other than these developed SNPs, the ones detected from transcriptome analysis can also be used in future large-scale genotyping in mapping and/or validation populations. Overall speaking, the establishment of the KASP genotyping method will assist the development of a SNP genotyping platform for TK molecular breeding in near the future and will realize future MAS in a more labor- and cost-efficient way.
Not tied to molecular breeding, colchicine-induced polyploid production was also done to improve rubber concentration in TK. We found an increase in rubber concentration and a decrease in inulin concentration in tetraploid plants compared to diploid plants. However, no change in rubber production per root was observed. This may be due to the lagging poisoning effects of the colchicine treatments because root stunting also was observed in diploids after colchicine treatment. We developed a highly efficient pre- screening methodology based on the abnormal leaf morphology and can select putative
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tetraploid seedlings with a high success rate. This will greatly reduce the time and genotypes moving to polyploid confirmation procedures versus using flow cytometry. Optimal conditions for TK tetraploid induction were established. The increase of rubber concentration in TK tetraploids may provide a promising breeding future for TK if root growth recovers or is enhanced in progeny.
Collectively, this research enriches current genomic resources in TK and explores the genetic parameters of traits of interest, providing breeders with decision-making information and reasonable breeding targets. With the rapid development of next- generation sequencing (NGS) strategies and SNP marker genotyping platforms, MAS may prove useful in TK to accelerate breeding and domestication procedures. In addition, the development of genetic engineering biotechnologies (e.g. CRISPR/Cas9) may also be integrated in MAS to contribute to, or create, novel traits when accelerating TK breeding and domestication. However, more work is needed to fully dissect genetic components controlling rubber production. This includes well-developed mapping populations and validation populations, a more effective and efficient phenotyping strategy, and well- designed analysis pipelines for quantitative trait loci (QTL) mapping or genome-wide association analysis (GWAS).