Comparative RNA-Seq analysis of the root revealed transcriptional regulation system for aluminum tolerance in contrasting indica rice of North East India

Expression pattern of aluminum (Al) tolerance genes is one of the major determinants of Al avoidance/tolerance within plant cultivars. We have performed transcriptome analysis of two contrasting (Al-tolerant, Disang; Al-sensitive, Joymati) cultivars of India's North Eastern region, an indica rice diversity hotspot, on exposure to excess Al3+ treatment in acidic condition. Co-expression analysis and SNPs enrichment analysis proposed the role of both trans-acting and cis-acting polymorphisms in Al signaling in the Al-tolerant cultivar. We proposed ten major genes, including arginine decarboxylase, phytase, and beta-glucosidase aggregating factor as candidates responsible for Al tolerance based on transcriptome analysis. Al3+ stress led to changes in the alternative splicing profile of the Al-tolerant cultivar. These studies demonstrated the transcriptional variations affiliated to Al avoidance/tolerance in contrasting indica rice of North East India and provided us with several candidate genes responsible for Al tolerance.

Automated summary

The expression pattern of aluminum tolerance genes plays a crucial role in determining aluminum avoidance/tolerance in plant cultivars. Transcriptome analysis of contrasting indica rice cultivars in India's North Eastern region revealed transcriptional variations associated with aluminum avoidance/tolerance and identified several candidate genes responsible for aluminum tolerance. The study suggests the involvement of both trans-acting and cis-acting polymorphisms in aluminum signaling in the aluminum-tolerant cultivar.