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Abstract 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.

Abstract The fate of doubled genes, from allopolyploid or autopolyploid origin, is controlled at multiple levels, resulting in the modern day cultivars. We studied the root growth of 3 different triploid banana cultivars under control and osmotic stress conditions. The root growth of the allopolyploid ABB cultivar was 42% higher under control and 61% higher under osmotic stress. By integrating transcriptomics and proteomics, we studied the gene expression of all 3 cultivars, resulting in 2,749 identified root proteins. 383 gene loci displayed genotype specific differential expression whereof 252 showed at least one Single Amino Acid Polymorphism (SAAP). In the ABB cultivar, allele expressions supposedly follow a 1/3 and 2/3 pattern for respectively the A and the B allele. Using transcriptome read alignment to assess the homeoallelic contribution we found that 63% of the allele specific genes deviated from this expectation. 32 gene loci even did not express the A allele. The identified ABB allele- specific proteins correlate well with the observed growth phenotype as they are enriched in energy related functions such as ATP metabolic processes, nicotinamide nucleotide metabolic processes, and glycolysis.

Water deficit is one of the world’s major constraints in agriculture and will aggravate in the future. Banana (Musa spp.) is an important crop that needs vast amounts of water for optimal production. The International Transit Center of Bioversity International holds the world’s biggest collection of banana biodiversity (>1,500 accessions). The long-term aim of this research is to evaluate the potential within this collection for climate smart agricultural usage. Therefore, we developed a phenotyping setup under controlled environmental conditions and we selected 32 representatives of the Musa biodiversity (29 cultivars and 3 wild relatives) for evaluation. The best performing genotypes accumulated six to seven times more biomass than the least performing. Eight genotypes (five ABB, one AAB, and two AAA) invest under osmotic stress significantly more in root growth than in leaf growth. We predict therefore that these genotypes have potential for high productivity under rain fed conditions with a short dry season. To gain more insight in the transpiration physiology, we gravimetrically monitored individual plant transpiration over the diurnal period. All analyzed genotypes showed a marked reduction in transpiration rate in the afternoon. Moreover, the timing of this onset, as well as its impact on total transpiration, was genotype dependent. This phenomenon was more pronounced in 13 genotypes (eight ABB, two AAB, two AA, one BB). Banana is a crop originating from the humid tropics and has developed a strong root pressure to maintain an efficient water and nutrient transport even under saturated relative humidity conditions. Therefore, we hypothesize that the diurnal transpiration decline contributes to a higher water use efficiency without compromising the nutrient transport. Of the eight genotypes that had the best growth under osmotic stress, all analyzed ABB cultivars have a lower maximal transpiration rate, keep this maximal transpiration for a shorter time and therefore consume less water per day. We conclude that lab models are very useful to study the biodiversity and to identify different traits that contribute to a better drought tolerance/avoidance. We encourage researchers investigating other crops to start exploring their collections.

Banana (Musa spp.), a perennial (sub-)tropical crop, suffers from seasonal droughts, which are typical of rain-fed agriculture. This study aimed at understanding the effect of seasonal drought on early growth, flowering and yield traits in bananas grown in the East African highlands. A field experiment was set up in North Tanzania using four genotypes from different geographical origins and two different ploidy levels. The treatments considered were exclusively rain-fed versus rain supplemented with irrigation. Growth in plant girth and leaf area were promising traits to detect the early effect of water deficit. Seasonal drought slowed down vegetative growth, thus significantly decreasing plant girth, plant height and the number of suckers produced when compared to irrigated plants. It also delayed flowering time and bunch maturity and had a negative effect on yield traits. However, the results depended on the genotype and crop cycle and their interaction with the treatments. “Nakitengwa”, an East African highland banana (EAHB; AAA genome group), which is adapted to the region, showed sensitivity to drought in terms of reduced bunch weight and expected yield, while “Cachaco” (ABB genome group) showed less sensitivity to drought but had a poorer yield than “Nakitengwa”. Our study confirms that seasonal drought has a negative impact on banana production in East Africa, where EAHBs are the most predominant type of bananas grown in the region. We also show that a drought-tolerant cultivar not adapted to the East African highlands had a low performance in terms of yield. We recommend a large-scale screening of diploid bananas to identify drought-tolerant genotypes to be used in the improvement of locally adapted and accepted varieties.