Mining the Musa biodiversity for drought tolerance: allele discovery via integrated phenomics, proteomics and transcriptomics

Banana (Musa spp.) is one of the most produced fruits in the world, the production exceeded 122 million tons in 2013. For optimal production the crop requires: 1200–2690 mm water/year, depending on the agro-ecological zone. The limited genetic diversity in commercial plantations renders the crop extremely vulnerable for (a)biotic stress, like drought. However, worldwide a huge (uncharacterized) biodiversity is available, and we believe optimal exploration and exploitation of this diversity can alleviate issues with drought and also with pests and diseases. The International Transit Center of Bioversity International holds the world’s biggest collection of banana biodiversity (>1500 accessions) which is hosted by the Laboratory for Tropical Crop Improvement (KU Leuven).

The general aim of my doctoral research is to evaluate drought tolerance within a diverse set of edible bananas and to identify potential related alleles. These are important markers for future drought tolerance breeding purposes and allow characterization of the banana biodiversity collection with regard to water scarcity. We already established proof of concept experiments to identify molecular markers for drought tolerance at transcript and protein level. Now we scale up the effort to guide more detailed marker selection, and get a more detailed view of the response to drought within a bigger subset of the banana biodiversity.

In our approach the phenotype is the crucial starting point. A first phenotyping model is based on quick screening of many varieties, so that a first general drought tolerance classification can be done. Secondly a detailed, dynamic phenotypic picture is taken, allowing to study the drought phenotype precisely in time and closer to the agronomic reality. Finally harvest data are collected from experimental fields to validate the phenotyping models.

To identify potential tolerance related markers/alleles we integrate variables on three levels: plant phenotype, transcriptome, and proteome. This enables to correlate the presence of specific alleles to tolerant phenotypes. The different allelic variants and the processes they belong to are studied and learn us more about the general drought response in banana. More tolerant and sensitive genotypes are being characterized via mRNA seq to validate the correlations between the presence of a unique allele and the tolerant phenotype. In a next step potential drought tolerance related alleles are further validated by qRT-PCR, or SRM, in independent experiments using our experimental setup closer to the agronomic reality. Altogether the characterisation of the Musa biodiversity for drought tolerance is established by a thorough search within three tiers of the central dogma, the phenome, proteome and the transcriptome.