Charting oat (Avena sativa) embryo and endosperm transcription factor expression reveals differential expression of potential importance for seed development

Abstract

Uniquely, oat, among cereals, accumulates an appreciable amount of oil in the endosperm together with starch. Oat is also recognized for its soluble fibers in the form of β-glucans. Despite high and increasing interest in oat yield and quality, the genetic and molecular understanding of oat grain development is still very limited. Transcription factors (TFs) are important regulatory components for plant development, product quality and yield. This study aimed to develop a workflow to determine seed tissue specificity of transcripts encoding transcription factors to reveal differential expression of potential importance for storage compound deposition and quality characters in oat. We created a workflow through the de novo assembly of sequenced seed endosperm and embryo, and publicly available oat seed RNAseq dataset, later followed by TF identification. RNAseq data were assembled into 33,878 transcripts with approximately 90% completeness. A total of 3875 putative TF encoding transcripts were identified from the oat hybrid assemblies. Members of the B3, bHLH, bZIP, C3H, ERF, NAC, MYB and WRKY families were the most abundant TF transcripts. A total of 514 transcripts which were differentially expressed between embryo and endosperm were identified with a threshold of 16-fold expression difference. Among those, 36 TF transcript homologs, belonging to 7 TF families, could be identified through similarity search in wheat embryo and endosperm EST libraries of NCBI Unigene database, and almost all the closest homologs were specifically expressed in seed when explored in WheatExp database. We verified our findings by cloning, sequencing and finally confirming differential expression of two TF encoding transcripts in oat seed embryo and endosperm. The developed workflow for identifying tissue-specific transcription factors allows further functional characterization of specific genes to increase our understanding of grain filling and quality.

Tissue-Specific Transcriptome Analysis Reveals Candidate Transcripts Associated with the Process of Programmed B Chromosome Elimination in Aegilops speltoides

“…Nevertheless, we were able to recover a total fraction of~65% BUSCO-confirmed genes (including fragmented and complete). Comparing our findings to a recently published study in an oat embryonic transcriptome detecting 60% complete and fragmented orthologues [15], the BUSCO results for the tissue-specific Ae. speltoides transcriptome are highly similar.…”

Single-Molecule Real-Time Sequencing of the Madhuca pasquieri (Dubard) Lam. Transcriptome Reveals the Diversity of Full-Length Transcripts

“…TFs are important regulatory components for seed germination and plant development [69], and many TF families, including WRKY, MYB, NAC, and bHLH, have been studied extensively in model plants and crops [70], but fewer studied in non-model plants [71]. For example, members of the MYB (HORVU0Hr1G018970, HORVU2Hr1G010450) and NAC (HORVU2Hr1G077320) family were found associated with regulating germination or root development in barley (Hordeum vulgare) [72].…”

First the seed: Genomic advances in seed science for improved crop productivity and food security

“…This hightemporal resolution study will certainly provide an exciting resource for future functional studies that will shed light on the genetic regulation of seed development. Analogously, by availing of de novo assembly of sequenced seed endosperm and embryo and a publicly available oat seed RNA sequencing dataset, Kushwaha et al (2019) aimed to determine seed tissue specificity of transcripts encoding transcription factors (TFs) to identify differential expression of potential importance for storage compound deposition and quality characters in oat. They detected 3,875 putative TF encoding transcripts, predominantly B3, bHLH, bZIP, C3H, ERF, MYB, and WRKY families, of which, 514 transcripts had 16-fold difference in expression between embryo and endosperm, with 36 TF transcript homologs also reported in wheat seed database.…”