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.
Highlights
Bananas and plantains (Musa spp.) are a major allopolyploid crop with a yearly production of ±145 million tonnes (2014, FAOstat), spread over thehumid tropics, an estimated 85% of which coming from smallholder plots in the developing world[1]
The high degree of heterozygosity and the amount of replicated sequence reads in polyploid crops is a great challenge for effective single nucleotide polymorphism (SNP) calling[8,21]
In banana GWAS has been successfully applied in diploids for the seedless phenotype, a trait underpinned by a limited number of genes[12]
Summary
Bananas and plantains (Musa spp.) are a major allopolyploid crop with a yearly production of ±145 million tonnes (2014, FAOstat), spread over the (sub-)humid tropics, an estimated 85% of which coming from smallholder plots in the developing world[1]. Flexibility of plants towards the environment is naturally determined by genetic diversity (G), and a deeper understanding thereof towards the phenotype is a priority[7,8] It is a major objective for crop scientists to identify sources of natural variation with potential to rise the tolerance towards unfavourable (a)biotic constraints while minimizing the yield penalty[8]. Many other important food, feed, or energy crops and their wild relatives are highly relevant in the quest for sustainable cultivars Among these are numerous polyploid crops with complex heterologous genomes. The dissimilarity between the Musa acuminata and the draft Musa balbisiana reference genomes is 1 SNP per 39 bp[13] Polyploid crops such as banana are characterized by a broad genetic diversity, acquired by genome merging and doubling[17]. Since not all cultivars of interest carry the reference sequence, mapping efficiency biases can still occur when one reference genome is more closely linked to a constituting genome than the other[23]
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