Improvement of strawberry (Fragaria × ananassa) fruit flavor is an important goal in breeding programs. To investigate genetic factors controlling this complex trait, a strawberry mapping population derived from genotype ‘1392’, selected for its superior flavor, and ‘232’ was profiled for volatile compounds over 4 years by headspace solid phase microextraction coupled to gas chromatography and mass spectrometry. More than 300 volatile compounds were detected, of which 87 were identified by comparison of mass spectrum and retention time to those of pure standards. Parental line ‘1392’ displayed higher volatile levels than ‘232’, and these and many other compounds with similar levels in both parents segregated in the progeny. Cluster analysis grouped the volatiles into distinct chemically related families and revealed a complex metabolic network underlying volatile production in strawberry fruit. Quantitative trait loci (QTL) detection was carried out over 3 years based on a double pseudo-testcross strategy. Seventy QTLs covering 48 different volatiles were detected, with several of them being stable over time and mapped as major QTLs. Loci controlling γ-decalactone and mesifurane content were mapped as qualitative traits. Using a candidate gene approach we have assigned genes that are likely responsible for several of the QTLs. As a proof of concept we show that one homoeolog of the O-methyltransferase gene (FaOMT) is the locus responsible for the natural variation of mesifurane content. Sequence analysis identified 30 bp in the promoter of this FaOMT homoeolog containing putative binding sites for basic/helix-loop-helix, MYB, and BZIP transcription factors. This polymorphism fully cosegregates with both the presence of mesifurane and the high expression of FaOMT during ripening.

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. 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. 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.

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.

ISHS XXIX International Horticultural Congress on Horticulture: Sustaining Lives, Livelihoods and Landscapes (IHC2014): IX International Symposium on Banana: ISHS-ProMusa Symposium on Unravelling the Banana's Genomic Potential Abiotic stress research in crops using -omics approaches: drought stress and banana in the spotlight

Scientific Reports 6: Article number: 22583; published online: 03 March 2016; updated: 20 May 2016. In this Article, the Accession codes were omitted from the Additional Information section: Data availability: The short reads of RNA-seq were deposited in NCBI’s Sequence Read Archive (SRA) database with accession numbers from SRX1473480 to SRX1473497 (http://www.