Identification of Transposable Elements in Conifer and Their Potential Application in Breeding

Wang, Junhui; Lu, Nan; Yi, Fei; Xiao, Yumei

doi:10.1177/1176934320930263

Cited by 13 publications

(11 citation statements)

References 28 publications

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“…Responsible for major changes in the genetic architecture (e.g., rearrangements, duplication, gene breaking, and the origin of new genes) (Bennetzen, 2005; Flagel and Wendel, 2009; Lisch, 2013), TEs are usually neutral. However, such elements possess mutagenic potential due to epigenetic mechanisms and are able to alter regulatory networks and confer genetic adaptations, leading to important phenotypic variations (Lisch, 2013; Wei and Cao, 2016; Wu et al, 2020); this has currently received great attention in genetic improvement programs for several species (Domínguez et al, 2020; Lee et al, 2006; Wang et al, 2020). In Hbr, Wu et al (2020) showed that TEs located in gene regulatory regions in Hbr were involved in latex production through cis regulation, which would explain the differential gene expression among contrasting genotypes.…”

Section: Discussionmentioning

confidence: 99%

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Santos

Aono

Francisco

et al. 2022

Preprint

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The protein kinase (PK) superfamily constitutes one of the largest and most conserved protein families in eukaryotic genomes, comprising core components of signaling pathways in cell regulation. Despite its remarkable relevance, only a few kinase families have been studied in Hevea brasiliensis. A comprehensive characterization and global expression analysis of the PK superfamily, however, is currently lacking. In this study, we identified and characterized the entire set of PKs, also known as the kinome, present in the Hevea genome. A total of 1,809 PK genes were identified using the current reference genome assembly at the scaffold level, and 1,379 PK genes were identified using the latest chromosome-level assembly and combined into a single set of 2,842 PKs. These proteins were further classified into 20 different groups and 122 families, exhibiting high compositional similarities among family members and with two phylogenetically close species (Manihot esculenta and Ricinus communis). Different RNA-sequencing datasets were employed to identify tissue-specific expression patterns and potential correspondences between different rubber tree genotypes. In addition, coexpression networks under several abiotic stress conditions, such as cold, drought and latex overexploitation, were employed to elucidate associations between families and tissues/stresses. Through the joint investigation of tandemly duplicated kinases, transposable elements, gene expression patterns, and coexpression events, we provided insights into the understanding of the cell regulation mechanisms in response to several conditions, which can often lead to a significant reduction in rubber yield.

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Section: Discussionmentioning

confidence: 99%

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Santos

Aono

Francisco

et al. 2022

Preprint

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“…In rubber trees, TEs may be related to the differential expression observed in some commercial clones, affecting important processes such as rubber production (Wu et al, 2020). As pointed out by Wang et al (2020), the identification of TEs associated with functional genes related to important characteristics suggest that they can be used as molecular markers in MAS, contributing significantly to the genetic improvement of woody trees. In this sense, our findings supply a wide range of genomic resources for breeding.…”

Section: Discussionmentioning

confidence: 99%

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

Aono

Silva

et al. 2021

Preprint

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Hevea brasiliensis (rubber tree) is a large tree species of the Euphorbiaceae family with inestimable economic importance. Rubber tree breeding programs currently aim to improve growth and production, and the use of early genotype selection technologies can accelerate such processes, mainly with the incorporation of genomic tools, such as marker-assisted selection (MAS). However, few quantitative trait loci (QTLs) have been used successfully in MAS for complex characteristics. Recent research shows the efficiency of genome-wide association studies (GWAS) for locating QTL regions in different populations. In this way, the integration of GWAS, RNA-sequencing (RNA-Seq) methodologies, coexpression networks and enzyme networks can provide a better understanding of the molecular relationships involved in the definition of the phenotypes of interest, supplying research support for the development of appropriate genomic based strategies for breeding. In this context, this work presents the potential of using combined multiomics to decipher the mechanisms of genotype and phenotype associations involved in the growth of rubber trees. Using GWAS from a genotyping-by-sequencing (GBS) Hevea population, we were able to identify molecular markers in QTL regions with a main effect on rubber tree plant growth under constant water stress. The underlying genes were evaluated and incorporated into a gene coexpression network modelled with an assembled RNA-Seq-based transcriptome of the species, where novel gene relationships were estimated and evaluated through in silico methodologies, including an estimated enzymatic network. From all these analyses, we were able to estimate not only the main genes involved in defining the phenotype but also the interactions between a core of genes related to rubber tree growth at the transcriptional and translational levels. This work was the first to integrate multiomics analysis into the in-depth investigation of rubber tree plant growth, producing useful data for future genetic studies in the species and enhancing the efficiency of the species improvement programs.

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“…In particular, changes in methylation of transposable elements can be responsible for the variability of traits [157]. This is especially important for conifers, whose large genomes contain a high number of transposable elements, which provide vast potential genetic resources [158].…”

Section: Perspectives Of Gs In Forestrymentioning

confidence: 99%

Genomic Selection for Forest Tree Improvement: Methods, Achievements and Perspectives

Lebedev

Лебедева

Chernodubov

et al. 2020

Forests

100

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The breeding of forest trees is only a few decades old, and is a much more complicated, longer, and expensive endeavor than the breeding of agricultural crops. One breeding cycle for forest trees can take 20–30 years. Recent advances in genomics and molecular biology have revolutionized traditional plant breeding based on visual phenotype assessment: the development of different types of molecular markers has made genotype selection possible. Marker-assisted breeding can significantly accelerate the breeding process, but this method has not been shown to be effective for selection of complex traits on forest trees. This new method of genomic selection is based on the analysis of all effects of quantitative trait loci (QTLs) using a large number of molecular markers distributed throughout the genome, which makes it possible to assess the genomic estimated breeding value (GEBV) of an individual. This approach is expected to be much more efficient for forest tree improvement than traditional breeding. Here, we review the current state of the art in the application of genomic selection in forest tree breeding and discuss different methods of genotyping and phenotyping. We also compare the accuracies of genomic prediction models and highlight the importance of a prior cost-benefit analysis before implementing genomic selection. Perspectives for the further development of this approach in forest breeding are also discussed: expanding the range of species and the list of valuable traits, the application of high-throughput phenotyping methods, and the possibility of using epigenetic variance to improve of forest trees.

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Identification of Transposable Elements in Conifer and Their Potential Application in Breeding

Cited by 13 publications

References 28 publications

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

The rubber tree kinome: genome-wide characterization and insights into coexpression patterns associated with abiotic stress responses

Unravelling Rubber Tree Growth by Integrating GWAS and Biological Network-Based Approaches

Genomic Selection for Forest Tree Improvement: Methods, Achievements and Perspectives

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