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Sample of genes differentially expressed in ‘Cachaco’ (ABB) compared to AAA cultivars (‘Mbwazirume’ and ‘Grande Naine’). (DOCX 18 kb)

Chromosome intervals (defined on genes coordinates) showing B:A ratio deviating from the expected genomic constitution. CDM indicates the three cultivars sharing the same pattern of deviating regions (‘Cachaco’, ‘Dole’ and ‘Monthan’). (DOCX 16 kb)

Histograms representing the paralog included expression (normalized read count, Y axis) for 58 genes having significant higher expression in ‘Cachaco’ (Ca) than in ‘Grande Naine’ (GN) and ‘Mbwazirume’ (Mb). Blue color represents expression level of DEG, other colors expression level of respective paralogs. (PPTX 146 kb)

Background Bananas (Musa spp.) are an important crop worldwide. Most modern cultivars resulted from a complex polyploidization history that comprised three whole genome duplications (WGDs) shaping the haploid Musa genome, followed by inter- and intra-specific crosses between Musa acuminata and M. balbisiana (A and B genome, respectively). Unresolved hybridizations finally led to banana diversification into several autotriploid (AAA) and allotriploid cultivars (AAB and ABB). Using transcriptomic data, we investigated the impact of the genome structure on gene expression patterns in roots of 12 different triploid genotypes covering AAA, AAB and ABB subgenome constitutions. Results We demonstrate that (i) there are different genome structures, (ii) expression patterns go beyond the predicted genomic groups, and (iii) the proportion of the B genome influences the gene expression. The presence of the B genome is associated with a higher expression of genes involved in flavonoid biosynthesis, fatty acid metabolism, amino sugar and nucleotide sugar metabolism and oxidative phosphorylation. There are cultivar-specific chromosome regions with biased B:A gene expression ratios that demonstrate homoeologous exchanges (HE) between A and B sub-genomes. In two cultivars, aneuploidy was detected. We identified 3674 genes with a different expression level between allotriploid and autotriploid with ~ 57% having recently duplicated copies (paralogous). We propose a Paralog Inclusive Expression (PIE) analysis that appears to be suitable for genomes still in a downsizing and fractionation process following whole genome duplications. Our approach allows highlighting the genes with a maximum likelihood to affect the plant phenotype. Conclusions This study on banana is a good case to investigate the effects of alloploidy in crops. We conclude that allopolyploidy triggered changes in the genome structure of a crop and it clearly influences the gene. Electronic supplementary material The online version of this article (10.1186/s12864-019-5618-0) contains supplementary material, which is available to authorized users.

Water shortage is the largest limiting abiotic factor in agriculture and will aggravate in the future. Because of the complexity there is not one conclusive definition of drought. Therefore it is challenging to identify the right parameter and stress intensity for drought tolerance evaluation. This paper contributes to tackle this challenge by exploring the effect of water deficit on transpiration efficiency (TE). In total, six triploid banana (Musa spp.) cultivars were characterized during well-watered and two different water deficit conditions. We developed a concept to evaluate both TE and growth, since selection for high TE is often associated with slow growth. TE increased for all cultivars when stressed and a clear genotypic variation in TE during water deficit could be discerned. ‘Kayinja’ (ABB) and ‘Sukali Ndizi’ (AAB) were ranked as the most efficient cultivars and the East African highland cultivar ‘Mpologoma’ (AAA) exhibited the least transpiration efficient phenotype. Selection for high TE did not lead to selection of slow growers during well-watered and mild stress conditions. High TE varieties are thus projected to bring forth good yield under well-watered and water deficit conditions.

To explore the transcriptomic global response to osmotic stress in roots, 18 mRNA-seq libraries were generated from three triploid banana genotypes grown under mild osmotic stress (5% PEG) and control conditions. Illumina sequencing produced 568 million high quality reads, of which 70-84% were mapped to the banana diploid reference genome. Using different uni- and multivariate statistics, 92 genes were commonly identified as differentially expressed in the three genotypes. Using our in house workflow to analyze GO enriched and underlying biochemical pathways, we present the general processes affected by mild osmotic stress in the root and focus subsequently on the most significantly overrepresented classes associated with: respiration, glycolysis and fermentation. We hypothesize that in fast growing and oxygen demanding tissues, mild osmotic stress leads to a lower energy level, which induces a metabolic shift towards (i) a higher oxidative respiration, (ii) alternative respiration and (iii) fermentation. To confirm the mRNA-seq results, a subset of twenty up-regulated transcripts were further analysed by RT-qPCR in an independent experiment at three different time points. The identification and annotation of this set of genes provides a valuable resource to understand the importance of energy sensing during mild osmotic stress.

The effects of abiotic stress on banana production become increasingly important, but the molecular processes behind tolerance still remain largely unknown. As the genome sequence is now publically available and cutting-edge high-throughput -omics technologies emerge, there lay multiple opportunities in the offing to close the knowledge gap. This chapter gives an overview of the molecular work that has already been performed on abiotic stress tolerance in banana. This research is mostly oriented towards cold and drought, while that on nutrient deficiencies is still lagging behind. Promising results as well as important gaps are formulated, and recommendations for future abiotic stress tolerance research are proposed. We show how new -omics technologies and the integration thereof enable a holistic view on abiotic stress tolerance in banana and can enhance our knowledge. Additionally, special emphasis is placed on the ultimate importance of phenotyping and a good definition of tolerance in the context of decent molecular research in this area.

Introduction of microbial trehalose biosynthesis enzymes has been reported to enhance abiotic stress resistance in plants but also resulted in undesirable traits. Here, we present an approach for engineering drought stress tolerance by modifying the endogenous trehalase activity in Arabidopsis (Arabidopsis thaliana). AtTRE1 encodes the Arabidopsis trehalase, the only enzyme known in this species to specifically hydrolyze trehalose into glucose. AtTRE1-overexpressing and Attre1 mutant lines were constructed and tested for their performance in drought stress assays. AtTRE1-overexpressing plants had decreased trehalose levels and recovered better after drought stress, whereas Attre1 mutants had elevated trehalose contents and exhibited a drought-susceptible phenotype. Leaf detachment assays showed that Attre1 mutants lose water faster than wild-type plants, whereas AtTRE1-overexpressing plants have a better water-retaining capacity. In vitro studies revealed that abscisic acid-mediated closure of stomata is impaired in Attre1 lines, whereas the AtTRE1 overexpressors are more sensitive toward abscisic acid-dependent stomatal closure. This observation is further supported by the altered leaf temperatures seen in trehalase-modified plantlets during in vivo drought stress studies. Our results show that overexpression of plant trehalase improves drought stress tolerance in Arabidopsis and that trehalase plays a role in the regulation of stomatal closure in the plant drought stress response.