Journal Article

Reproductive developmental transcriptome analysis of Tripidium ravennae (Poaceae)

Ranney, Thomas, Liu, Wusheng, Ashrafi, Hamid, Touchell, Darren, Zhao, Fangzhou, Maren, Nathan, Aryal, Rishi

2021

Overview

Background Tripidium ravennae is a cold-hardy, diploid species in the sugarcane complex ( Poaceae subtribe Saccharinae ) with considerable potential as a genetic resource for developing improved bioenergy and ornamental grasses. An improved understanding of the genetic regulation of reproductive processes (e.g., floral induction, inflorescence development, and seed development) will enable future applications of precision breeding and gene editing of floral and seed development. In particular, the ability to silence reproductive processes would allow for developing seedless forms of valuable but potentially invasive plants. The objective of this research was to characterize the gene expression environment of reproductive development in T. ravennae. Results During the early phases of inflorescence development, multiple key canonical floral integrators and pathways were identified. Annotations of type II subfamily of MADS-box transcription factors, in particular, were over-represented in the GO enrichment analyses and tests for differential expression (FDR p -value < 0.05). The differential expression of floral integrators observed in the early phases of inflorescence development diminished prior to inflorescence determinacy regulation. Differential expression analysis did not identify many unique genes at mid-inflorescence development stages, though typical biological processes involved in plant growth and development expressed abundantly. The increase in inflorescence determinacy regulatory elements and putative homeotic floral development unigenes at mid-inflorescence development coincided with the expression of multiple meiosis annotations and multicellular organism developmental processes. Analysis of seed development identified multiple unigenes involved in oxidative-reductive processes. Conclusion Reproduction in grasses is a dynamic system involving the sequential coordination of complex gene regulatory networks and developmental processes. This research identified differentially expressed transcripts associated with floral induction, inflorescence development, and seed development in T. ravennae . These results provide insights into the molecular regulation of reproductive development and provide a foundation for future investigations and analyses, including genome annotation, functional genomics characterization, gene family evolutionary studies, comparative genomics, and precision breeding.

• Publisher: BioMed Central,BioMed Central Ltd,Springer Nature B.V,BMC
• Subject: Alternative energy sources / Analysis / Animal Genetics and Genomics / Annotations / Biological activity / Biomedical and Life Sciences / Coordination compounds / Developmental stages / Differential gene expression / Diploids / Floral transition / Flowering / Gene expression / Gene Expression Profiling / Gene Expression Regulation, Plant / Genetic aspects / Genetic modification / Genetic resources / Genome editing / Genomics / Grasses / Growth / Inflorescence / Integrators / Invasive plants / Kinases / Life Sciences / Meiosis / Metabolism / Microarrays / Microbial Genetics and Genomics / Morphogenesis / Next-generation sequencing / Plant Breeding / Plant Genetics and Genomics / Plant growth / Plant reproduction / Plants / Poaceae / Proteins / Proteomics / Regulatory sequences / Reproduction / RNA sequencing / Sugarcane / Transcription factors / Transcriptome sequencing / Transcriptomes / Tripidium ravennae / Varieties