AUTHOR=Thirugnanasambandam Prathima Perumal , Singode Avinash , Thalambedu Lakshmi Pathy , Athiappan Selvi , Krishnasamy Mohanraj , Purakkal Sobhakumari Valiya , Govind Hemaprabha , Furtado Agnelo , Henry Robert 

TITLE=Long read transcriptome sequencing of a sugarcane hybrid and its progenitors, Saccharum officinarum and S. spontaneum

JOURNAL=Frontiers in Plant Science

VOLUME=14

YEAR=2023

URL=https://www.frontiersin.org/journals/plant-science/articles/10.3389/fpls.2023.1199748

DOI=10.3389/fpls.2023.1199748

ISSN=1664-462X

ABSTRACT=<p>Commercial sugarcane hybrids are derivatives from <italic>Saccharum officinarum</italic> and <italic>Saccharum spontaneum</italic> hybrids containing the full complement of <italic>S. officinarum</italic> and a few <italic>S. spontaneum</italic> chromosomes and recombinants with favorable agronomic characters from both the species. The combination of the two sub-genomes in varying proportions in addition to the recombinants presents a challenge in the study of gene expression and regulation in the hybrid. We now report the transcriptome analysis of the two progenitor species and a modern commercial sugarcane hybrid through long read sequencing technology. Transcripts were profiled in the two progenitor species <italic>S. officinarum</italic> (Black Cheribon), and <italic>S. spontaneum</italic> (Coimbatore accession) and a recent high yielding, high sugar variety Co 11015. The composition and contribution of the progenitors to a hybrid with respect to sugar, biomass, and disease resistance were established. Sugar related transcripts originated from <italic>S. officinarum</italic> while several stress and senescence related transcripts were from <italic>S. spontaneum</italic> in the hybrid. The hybrid had a higher number of transcripts related to sugar transporters, invertases, transcription factors, trehalose, UDP sugars, and cellulose than the two progenitor species. Both <italic>S. officinarum</italic> and the hybrid had an abundance of novel genes like sugar phosphate translocator, while <italic>S. spontaneum</italic> had just one. In general, the hybrid shared a larger number of transcripts with <italic>S. officinarum</italic> than with <italic>S. spontaneum</italic>, reflecting the genomic contribution, while the progenitors shared very few transcripts between them. The common isoforms among the three genotypes and unique isoforms specific to each genotype indicate that there is a high scope for improvement of the modern hybrids by utilizing novel gene isoforms from the progenitor species.</p>