Gene transcript analysis in drought stressed ‘AAA’ and ‘ABB’ bananas using next generation sequencing technologies

Abstract

The main purpose of this study was to determine differences in gene expression and allelic heterozygosity in two banana genotypes, Mbwazirume ‘AAA’ which is susceptible to drought stress and Cachaco ‘ABB’ which is tolerant when exposed to drought stress. This was achieved using data from 454 and Illumina sequencing platforms. Drought stress tolerance in bananas has been associated with the B genome but no linkage between gene expression and drought had been illustrated. This has been in part caused by lack of a reference genome/reference transcriptome making it hard to conduct gene expression studies. In this study a reference transcriptome was generated using 454-pyrosequencing technology that comprises of 21201 contigs of lengths ranging between 500-4000 bp. During the course of this project the DH Pahang genome from the CIRAD team was accessed, which together with the reference transcriptome enabled a comprehensive analysis of gene expression and allelic heterozygosity in the two genotypes. Mbwazirume and Cachaco share many genes but what differs is the expression level of these genes. Many genes that are associated with drought tolerance were up-regulated in Cachaco and down-regulated in Mbwazirume. In cases where both genotypes showed down-regulation such as expression of aquaporins, Cachaco maintained a higher level than Mbwazirume. Transcription factors such as MYB44, MYC4, NAC, bZIP, DREB1 and DREB3 were up-regulated in tissues of Cachaco and down-regulated in Mbwazirume. The same trend was observed for genes for antioxidant enzymes and cell cycle regulating proteins. The ability of Cachaco leaves to express high levels of SIC-SGP with reduced expression of LSRP and chlorophyll catabolic enzymes would help it retain more green leaves under dry conditions. Many SNPs were detected in Cachaco, with majority being heterozygous. This was attributed to the presence of two copies of the B genome. It is possible that some of these alleles affect gene activity and efficiency of gene transcription, which results in differences in response to drought stress.