Impact of polyploidy on fertility variation of Mediterranean Arundo L. (Poaceae)

Hardion, Laurent; Verlaque, Régine; Rosato, Marcela; Rosselló, Josep A.; Vila, Bruno

doi:10.1016/j.crvi.2015.03.013

Cited by 27 publications

(38 citation statements)

References 41 publications

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“…Also the majority of the rice homologs of differentially expressed A. donax unigenes from the C 2 H 2 family (LOC_Os03g55540, LOC_Os03g13600, LOC_Os03g60570, LOC_Os09g38340) were previously identified as drought responsive [ 66 ], indicating their conserved role in Poaceae. Two among them and an additional C 2 H 2 gene not previously identified (LOC_Os03g10140, LOC_Os09g38340, LOC_Os09g38790) are known to control the vegetative to floral phase transition in monocots [ 67 , 68 ], indicating that responsiveness of C 2 H 2 genes to water deprivation may be relictual in A. donax : while other species from the Arundo genus are fertile and could benefit from accelerating seed setting as a drought-escape strategy, A. donax is fully sterile [ 69 ] and no clear selective advantage seems to be associated to this trait. Therefore, loss of function mutations of C 2 H 2 or other flowering time TFs could be interesting candidates to extend the vegetative phase and, thus, biomass accumulation in A. donax [ 24 ].…”

Section: Resultsmentioning

confidence: 99%

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq

Poli

Sablok

et al. 2016

Biotechnol Biofuels

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BackgroundArundo donax L. (Poaceae) is considered one of the most promising energy crops in the Mediterranean region because of its high biomass yield and low input requirements, but to date no information on its transcriptional responses to water stress is available.ResultsWe obtained by Illumina-based RNA-seq the whole root and shoot transcriptomes of young A. donax plants subjected to osmotic/water stress with 10 and 20 % polyethylene glycol (PEG; 3 biological replicates/organ/condition corresponding to 18 RNA-Seq libraries), and identified a total of 3034 differentially expressed genes. Blast-based mining of stress-related genes indicated the higher responsivity of roots compared to shoots at the early stages of water stress especially under the milder PEG treatment, with a majority of genes responsive to salt, oxidative, and dehydration stress. Analysis of gene ontology terms underlined the qualitatively different responses between root and shoot tissues. Among the most significantly enriched metabolic pathways identified using a Fisher’s exact test with FDR correction, a crucial role was played in both shoots and roots by genes involved in the signaling cascade of abscisic acid. We further identified relatively large organ-specific differences in the patterns of drought-related transcription factor AP2-EREBP, AUX/IAA, MYB, bZIP, C2H2, and GRAS families, which may underlie the transcriptional reprogramming differences between organs. Through comparative analyses with major Poaceae species based on Blast, we finally identified a set of 53 orthologs that can be considered as a core of evolutionary conserved genes important to mediate water stress responses in the family.ConclusionsThis study provides the first characterization of A. donax transcriptome in response to water stress, thus shedding novel light at the molecular level on the mechanisms of stress response and adaptation in this emerging bioenergy species. The inventory of early-responsive genes to water stress identified could constitute useful markers of the physiological status of A. donax and be a basis for the improvement of its productivity under water limitation. The full water-stressed A. donax transcriptome is available for Blast-based homology searches through a dedicated web server (http://ecogenomics.fmach.it/arundo/).Electronic supplementary materialThe online version of this article (doi:10.1186/s13068-016-0471-8) contains supplementary material, which is available to authorized users.

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Section: Resultsmentioning

confidence: 99%

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq

Poli

Sablok

et al. 2016

Biotechnol Biofuels

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“…MIR1430 family expansion may predate A . donax loss of fertility associated to polyploidization 69 , when transition to the reproductive phase likely still constituted a relevant stress-escape strategy for this species. Another possibility is that the likely lineage-specific expansion of MIR1430 gene family may be related to suppression of fungal resistance, as differential repression of NF-YA genes by MIR169 has been found to negatively regulate rice immunity against the blast fungus M .…”

Section: Discussionmentioning

confidence: 99%

In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.

Jike

Sablok

Bertorelle

et al. 2018

Sci Rep

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MicroRNAs (miRNAs) are small non-coding RNA molecules involved in the post-transcriptional regulation of gene expression in plants. Arundo donax L. is a perennial C3 grass considered one of the most promising bioenergy crops. Despite its relevance, many fundamental aspects of its biology still remain to be elucidated. In the present study we carried out the first in silico mining and tissue-specific characterization of microRNAs and their putative targets in A. donax. We identified a total of 141 miRNAs belonging to 14 families along with the corresponding primary miRNAs, precursor miRNAs and a total of 462 high-confidence predicted targets and novel target sites were validated by 5′-race. Gene Ontology functional annotation showed that miRNA targets are constituted mainly by transcription factors, but three of the newly validated targets are enzymes involved in novel functions like RNA editing, acyl lipid metabolism and post-Golgi trafficking. Folding variability of pre-miRNA loops and phylogenetic analyses indicate variable selective pressure acting on the different miRNA families. The set of miRNAs identified in this study will pave the road to further miRNA research in Arundo donax and contribute towards a better understanding of miRNA-mediated gene regulatory processes in other bioenergy crops.

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“…Although polyploidisation may have contributed to the emergence of different morphotypes, it may have only partially influenced the reproductive system and the lack of fertility. As pointed out by Hardion, Verlaque, Rosato, Rosselló, and Vila (), other factors may have induced the sterility in A. donax , such as the bioclimatic disequilibrium experienced during the spread to and through the Mediterranean.…”

Section: Discussionmentioning

confidence: 94%

Multiple evolutionary lineages detected in giant reed (Arundo donax L.): Applied and evolutionary perspectives

Zecca

Tommasi

Grassi

2020

Annals of Applied Biology

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Identification of independent evolutionary lineages is a modern challenge for biologists especially in crops with high potential. Molecular methods, usually used to explore intraspecific variation, also offer important information regarding how and when lineages have evolved and spread. Today, several tools to define the demarcation of lineages based on single or multi-locus data are available, permitting objective results to be obtained. We tested nuclear and plastid loci using five different approaches to delimit the major lineages and estimate the divergence times in giant reed (Arundo donax L.). It is an emerging energy crop, widespread in sub-tropical and temperate regions but particularly aggressive outside its native range. Our results support the presence of six lineages distributed from the Asian regions to the Mediterranean basin and indicate the western and southern edges of the Qinghai-Tibet Plateau as the putative area of origin and source of ancient and cryptic lineages. We suppose it could be an area that has fertile populations. These results should be considered in breeding programmes to produce new cultivars, especially because the absence of fertility for Mediterranean giant reed lineages reduces the opportunity of crop improvement. Moreover, the description of multiple lineages and identifying its putative ancestral area may be helpful to researchers working on invasiveness management, phytoremediation programmes and conservation biology.

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Impact of polyploidy on fertility variation of Mediterranean Arundo L. (Poaceae)

Cited by 27 publications

References 41 publications

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq

Dissection of early transcriptional responses to water stress in Arundo donax L. by unigene-based RNA-seq

In silico identification and characterization of a diverse subset of conserved microRNAs in bioenergy crop Arundo donax L.

Multiple evolutionary lineages detected in giant reed (Arundo donax L.): Applied and evolutionary perspectives

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