Drought tolerance conferred to sugarcane by association with Gluconacetobacter diazotrophicus: a transcriptomic view of hormone pathways

Sugarcane interacts with particular types of beneficial nitrogen-fixing bacteria that provide fixed-nitrogen and plant growth hormones to host plants, promoting an increase in plant biomass. Other benefits, as enhanced tolerance to abiotic stresses have been reported to some diazotrophs. Here we aim to study the effects of the association between the diazotroph Gluconacetobacter diazotrophicus PAL5 and sugarcane cv. SP70-1143 during water depletion by characterizing differential transcriptome profiles of sugarcane. RNA-seq libraries were generated from roots and shoots of sugarcane plants free of endophytes that were inoculated with G. diazotrophicus and subjected to water depletion for 3 days. A sugarcane reference transcriptome was constructed and used for the identification of differentially expressed transcripts. The differential profile of non-inoculated SP70-1143 suggests that it responds to water deficit stress by the activation of drought-responsive markers and hormone pathways, as ABA and Ethylene. qRT-PCR revealed that root samples had higher levels of G. diazotrophicus 3 days after water deficit, compared to roots of inoculated plants watered normally. With prolonged drought only inoculated plants survived, indicating that SP70-1143 plants colonized with G. diazotrophicus become more tolerant to drought stress than non-inoculated plants. Strengthening this hypothesis, several gene expression responses to drought were inactivated or regulated in an opposite manner, especially in roots, when plants were colonized by the bacteria. The data suggests that colonized roots would not be suffering from stress in the same way as non-inoculated plants. On the other hand, shoots specifically activate ABA-dependent signaling genes, which could act as key elements in the drought resistance conferred by G. diazotrophicus to SP70-1143. This work reports for the first time the involvement of G. diazotrophicus in the promotion of drought-tolerance to sugarcane cv. SP70-1143, and it describes the initial molecular events that may trigger the increased drought tolerance in the host plant

Sugarcane transcriptome analysis in response to infection caused by <i>Acidovorax avenae</i> subsp. <i>avenae</i>

<div><p>Sugarcane is an important tropical crop mainly cultivated to produce ethanol and sugar. Crop productivity is negatively affected by <i>Acidovorax avenae</i> subsp <i>avenae</i> (<i>Aaa</i>), which causes the red stripe disease. Little is known about the molecular mechanisms triggered in response to the infection. We have investigated the molecular mechanism activated in sugarcane using a RNA-seq approach. We have produced a <i>de novo</i> transcriptome assembly (TR7) from sugarcane RNA-seq libraries submitted to drought and infection with <i>Aaa</i>. Together, these libraries present 247 million of raw reads and resulted in 168,767 reference transcripts. Mapping in TR7 of reads obtained from infected libraries, revealed 798 differentially expressed transcripts, of which 723 were annotated, corresponding to 467 genes. GO and KEGG enrichment analysis showed that several metabolic pathways, such as code for proteins response to stress, metabolism of carbohydrates, processes of transcription and translation of proteins, amino acid metabolism and biosynthesis of secondary metabolites were significantly regulated in sugarcane. Differential analysis revealed that genes in the biosynthetic pathways of ET and JA PRRs, oxidative burst genes, NBS-LRR genes, cell wall fortification genes, SAR induced genes and pathogenesis-related genes (PR) were upregulated. In addition, 20 genes were validated by RT-qPCR. Together, these data contribute to a better understanding of the molecular mechanisms triggered by the <i>Aaa</i> in sugarcane and opens the opportunity for the development of molecular markers associated with disease tolerance in breeding programs.</p></div

Validation of RNA-seq analysis by qRT-PCR using genes from different pathways.

<p>Two biological replicates were used. Gene names correspond to those listed in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166473#pone.0166473.s009" target="_blank">S9</a> and <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166473#pone.0166473.s010" target="_blank">S10</a> Tables. Relative expression by qRT-PCR. The bars represent the relative expression of three technical replicates (n = 3) and standard deviation (Green bars: replicate 1 and blue bars: replicate 2). The relative expression values above the dotted line are upregulated genes, whereas below line correspond to downregulated genes. GAPDH was used as a reference gene for normalization of gene-expression data. These 20 genes validated in replicates were grouped into four categories, <b>(A)</b> genes related to stress, <b>(B)</b> genes that coding to several pathways, <b>(C)</b> primary carbohydrate metabolism pathways genes and <b>(D)</b> genes encoding for PRRs. The values of the quantitative method ΔΔCt can be seen in <a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0166473#pone.0166473.s010" target="_blank">S10 Table</a></p

