Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants

Background: Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown. Results: Using Vitis vinifera embryogenic callus, we explored the impact of biotic stressors on transposon transcription through the exposure of the callus to live cultures of an endemic grapevine yeast, Hanseniaspora uvarum. We found that only 1.7–2.5% of total annotated TE loci were transcribed, of which 5–10% of these were full-length, and the expressed TE loci exhibited a strong location bias towards expressed genes. These trends in transposon transcription were also observed in RNA-seq data from Arabidopsis thaliana wild-type plants but not in epigenetically compromised Arabidopsis ddm1 mutants. Moreover, differentially expressed TE loci in the grapevine tended to share expression patterns with co-localised differentially expressed genes. Utilising nanopore cDNA sequencing, we found a strong correlation between the inclusion of intronic TEs in gene transcripts and the presence of premature termination codons in these transcripts. Finally, we identified low levels of full-length transcripts deriving from structurally intact TE loci in the grapevine model. Conclusion: Our observations in two disparate plant models representing clonally and seed propagated plant species reveal a closely connected transcriptional relationship between TEs and co-localised genes, particularly when epigenetic silencing is not compromised. We found that the stress treatment alone was insufficient to induce large-scale full-length transcription from structurally intact TE loci, a necessity for non-autonomous and autonomous mobilisation

Comprehensive analysis of both long and short read transcriptomes of a clonal and a seed-propagated model plant species reveal the prerequisites for transcriptional activation of autonomous and non-autonomous transposons in plants

Transposable element (TE) transcription is a precursor to its mobilisation in host genomes. However, the characteristics of expressed TE loci, the identification of self-competent transposon loci contributing to new insertions, and the genomic conditions permitting their mobilisation remain largely unknown

Elevated transcription of transposable elements is accompanied by het-siRNA-driven de novo DNA methylation in grapevine embryogenic callus

Background: Somatic variation is a valuable source of trait diversity in clonally propagated crops. In grapevine, which has been clonally propagated worldwide for centuries, important phenotypes such as white berry colour are the result of genetic changes caused by transposable elements. Additionally, epiallele formation may play a role in determining geo-specific (‘terroir’) differences in grapes and thus ultimately in wine. This genomic plasticity might be co-opted for crop improvement via somatic embryogenesis, but that depends on a species-specific understanding of the epigenetic regulation of transposable element (TE) expression and silencing in these cultures. For this reason, we used whole-genome bisulphite sequencing, mRNA sequencing and small RNA sequencing to study the epigenetic status and expression of TEs in embryogenic callus, in comparison with leaf tissue. Results: We found that compared with leaf tissue, grapevine embryogenic callus cultures accumulate relatively high genome-wide CHH methylation, particularly across heterochromatic regions. This de novo methylation is associated with an abundance of transcripts from highly replicated TE families, as well as corresponding 24 nt heterochromatic siRNAs. Methylation in the TE-specific CHG context was relatively low over TEs located within genes, and the expression of TE loci within genes was highly correlated with the expression of those genes. Conclusions: This multi-‘omics analysis of grapevine embryogenic callus in comparison with leaf tissues reveals a high level of genome-wide transcription of TEs accompanied by RNA-dependent DNA methylation of these sequences in trans. This provides insight into the genomic conditions underlying somaclonal variation and epiallele formation in plants regenerated from embryogenic cultures, which is an important consideration when using these tissues for plant propagation and genetic improvement

The addition of an organosilicone surfactant to Agrobacterium suspensions enables efficient transient transformation of in vitro grapevine leaf tissue at ambient pressure

Transient Agrobacterium-mediated transformation of plant tissue has become a standard technique for rapid in vivo analysis of gene expression and function. In grapevine, the efficacy of transient leaf transformation is limited by the ability of bacterial suspensions to penetrate into the tissue. Current protocols therefore use the temporary application of a vacuum or site-specific syringe infiltration to improve transformation efficiencies. We show that supplementing Agrobacterium suspensions with a commercially available organosilicone surfactant (Pulse® penetrant) elevates transformation efficiency at ambient pressure. The transformation efficiency of leaf tissue of in vitro grown Vitis vinifera ‘Sauvignon blanc’ plantlets submerged in Agrobacterium suspension was increased 65-fold by the addition of Pulse® penetrant at low concentration (0.03 % v/v). A quick and precise determination of transformation efficiency was achieved by measuring red pigmentation of cells transiently transformed with the transcriptional activator of anthocyanin biosynthesis, VvMYBA1. A variable increase in transformation efficiency was also observed in eight commercial wine grape varieties and one rootstock variety. Pulse® penetrant can therefore be used to achieve transient transformation of grapevine by simply dipping in vitro leaf material into bacterial suspension culture

