Iso-Seq analysis of the flag leaf and first node of Karuppanel (a high grain zinc content rice variety) and MTU 1010 (a widely cultivated mega variety with low grain zinc content) at 10 and 20 days after anthesis to identify differentially expressed full-length transcripts and alternative splicing events regulating zinc uptake, transport, and remobilization during grain filling.
Karuppanel, recognized as a promising donor for high zinc accumulation in the rice endosperm, has been identified under the ICAR "CRP - Biofortification" project for its potential in developing biofortified rice varieties with enhanced grain zinc content. To elucidate the genetic mechanisms governing zinc uptake, transport, and accumulation, transcriptome sequencing was performed on the flag leaf and first node of Karuppanel and the widely cultivated low-zinc mega variety, MTU 1010, at two time intervals: ten and twenty days after anthesis, using the PacBio Iso-Seq Sequel platform. Three biological replicates per tissue were sequenced, generating high-quality long reads. The sequencing data were pre-processed, aligned to the Karuppanel reference genome, collapsed to identify unique isoforms, and quantified. Further downstream analysis included differential gene expression profiling, Gene Ontology (GO) enrichment, KEGG pathway analysis, and alternative splicing event identification, providing insights into the molecular networks regulating zinc accumulation in rice.