cat

cat3 nCat has several meanings peculiar to Newfoundland and Labrador or at least, to the Canadian Atlantic area. Since one usage of _cat_ derives from _catamaran_, I will list these terms in sequence. _cat_ n. 1. _Nfld., S. & C. Lab_. [elliptical] A _catermaran_ (def. 1) q.v. 2. likely as short form for _catamount_, the European wildcat of Britain (< _cat a' mount_ "mountain cat" < _A.S. catt_ ; reinforced by Wolen _cath_, In., Gael _cat_, Latin _catta_; thought ultimately to be Celtic, but note Arabic _gitt_, Turkish _Kedi_, a cat] The Canada Lynx,_ Lynx canadenais_; its flesh or palt. Also called _gatamount, mountain cat [underlined], great cat_ q.v. 3. _esp. Lab_ [likely < British dial. _cat_, any furry, small cat-like animal (Irish, Gael. _cat_ is same dial. sense); see also under def. 2. Note English _polecat_ the fitch or "stinking marten".] A marten, fisher or mink, or the pelt of any of these. See also _cat house, cat killer, cat path n. 4. _sealing;_ _esp. Nfld._ [< cat n. (as above); likely infl by kit n., a young or small animal (?< _kitten_ or akin to Scots, N. Eng. _chit_, child) a) Sepcifically, (over) [reverse] a still-born whitecoat or harp-seal, its scalp or pelt. 5. _Atlantic Provs_. , _B.C. coast; rare_ [ellipt. (< the cat-urine odour characteristic of its crushed needles] A "cat-spruce"; a white spruce. 6. _esp. Nfld._ [ellipt.] The catfish, also called ocean cat and Spotted Wolf-fish, _Anarhichas minor._ 7. _esp. Nfld_ [ellipt.] The sea cat or Ocean Pout, _Macrozoarces americanus._ _Catamaran_ n. 1. _esp. Nfld_ [ <s.w. Eng. rural dial. _catamaran_, anything roughly or awkardly construct < cat, thing (< O.E. _catal_, chattel, thing) + *_amaran_, wild, rough botched (< AS _amarran_ v., botch, mar; ? reincforced by French _marron_, wild, untamed)] A runnered work-sled of any type, esp. a strong broad sledge with wooden runners used n haulng wood or lumber. 2. [supposedly < Tamil _kattumaram_, tied loga ( < _kattu_ v., tis + _maram_ tree) but perhaps as in def. 1] a) _Atlantic Provs.; archaic_ A long raft; b) _esp. N. Lab. ; rare_ Two kayaks or small boats joined together for seaworthiness. _catamaran_ v.t. _esp. N. Lab.; now rare_ [< the noun q.v.] Join two kayaks or other small boats together for seawothiness when travelling on the ocean.W.J. KIRWIN DEC 1972JH DEC 1972Used I and SupUsed I and SupNot usedWHITE-COAT, HARP, HOODChecked by Cathy Wismeman on Wed 15 Apr 2015; Reverse side of C_1362

Statistics of DETs annotated by TRAPID.

<p>Statistics of DETs annotated by TRAPID.</p

Genes known to be upregulated in response to water deprivation and their expression in Drought dataset comparison for root and shoot tissues.

<p>Numbers show the log₂ fold change of DE genes.</p><p>Genes known to be upregulated in response to water deprivation and their expression in Drought dataset comparison for root and shoot tissues.</p

The ten most frequently occurred protein domains in the sequence of sugarcane infected by <i>Aaa</i>.

<p>The ten most frequently occurred protein domains in the sequence of sugarcane infected by <i>Aaa</i>.</p

Summary of reads and genes (loci) mapped in each generated library.^*

<p>* Bases in deletions or insertions were not counted here.</p>a<p>Number of reads obtained after Illumina sequencing and filtering.</p>b<p>Number of reads mapped against reference transcriptome.</p>c<p>Number of loci from a total of 87,827 loci mapped.</p><p>Summary of reads and genes (loci) mapped in each generated library.^{<a href="http://www.plosone.org/article/info:doi/10.1371/journal.pone.0114744#nt103" target="_blank">*</a>}</p

The top six up- and downregulated differentially expressed genes in sugarcane infected by <i>Aaa</i>.

<p>The top six up- and downregulated differentially expressed genes in sugarcane infected by <i>Aaa</i>.</p

Summary of Illumina transcriptome sequence data and quality control.

<p>* percentage of reads left after trimming and filtering.</p><p>Summary of Illumina transcriptome sequence data and quality control.</p