Harnessing the value of bud-sport mutations

Despite a low contribution by volume to the global market, the New Zealand wine industry has managed to build a respected international reputation. This has largely been achieved by exporting wines that present flavour profiles that are both interesting and sometimes unusual for their variety. By taking advantage of the diversity of flavours that can be obtained from established varieties, the local wine industry has been able to place itself at the high-value end of the market. However, in order to maintain this reputation as the industry matures, a continued effort to offer unique and diverse wine styles will be essential

The effect of pre-budbreak cane girdling on the physical and phenological development of the inner and outer arm in Vitis vinifera L. 'Sauvignon blanc' inflorescence structures

The development of inflorescence primordia (IP) into floral bearing structures is influenced by many environmental and genetic factors. We hypothesise that carbohydrate (CHO) availability at budbreak (BB) has a strong influence on IP development, especially during the initial stages of shoot growth when pre-formed IP emerge from dormant buds and may be dependent on reserve CHOs for further branching and development. Carbohydrate availability to developing grapevine buds (Vitis vinifera L. 'Sauvignon blanc') was manipulated by girdling canes two weeks before BB. Dates of flowering, flower number, berry number and grape berry soluble solids (SS) were measured for the inner and outer arm bunch components of basal and apical bunches separately. Restricting pre-BB CHOs resulted in the abortion of some pre-formed inflorescences and reduced branching of the inflorescences that did develop. In general, berry SS were greatest for the basal inner arm, followed by those of the apical bunch inner arm, then those of the basal bunch outer arm, then lastly by those of the apical bunch outer arm. However, this was influenced by the relative berry numbers between the inner and outer arm. Bunches with more similar berry numbers on the inner and outer arms had more synchronous flowering and uniform SS, where the differences in SS were largely a reflection of the timing of flowering of the various inflorescence components and may be an important source of variation in SS within a vine at harvest

Utilisation of transposons to alter genomic and epigenomic diversity in crop plants

Plant genetic improvement relies on the presence of a wide range of genetic variation in both form and function to deliver phenotypes of importance to agriculture and horticulture. Often, however, this pool of important allelic variation is constrained either through previous breeding efforts or a lack of suitable populations from which to draw allelic diversity to generate new phenotypes for key agronomic and quality traits. With the democratisation of sequencing technologies and the concomitant drop in sequencing costs an ever growing range of plant genomes are being sequenced uncovering the underlying drivers of genetic variation. Among the many forms of genome variation contributing to phenotype, it is becoming clear that transposons are a key driver of genetic and phenotypic diversity in crop systems. Aside from obvious roles in loss-offunction mutation through insertion, transposons have also been shown to be potent manipulators of gene regulatory networks via genetic and epigenetic pathways. Our work has focused on understanding the roles of transposons in 2 crop plants, grapevine (Vitis Vinifera), and Hops (Humulus lupulus) as well as Pilosella (Mendel’s Hawkweed) and the native Australian tobacco, Nicotiana benthamiana. We have recently shown transposons are the causative agent for parthenogenesis in Piosella. In addition we have proven it is possible to elevate and capture new transposable element activity in crop plants and are currently evaluating the impact of this activity in genetic, epigenetic and phenotypic contexts. We present a case for the importance of transposons in providing new and novel sources of (epi)genetic variation, which in combination with high throughput sequencing allows both the identification of novel insertions and their exploitation of insertions impacting phenotype, to drive genetic gain in a wide range of plant species

Genetic parameters for fruit mineral content in an interspecific pear (Pyrus spp.) population

There is a lack of data and information on mineral content in pear fruit and none on the genetic parameters related to these individual elements. The aim of this research was to report mineral composition of pear fruit and to determine the quantitative genetic parameters of mineral content in fruit from interspecific pear populations. There was a high genetic component involved in the accumulation of boron and aluminium in the fruit, with heritabilities of as much as 0.72. Iron had a positive genetic correlation with accumulation of zinc (0.72) and sulphur (0.71), while chromium had a negative correlation with nickel (−0.77), phosphorus (−0.70) and magnesium (−0.4) accumulation. Parents of the same origin (Asian or European) had similar estimated breeding values for total mineral content. Macro element mineral content of fruit was: 4% calcium, 13% phosphorus, 76% potassium, 5% magnesium and 2% sulphur and for micro element mineral content 39% boron, 12% iron, 8% zinc, 4% manganese, 7% copper, 0.4% chromium, 9% nickel and 21% aluminium

The vines are mutating. What does that mean for our industry?

Co-funding from New Zealand Wine, Plant and Food Research and Lincoln University has made possible research into a previously unknown type of genetic differences among the elite clones grown by the NZ wine industry