Evolutionary transgenomics: prospects and challenges

Correa, Raúl; Baum, David A.

doi:10.3389/fpls.2015.00858

Cited by 5 publications

(2 citation statements)

References 67 publications

(86 reference statements)

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“…Nitrogen (N) is one of the essential elements required by plants and plays key roles in their growth, development and morphological composition [ 1 , 2 ]. In most higher plants, nitrate (NO 3 − ) and ammonium (NH 4 + ) are the main forms of inorganic N resources absorbed by plant roots from the soil [ 3 , 4 ].…”

Section: Introductionmentioning

confidence: 99%

Nitrate/ammonium-responsive microRNA-mRNA regulatory networks affect root system architecture in Populus × canescens

Zhou

2022

BMC Plant Biol

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Background Nitrate (NO3−) and ammonium (NH4+) are the primary forms of inorganic nitrogen (N) taken up by plant roots, and a lack of these N sources commonly limits plant growth. To better understand how NO3− and NH4+ differentially affect root system architecture, we analyzed the expression profiles of microRNAs and their targets in poplar roots treated with three forms of nitrogen S1 (NO3−), S2 (NH4NO3, normal), and S3 (NH4+) via RNA sequencing. Results The results revealed a total of 709 miRNAs. Among them, 57 significantly differentially expressed miRNAs and 28 differentially expressed miRNA-target pairs showed correlated expression profiles in S1 vs. S2. Thirty-six significantly differentially expressed miRNAs and 12 differentially expressed miRNA-target pairs showed correlated expression profiles in S3 vs. S2. In particular, NFYA3, a target of upregulated ptc-miR169i and ptc-miR169b, was downregulated in S1 vs. S2, while NFYA1, a target of upregulated ptc-miR169b, was downregulated in S3 vs. S2 and probably played an important role in the changes in root morphology observed when the poplar plants were treated with different N forms. Furthermore, the miRNA-target pairs ptc-miR169i/b-D6PKL2, ptc-miR393a-5p-AFB2, ptc-miR6445a-NAC14, ptc-miR172d-AP2, csi-miR396a-5p_R + 1_1ss21GA-EBP1, ath-miR396b-5p_R + 1-TPR4, and ptc-miR166a/b/c-ATHB-8 probably contributed to the changes in root morphology observed when poplar plants were treated with different N forms. Conclusions These results demonstrate that differentially expressed miRNAs and their targets play an important role in the regulation of the poplar root system architecture by different N forms.

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Section: Introductionmentioning

confidence: 99%

Nitrate/ammonium-responsive microRNA-mRNA regulatory networks affect root system architecture in Populus × canescens

Zhou

2022

BMC Plant Biol

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“…The test for sufficiency can be extended to a forward screen to find novel genes contributing to morphological divergence between species, as initially proposed under the term transgenomics (Baum, 2002 ; Correa and Baum, 2015 ). A proof-of-concept study reported the introduction of ca.…”

Section: Other Notable Applicationsmentioning

confidence: 99%

Interspecies Gene Transfer as a Method for Understanding the Genetic Basis for Evolutionary Change: Progress, Pitfalls, and Prospects

Nikolov

Tsiantis

2015

Front. Plant Sci.

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The recent revolution in high throughput sequencing and associated applications provides excellent opportunities to catalog variation in DNA sequences and gene expression between species. However, understanding the astonishing diversity of the Tree of Life requires understanding the phenotypic consequences of such variation and identification of those rare genetic changes that are causal to diversity. One way to study the genetic basis for trait diversity is to apply a transgenic approach and introduce genes of interest from a donor into a recipient species. Such interspecies gene transfer (IGT) is based on the premise that if a gene is causal to the morphological divergence of the two species, the transfer will endow the recipient with properties of the donor. Extensions of this approach further allow identifying novel loci for the diversification of form and investigating cis- and trans-contributions to morphological evolution. Here we review recent examples from both plant and animal systems that have employed IGT to provide insight into the genetic basis of evolutionary change. We outline the practice of IGT, its methodological strengths and weaknesses, and consider guidelines for its application, emphasizing the importance of phylogenetic distance, character polarity, and life history. We also discuss future perspectives for exploiting IGT in the context of expanding genomic resources in emerging experimental systems and advances in genome editing.

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RETRACTED ARTICLE: An assessment of transgenomics as a tool for gene discovery in Populus euphratica Oliv.

et al. 2018

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Transgenomics for gene discovery in Populus euphratica. Transgenomics, a member of the omics family of methodologies, is characterized as the introduction of DNA from one organism into another on a genome-wide scale followed by the identification of recipients with altered phenotypes. This strategy allows investigators to identify the gene(s) involved in these phenotypic changes. It is particularly promising for woody plants that have a long life cycle and for which molecular tools are limited. In this study, we constructed a large-insert binary bacterial artificial chromosome library of Populus euphratica, a stress-tolerant poplar species, which included 55,296 clones with average insert sizes of about 127 kb. To date, 1077 of the clones have been transformed into Arabidopsis thaliana via Agrobacterium by the floral dip method. Of these, 69 transgenic lines showed phenotypic changes represented by diverse aspects of plant form and development, 22 of which were reproducibly associated with the same phenotypic change. One of the clones conferring transgenic plants with increased salt tolerance, 002A1F06, was further analyzed and the 127,284 bp insert in this clone harbored eight genes that have been previously reported to be involved in stress resistance. This study demonstrates that transgenomics is useful in the study of functional genomics of woody plants and in the identification of novel gene(s) responsible for economically important traits. Thus, transgenomics can also be used for validation of quantitative trait loci mapped by molecular markers.

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Evolutionary transgenomics: prospects and challenges

Cited by 5 publications

References 67 publications

Nitrate/ammonium-responsive microRNA-mRNA regulatory networks affect root system architecture in Populus × canescens

Nitrate/ammonium-responsive microRNA-mRNA regulatory networks affect root system architecture in Populus × canescens

Interspecies Gene Transfer as a Method for Understanding the Genetic Basis for Evolutionary Change: Progress, Pitfalls, and Prospects

RETRACTED ARTICLE: An assessment of transgenomics as a tool for gene discovery in Populus euphratica Oliv.

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